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Automated structure solution with AutoSol
Author(s)
PurposeThe AutoSol Wizard uses HYSS, SOLVE, Phaser, RESOLVE, TEXTAL, xtriage and phenix.refine to solve a structure and generate experimental phases with the MAD, MIR, SIR, or SAD methods. The Wizard begins with datafiles (.sca, .hkl, etc) containing amplitidues of structure factors, identifies heavy-atom sites, calculates phases, carries out density modification and NCS identification, and builds and refines a preliminary model. UsageThe AutoSol Wizard can be run from the PHENIX GUI, from the command-line, and from keyworded script files. All three versions are identical except in the way that they take commands from the user. See Running a Wizard from a GUI, the command-line, or a script for details of how to run a Wizard. The command-line version will be described here, except for MIR and multiple datasets, which can only be run with the GUI or with a script. How the AutoSol Wizard worksThe basic steps that the AutoSol Wizard carries out are described below. They are: Setting up inputs, Analyzing and scaling the data, Finding heavy-atom (anomalously-scattering atom) sites, Scoring of heavy-atom solutions, Phasing, Density modification (including NCS averaging), and Preliminary model-building and refinement. The data for structure solution are grouped into Datasets and solutions are stored in Solution objects. Setting up inputsThe AutoSol Wizard expects the following basic information: (1) a datafile name (w1.sca or data=w1.sca) (2) a sequence file (seq.dat or seq_file=seq.dat) (3) how many sites to look for (2 or sites=2) (4) what the anomalously-scattering atom is (Se or atom_type=Se) (5) If you have SAD or MAD data, then it is helpful to add f_prime and f_double_prime for each wavelength. You can also specify many other parameters, including resolution, number of sites, whether to search in a thorough or quick fashion, how thoroughly to build a model, etc. If you have a heavy-atom solution from a previous run or another approach, you can read it in directly as well. Datasets and Solutions in AutoSolAutoSol breaks down the data for a structure solution into datasets, where a dataset is a set of data that corresponds to a single set of heavy-atom sites. An entire MAD dataset is a single dataset. An MIR structure solution consists of several datasets (one for each native-derivative combination). A MAD + SIR structure has one dataset for the MAD data and a second dataset for the SIR data. The heavy-atom sites for each dataset are found separately (but using difference Fouriers from any previously-solved datasets to help). In the phasing step all the information from all datasets is merged into a single set of phases. The AutoSol wizard uses a "Solution" object to keep track of heavy-atom solutions and the phased datasets that go with them. There are two types of Solutions: those which consist of a single dataset (Primary Solutions) and those that are combinations of datasets (Composite Solutions). "Primary" Solutions have information on the datafiles that were part of the dataset and on the heavy-atom sites for this dataset. Composite Solutions are simply sets of Primary Solutions, with associated origin shifts. The hand of the heavy-atom or anomalously-scattering atom substructure is part of a Solution, so if you have two datatsets, each with two Solutions related by inversion, then AutoSol would normally construct four different Composite Solutions from these and score each one as described below. Analyzing and scaling the dataThe AutoSol Wizard analyzes input datasets with phenix.xtriage to identify twinning and other conditions that may require special care. The data is scaled with SOLVE. For MAD data, FA values are calculated as well. Note on anisotropy corrections: The AutoSol wizard will apply an anistropy correction to all the raw experimental data if any of the files in the first dataset read in have a very strong anisotropy. You can tell the Wizard how much anisotropy there must be before applying this correction by default using the keywords correct_aniso=True # (if True or False then always or never apply correction)
delta_b_for_auto_correct_aniso=20 # correct if range of anisotropic B
#is greater than 20
ratio_b_for_auto_correct_aniso=1.5 #correct if the ratio of the largest
#to smallest anisotropic B is greater than 1.5
If an anisotropy correction is applied then a separate refinement file must be specified if refinement is to be carried out. This is because it is best to refine against data that have not been corrected for anisotropy (instead applying the correction as part of refinement). Finding heavy-atom (anomalously-scattering atom) sitesThe AutoSol Wizard uses HYSS to find heavy-atom sites. The result of this step is a list of possible heavy-atom solutions for a dataset. For SIR or SAD data, the isomorphous or anomalous differences, respectively are used as input to HYSS. For MAD data, the anomalous differences at each wavelength, and the FA estimates of complete heavy-atom structure factors from SOLVE are each used as separate inputs to HYSS. Each heavy-atom substructure obtained from HYSS corresponds to a potential solution. In space groups where the heavy-atom structure can be either hand, a pair of enantiomorphic solutions is saved for each run of HYSS. Running AutoSol separately in related space groupsAutoSol will check for the opposite hand of the heavy-atom solution, and at the same time it will check for the opposite hand of your space group (It will invert the heavy-atom solution from HYSS and invert the hand of the space group at the same time). Therefore you do not need to run AutoSol twice for space groups that are chiral (for example P41). The corresponding inverse space groups will be checked automatically (P43 ). If there are possibilities for your space group other than the inverse hand of the space group, then you should test them all, one at a time. For example if you were not able to measure 00l reflections in a hexagonal space group, your space group might be P6, P61, P62, P63, P64 or P65. In this case you would have to run it in P6, P61 P62 and P63 (and then P65 and P64 will be done automatically as the inverses of P61 and P62). Normally only one of these will give a plausible solution. Scoring of heavy-atom solutionsPotential heavy-atom solutions are scored based on a set of criteria (CC, RFACTOR, SKEW, FOM, NCS_OVERLAP, TRUNCATION, REGIONS, SD; described below), using either a Bayesian estimate, a linear regression, or a Z-score system to put all the scores on a common scale and to combine them into a single overall score. The overall scoring method chosen (BAYES-CC or Z-SCORE) is determined by the value of the keyword overall_score_method. The default is BAYES-CC. Note that for all scoring methods, the map that is being evaluated, and the estimates of map-perfect-model correlation, refer to the experimental electron density map, not the density-modified map. Bayesian CC scores (BAYES-CC). Bayesian estimates of the quality of experimental electron density maps are obtained using data from a set of previously-solved datasets. The standard scoring criteria were evaluated for 1905 potential solutions in a set of 246 MAD, SAD, and MIR datasets. As each dataset had previously been solved, the correlation between the refined model and each experimental map (CC_PERFECT) could be calculated for each solution (after offsetting the maps to account for origin differences). Histograms were tabulated of the number of instances that a scoring criterion (e.g., SKEW) had various possible values, as a function of the CC_PERFECT of the corresponding experimental map to the refined model. These histograms yield the relative probability of measuring a particular value of that scoring criterion (SKEW), given the value of CC_PERFECT. Using Bayes' rule, these probabilities can be used to estimate the relative probabilities of values of CC_PERFECT given the value of each scoring criterion for a particular electron density map. The mean estimate (BAYES-CC) is reported (multiplied x 100), with a +/-2SD estimate of the uncertainty in this estimate of CC_PERFECT. The BAYES-CC values are estimated independently for each scoring criterion used, and also from all those selected with the keyword score_type_list and not selected with the keyword skip_score_list. Z-scores (Z-SCORE). The Z-score for one criterion for a particular solution is given by, Z= (Score - mean_random_solution_score)/(SD_of_random_solution_scores)where Score is the score for this solution, mean_random_solution_score is the mean score for a solution with randomized phases, and SD_of_random_solution_scores is the standard deviation of the scores of solutions with randomized phases. To create a total score based on Z-scores, the Z-scores for each criterion are simply summed. The principal scoring criteria are: (1) Correlation of map-phased electron density map with experimentally- phased map (CC). The statistical density modification in RESOLVE allows the calculation of map-based phases that are (mostly) independent of the experimental phases. The phase information in statistical density modification comes from two sources: your experimental phases and maximization of the agreement of the map with expectations (such as a flat solvent region). Normally the phase probabilities from these two sources are merged together, yielding your density-modified phases. This score is calculated based on the correlation of the phase information from these two sources before combining them, and is a good indication of the quality of the experimental phases. This criterion is used in scoring by default. (2) The R-factor for density modification (R-Factor). Statistical density modification provides an estimate of structure factors that is (mostly) independent of the measured structure factors, so the R-factor between FC and Fobs is a good measure of the quality of experimental phases. This criterion is used in scoring by default. (3) The skew (third moment or normalized <rho**3>) of the density in an electron density map is a good measure of its quality, because a random map has a skew of zero (density histograms look like a Gaussian), while a good map has a very positive skew (density histograms very strong near zero, but many points with very high density). This criterion is used in scoring by default. (4) Non-crystallographic symmetry (NCS overlap). The presence of NCS in a map is a nearly-positive indication that the map is good, or has some correct features. The AutoSol Wizard uses symmetry in heavy-atom sites to suggest NCS, and RESOLVE identifies the actual correlation of NCS-related density for the NCS overlap score. This score is used by default if NCS is present in the Z-score method of scoring. (5) Figure of merit (FOM). The figure of merit of phasing is a good indicator of the internal consistency of a solution. This score is not normalized by the SD of randomized phase sets (as that has no meaning; rather a standard SD=0.05 is used). This score is used by default if NCS is present in the Z-score method of scoring and in the Bayesian CC estimate method. (6) Map correlation after truncation (TRUNCATION). Dummy atoms (the same number as estimated non-hydrogen atoms in the structure) are placed in positions of high density of the map, and a new map is calculated based on these atomic positions. The correlation of these maps is calculated after adjusting an overall B-value for the dummy atoms to maximize the correlation. A good map will show a high correlation of these maps. This score is by default not used. (7) Number of contiguous regions per 100 A**3 comprising top 5% of density in map (REGIONS). The top 5% of points in the map are marked, and the number of contiguous regions that result are counted, and divided by the volume of the asymmetric unit, then multiplied by 100. A good map will have just a few contiguous regions at a high contour level, a poor map will have many isolated peaks. This score is by default not used. (8) Standard deviation of local rms density (SD). The local rms density in the map is calculated using a smoothing radius of 3 times the high-resolution cutoff (or 6 A, if less than 6A). Then the standard deviation of the local rms, normalized to the mean value of the local rms, is reported. This criteria will be high if there are regions of high local rms (the macromolecule) and separate regions of low local rms (the solvent) and low if the map is random. This score is by default not used. PhasingThe AutoSol Wizard uses Phaser to calculate experimental phases from SAD data, and SOLVE to calculate phases from MIR, MAD, and multiple-dataset cases. Density modification (including NCS averaging)The AutoSol Wizard uses RESOLVE to carry out density modification. It identifies NCS from symmetries in heavy-atom sites with RESOLVE and applies this NCS if it is present in the electron density map. Preliminary model-building and refinementThe AutoSol Wizard carries out one cycle of model-building and refinement after obtaining density-modified phases. The model-building can be with RESOLVE or with TEXTAL. The refinement is carried out with phenix.refine. Resolution limits in AutoSolThere are several resolution limits used in AutoSol. You can leave them all to default, or you can set any of them individually. Here is a list of these limits and how their default values are set: Output files from AutoSolWhen you run AutoSol the output files will be in a subdirectory with your run number: AutoSol_run_1_/ The key output files that are produced are:
How to run the AutoSol WizardRunning the AutoSol Wizard is easy. From the command-line you can type: phenix.autosol w1.sca seq.dat 2 Se f_prime=-8 f_double_prime=4.5 The AutoSol Wizard will assume that w1.sca is a datafile (because it ends in .sca and is a file) and that seq.dat is a sequence file, that there are 2 heavy-atom sites, and that the heavy-atom is Se. The f_prime and f_double_prime values are set explicitly You can also specify each of these things directly: phenix.autosol data=w1.sca seq_file=seq.dat sites=2 \ atom_type=Se f_prime=-8 f_double_prime=4.5 You can specify many more parameters as well. See the list of keywords, defaults and descriptions at the end of this page and also general information about running Wizards at Running a Wizard from a GUI, the command-line, or a script for how to do this. Some of the most common parameters are: sites=3 # 3 sites sites_file=sites.pdb # ha sites in PDB or fractional xyz format atom_type=Se # Se is the heavy-atom seq_file=seq.dat # sequence file (1-aa code, separate chains with >>>>) quick=True # try to find sites quickly data=w1.sca # input datafile f_prime=-5 # f-prime value for SAD f_double_prime=4.5 # f-double-prime value for SAD Model viewing during model-building with the Coot-PHENIX interfaceThe AutoSol Wizard allows you to view the current best model that is produced by the automated model-building process. This capability is identical to the view/edit model procedure available in the AutoBuild Wizard. Normally you would use it just to view the model in AutoSol, and to view and edit a model in AutoBuild . The PHENIX-Coot interface is accessible through the GUI and via the command-line. Using the GUI, when a model has been produced by the AutoSol Wizard, you can double-click the button on the GUI labelled View/edit files with coot to start Coot with your current map and model. If you are running from the command-line, you can open a new window and type: phenix.autobuild cootwhich will do the same (provided the necessary map and model are ready). When Coot has been loaded, your map and model will be displayed along with a PHENIX-Coot Interface window. If you want, you can edit your model and then save it, giving it back to PHENIX with the button labelled something like Save model as COMM/overall_best_coot_7.pdb. This button creates the indicated file and also tells PHENIX to look for this file and to try and include the contents of the model in the building process. In AutoSol, only the main-chain atoms of the model you save are considered, and the side-chains are ignored. Ligands and solvent in the model are ignored as well. As the AutoSol Wizard continues to build new models and create new maps, you can update in the PHENIX-Coot Interface to the current best model and map with the button Update with current files from PHENIX. ExamplesSAD datasetphenix.autosol w1.sca seq.dat 2 Se f_prime=-8 f_double_prime=4.5The sequence file is used to estimate the solvent content of the crystal and for model-building. Note that for a SAD dataset the value of f_prime and f_double_prime are not critical. If you are off by a factor of 2 on f_double_prime, the refined occupancies of heavy-atom sites might be 1/2 their correct values. SAD dataset specifying solvent fractionphenix.autosol w1.sca seq.dat 2 Se f_prime=-8 f_double_prime=4.5 \
solvent_fraction=0.45
This will force the solvent fraction to be 0.45. This illustrates a
general feature of the Wizards: they will try to estimate values of
parameters, but if you input them directly, they will use your input
values.
SAD dataset without model-buildingphenix.autosol w1.sca seq.dat 2 Se f_prime=-8 f_double_prime=4.5 \
build=False
This will carry out the usual structure solution, but will skip model-building
SAD dataset, building RNA instead of proteinphenix.autosol w1.sca seq.dat 2 Se f_prime=-8 f_double_prime=4.5 \
chain_type=RNA
This will carry out the usual structure solution, but will build an RNA
chain. For DNA, specify chain_type=DNA. You can only build one type of
chain at a time in the AutoSol Wizard. To build protein and DNA, use
the AutoBuild
Wizard and run it first with chain_type=PROTEIN, then
run it again specifying the protein
model as input_lig_file_list=proteinmodel.pdb
and with chain_type=DNA.
SAD dataset, selecting a particular dataset from an MTZ fileIf you have an input MTZ file with more than one anomalous dataset, you can type something like: phenix.autosol w1.mtz seq.dat 2 Se f_prime=-8 f_double_prime=4.5 \ labels='F SIGF DANO SIGDANO'This will carry out the usual structure solution, but will choose the input data columns based on the labels: 'F SIGF DANO SIGDANO'. If you run the AutoSol Wizard with SAD data and an MTZ file containing more than one anomalous dataset and don't tell it which one to use, all possible values of labels are printed out for you so that you can just paste the one you want in. You can also find out all the possible label strings to use by typing: phenix.autosol display_labels=w1.mtz # display all labels for w1.mtz MRSAD -- SAD dataset with an MR model; Phaser SAD phasing including the modelIf you are carrying out SAD phasing with Phaser, you can carry out a combination of molecular replacement phasing and SAD phasing (MRSAD) by adding a single new keyword to your AutoSol run: input_partpdb_file=MR.pdbIn this case the MR.pdb file will be used as a partial model in a maximum-likelihood SAD phasing calculation with Phaser to calculate phases and identify sites in Phaser, and the combined MR+SAD phases will be written out. NOTE: At the moment the AutoBuild Wizard is not equipped to use these combined phases optimally in iterative model-building, density modification and refinement, because they contain both experimental phase information and model information. It is therefore possible that the resulting phases are biased by your MR model, and that this bias will not go away during iterative model-building because it is continually fed back in. Using an MR model to find sites and as a source of phase information (method #2 for MRSAD)You can also combine MR information with SAD phases (see J. P. Schuermann and J. J. Tanner Acta Cryst. (2003). D59, 1731-1736 ) in PHENIX by running the three wizards AutoMR, AutoSol, and AutoBuild one after the other. This method does not use the partial model and the anomalous information in the SAD dataset simultaneously as the above Phaser maximum-likelihood method does. On the other hand, the phases obtained in this method are independent of the model, so that combining them afterwards does not introduce model bias. (It is not yet clear which is the better approach, so you may wish to try both.) Additionally, this approach can be used with any method for phasing. Here is a set of three simple commands to do this: First run AutoMR to find the molecular replacement solution, but don't rebuild it yet: phenix.automr gene-5.pdb infl.sca copies=1 \ RMS=1.5 mass=9800 rebuild_after_mr=FalseNow your MR solution is in AutoMR_run_1_/MR.1.pdb and phases are in AutoMR_run_1_/MR.1.mtz. Use these phases as input to AutoSol, along with some weak SAD data, still not building any new models: phenix.autosol data=infl.sca \ input_phase_file=AutoMR_run_1_/MR.1.mtz input_phase_labels="F PHIC FOM" \ seq_file=sequence.dat build=Falsenote that we have specified the data columns for F PHI and FOM in the input_phase_file. For input_phase_file you must specify all three of these (if you leave out FOM it will set it to zero). AutoSol will write an MTZ file with experimental phases to phaser_xx.mtz where xx depends on how many solutions are considered during the run. The next command for running AutoBuild you will need to edit depending on the value of xx: phenix.autobuild data=AutoSol_run_1_/phaser_2.mtz \ model=AutoMR_run_1_/MR.1.pdb seq_file=sequence.dat rebuild_in_place=FalseAutoBuild will now take the phases from your AutoSol run and combine them with model-based information from your AutoMR MR solution, and will carry out iterative density modification, model-building and refinement to rebuild your model. Note that you may wish to set rebuild_in_place=True, depending on how good your MR model is. SAD dataset, reading heavy-atom sites from a PDB file written by phenix.hyssphenix.autosol 11 Pb data=deriv.sca seq_file=seq.dat \ sites_file=deriv_hyss_consensus_model.pdbThis will carry out the usual structure solution process, but will read sites from deriv_hyss_consensus_model.pdb, try both hands, and carry on from there. If you know the hand of the substructure, you can fix it with have_hand=True. MAD datasetThe inputs for a MAD dataset need to specify f_prime and f_double_prime for each wavelength. It also must be clear what datafile goes with which wavelength. If you input an MTZ file with multiple datasets, then the order of those datasets is assumed to be the same as the order of the wavelengths. You may want to either select particular datasets from your MTZ file (see below) or split such an MTZ file into separate files for each dataset if this does not work in the way you expect. phenix.autosol seq_file=seq.dat sites=2 atom_type=Se \ peak.data=w1.sca peak.f_prime=-8 peak.f_double_prime=4.5 \ infl.data=w2.sca infl.f_prime=-9 infl.f_double_prime=1.9 \ high.data=w3.sca high.f_prime=-5 high.f_double_prime=3.0 MAD dataset, selecting particular datasets from an MTZ fileThis is similar to the case for SAD data.If you have an input MTZ file with more than one anomalous dataset, you can type something like: phenix.autosol seq_file=seq.dat sites=2 atom_type=Se \ peak.data=all_data.mtz peak.f_prime=-8 peak.f_double_prime=4.5 \ high.data=all_data.mtz high.f_prime=-5 high.f_double_prime=3.0 \ peak.labels='Fpeak SIGFpeak DANOpeak SIGDANOpeak' \ high.labels='Fhigh SIGFhigh DANOhigh SIGDANOhigh'This will carry out the usual structure solution, but will choose the input peak data columns based on the labels: 'Fpeak SIGFpeak DANOpeak SIGDANOpeak', and the high data from the ones labelled 'Fhigh SIGFhigh DANOhigh SIGDANOhigh'. As in the SAD case, you can find out all the possible label strings to use by typing: phenix.autosol display_labels=w1.mtz # display all labels for w1.mtz SIR datasetThe standard inputs for an SIR dataset are the native and derivative, the sequence file, the heavy-atom type, and the number of sites, as well as whether to use anomalous differences (or just isomorphous differences): phenix.autosol native.data=native.sca deriv.data=deriv.sca \ deriv.atom_type=I deriv.sites=2 deriv.inano=inanoThis will set the heavy-atom type to Iodine, look for 2 sites, and include anomalous differences. SAD with more than one anomalously-scattering atomYou can tell the AutoSol wizard to look for more than one anomalously- scattering atom. Specify one atom type (Se) in the usual way. Then specify any additional ones like this if you are running AutoSol from the command line: mad_ha_add_list="Br Pt" mad_ha_add_f_prime_list=" -7 -10" mad_ha_add_f_double_prime_list=" 4.2 12"There must be the same number of entries in each of these three keyword lists. During phasing Phaser will try to add whichever atom types best fit the scattering from each new site. This option is available for SAD phasing only. MIR datasetAn MIR dataset is a set of more than one datasets. This cannot be readily expressed in the command-line inputs, but you can specify it easily with the PHENIX AutoSol GUI or with a script. In a script file you can say: cell 93.796 79.849 43.108 90.000 90.000 90.00 # cell params thoroughness thorough # best to use thorough for MIR resolution 2.8 # Resolution expt_type sir # MIR dataset is set of SIR datasets input_seq_file sequence.dat ############## DATASET 1 ################ input_file_list rt_rd_1.sca auki_rd_1.sca # Native and deriv 1 nat_der_list Native Au # identify files by ha type inano_list noinano inano # say if ano diffs to be used n_ha_list 0 5 # number of heavy-atoms run_list start # read in datafiles for dataset run_list read_another_dataset # about to start a new dataset here ############## DATASET 2 ################ input_file_list rt_rd_1.sca hgki_rd_1.sca # Native and deriv 2 nat_der_list Native Hg inano_list noinano inano n_ha_list 0 5 ######################################### The script file carries out steps in the order that they are input. This allows us to read in one entire dataset, save it, then read in another one. The AutoSol Wizard will solve each dataset and then combine them and phase the combined datset with SOLVE Bayesian correlated phasing, taking into account any correlations among the non-isomorphism and heavy-atom sites for the various derivatives. SIR + SAD datasetsA combination of SIR and SAD datasets is almost the same as an MIR dataset in the AutoSol Wizard. You specify each dataset separately, and put "start" and "read_another_dataset" between the datasets: cell 93.796 79.849 43.108 90.000 90.000 90.00 # cell params resolution 2.8 # Resolution input_seq_file sequence.dat ############## DATASET 1 ################ expt_type sir # MIR dataset is set of SIR datasets input_file_list rt_rd_1.sca auki_rd_1.sca # Native and deriv 1 nat_der_list Native Au # identify files by ha type inano_list noinano inano # say if ano diffs to be used n_ha_list 0 5 # number of heavy-atoms run_list start # read in datafiles for dataset run_list read_another_dataset # about to start a new dataset here ############## DATASET 2 ################ expt_type sad # our second dataset is SAD input_file_list hgki_rd_1.sca # anom diffs for SAD dataset mad_ha_n 5 # 5 sites ######################################### The SIR and SAD datasets will be solved separately (but whichever one is solved first will use difference Fourier or anomalous difference Fourier's to locate sites for the other). Then phases will be combined by addition of Hendrickson-Lattman coefficients and the combined phases will be density modified. Possible ProblemsGeneral limitationsSpecific limitations and problems
Literature
Additional informationList of all AutoSol keywords
-------------------------------------------------------------------------------
Legend: black bold - scope names
black - parameter names
red - parameter values
blue - parameter help
blue bold - scope help
Parameter values:
* means selected parameter (where multiple choices are available)
False is No
True is Yes
None means not provided, not predefined, or left up to the program
"%3d" is a Python style formatting descriptor
-------------------------------------------------------------------------------
autosol
sites= None Number of heavy-atom sites. This is an alias for the keyword
mad_ha_n. (Command-line only)
sites_file= None PDB or plain-text file with ha sites. This is an alias for
the keyword ha_sites_file. (Command-line only)
atom_type= None Anomalously-scattering atom type. This is an alias for the
keyword mad_ha_type. (Command-line only)
seq_file= Auto Sequence file . This is an alias for the keyword
input_seq_file. (Command-line only)
quick= None Run everything quickly (thoroughness=quick) (Command-line only)
data= None Datafile. For command_line input it is easiest if each
wavelength of data is in a separate data file with obvious data
columns. File types that are easy to read include Scalepack sca files
, CNS hkl files, mtz files with just one wavelength of data, or just
native or just derivative. In this case the Wizard can read your data
without further information. If you have a datafile with many
columns, you can use the "labels" keyword to specify which data
columns to read. (It may be easier in some cases to use the GUI or to
split it with phenix.reflection_file_converter first, however.)
(Command-line only)
labels= None Specification string for data labels (Command_line only). To
find out what the appropriate strings are, type "phenix.autosol
display_labels=your-datafile-here.mtz"
f_prime= None F-prime value for any wavelength. (Command-line only)
f_double_prime= None F-doubleprime value for any wavelength. (Command_line
only)
special_keywords
write_run_directory_to_file= None Writes the full name of a run
directory to the specified file. This can
be used as a call-back to tell a script
where the output is going to go.
(Command-line only)
run_control
coot= None Set coot to True and optionally run=[run-number] to run Coot
with the current model and map for run run-number. In some wizards
(AutoBuild) you can edit the model and give it back to PHENIX to
use as part of the model-building process. If you just say coot
then the facts for the highest-numbered existing run will be
shown. (Command-line only)
ignore_blanks= None ignore_blanks allows you to have a command-line
keyword with a blank value like "input_lig_file_list="
stop= None You can stop the current wizard with "stopwizard" or "stop".
If you type "phenix.autobuild run=3 stop" then this will stop run
3 of autobuild. (Command-line only)
display_facts= None Set display_facts to True and optionally
run=[run-number] to display the facts for run run-number.
If you just say display_facts then the facts for the
highest-numbered existing run will be shown.
(Command-line only)
display_summary= None Set display_summary to True and optionally
run=[run-number] to show the summary for run
run-number. If you just say display_summary then the
summary for the highest-numbered existing run will be
shown. (Command-line only)
carry_on= None Set carry_on to True to carry on with highest-numbered
run from where you left off. (Command-line only)
run= None Set run to n to continue with run n where you left off.
(Command-line only)
copy_run= None Set copy_run to n to copy run n to a new run and continue
where you left off. (Command-line only)
display_runs= None List all runs for this wizard. (Command-line only)
delete_runs= None List runs to delete: 1 2 3-5 9:12 (Command-line only)
display_labels= None display_labels=test.mtz will list all the labels
that identify data in test.mtz. You can use the label
strings that are produced in AutoSol to identify which
data to use from a datafile like this: peak.data="F+
SIGF+ F- SIGF-" # the entire string in quotes counts
here You can use the individual labels from these
strings as identifiers for data columns in AutoSol and
AutoBuild like this: input_refinement_labels="FP SIGFP
FreeR_flags" # each individual label counts
dry_run= False Just read in and check parameter names
params_only= False Just read in and return parameter defaults
display_all= False Just read in and display parameter defaults
peak
data= None Datafile for peak wavelength. (Command_line only)
labels= None Specification string for data labels for peak wavelength.
(Command_line only). To find out what the appropriate strings
are, type "phenix.autosol display_labels=your-datafile-here.mtz"
f_prime= None F-prime value for peak wavelength. (Command_line only)
f_double_prime= None F-doubleprime value for peak wavelength.
(Command_line only)
infl
data= None Datafile for infl wavelength. (Command_line only)
labels= None Specification string for data labels for infl wavelength.
(Command_line only). To find out what the appropriate strings
are, type "phenix.autosol display_labels=your-datafile-here.mtz"
f_prime= None F-prime value for infl wavelength. (Command_line only)
f_double_prime= None F-doubleprime value for infl wavelength.
(Command_line only)
high
data= None Datafile for high wavelength. (Command_line only)
labels= None Specification string for data labels for high wavelength.
(Command_line only). To find out what the appropriate strings
are, type "phenix.autosol display_labels=your-datafile-here.mtz"
f_prime= None F-prime value for high wavelength. (Command_line only)
f_double_prime= None F-doubleprime value for high wavelength.
(Command_line only)
low
data= None Datafile for low wavelength. (Command_line only)
labels= None Specification string for data labels for low wavelength.
(Command_line only). To find out what the appropriate strings
are, type "phenix.autosol display_labels=your-datafile-here.mtz"
f_prime= None F-prime value for low wavelength. (Command_line only)
f_double_prime= None F-doubleprime value for low wavelength.
(Command_line only)
remote
data= None Datafile for remote wavelength. (Command_line only)
labels= None Specification string for data labels for remote wavelength.
(Command_line only). To find out what the appropriate strings
are, type "phenix.autosol display_labels=your-datafile-here.mtz"
f_prime= None F-prime value for remote wavelength. (Command_line only)
f_double_prime= None F-doubleprime value for remote wavelength.
(Command_line only)
native
data= None Datafile for native . (Command_line only)
labels= None Specification string for data labels for native .
(Command_line only). To find out what the appropriate strings
are, type "phenix.autosol display_labels=your-datafile-here.mtz
"
atom_type= Native Heavy-atom type for native . (Command_line only)
sites= 0 Number of heavy-atom sites for native . (Command_line only)
inano= *noinano inano anoonly Use anomalous differences for native .
(Command_line only)
deriv
data= None Datafile for deriv . (Command_line only)
labels= None Specification string for data labels for deriv .
(Command_line only). To find out what the appropriate strings
are, type "phenix.autosol display_labels=your-datafile-here.mtz
"
atom_type= I Heavy-atom type for deriv . (Command_line only)
sites= 2 Number of heavy-atom sites for deriv . (Command_line only)
inano= noinano *inano anoonly Use anomalous differences for deriv .
(Command_line only)
crystal_info
cell= 0.0 0.0 0.0 0.0 0.0 0.0 Enter cell parameter a b c alpha beta
gamma
chain_type= *Auto PROTEIN DNA RNA You can specify whether to build
protein, DNA, or RNA chains. At present you can only build
one of these in a single run. If you have both DNA and
protein, build one first, then run AutoBuild again,
supplying the prebuilt model in the "input_lig_file_list"
and build the other. NOTE: default for this keyword is Auto,
which means "carry out normal process to guess this
keyword". The process is to look at the sequence file and/or
input pdb file to see what the chain type is. If there are
more than one type, the type with the larger number of
residues is guessed. If you want to force the chain_type,
then set it to PROTEIN RNA or DNA.
change_sg= False You can change the space group. In AutoSol the Wizard
will use ImportRawData and let you specify the sg and cell.
In AutoMR the wizard will give you an entry form to specify
them. NOTE: This only applies when reading in new datasets.
It does nothing when changed after datasets are read in.
residues= None Number of amino acid residues in the au (or equivalent)
resolution= 0.0 High-resolution limit.Used as resolution limit for
density modification and as general default high-resolution
limit. If resolution_build or refinement_resolution are set
then they override this for model-building or refinement. If
overall_resolution is set then data beyond that resolution
is ignored completely.
sg= None Space Group symbol (i.e., C2221 or C 2 2 21)
solvent_fraction= None Solvent fraction (typically 0.4 - 0.6)
decision_making
acceptable_quality= 40.0 You can specify the minimum overall quality of
a model (as defined by overall_score_method) to be
considered acceptable
acceptable_secondary_structure_cc= 0.35 You can specify the minimum
correlation of density from a
secondary structure model to be
considered acceptable
create_scoring_table= False Choose whether you want a scoring table for
solutions A scoring table is slower but better
desired_coverage= 0.8 Choose what probability you want to have that the
correct solution is in your current list of top
solutions. A good value is 0.80. If you set a low
value (0.01) then only one solution will be kept at
any time; if you set a high value, then many solutions
will be kept (and it will take longer).
ha_iteration= False Choose whether you want to iterate the heavy-atom
search. With iteration, sites are found with HYSS, then
used to phase and carry out quick density-modification,
then difference Fourier is used to find sites again and
improve their accuracy.
hklperfect= None Enter an mtz file with idealized coefficients for map
This will be compared with all maps calculated during
structure solution
max_cc_extra_unique_solutions= 0.5 Specify the maximum value of CC
between experimental maps for two
solutions to consider them substantially
different. Solutions that are within the
range for consideration based on
desired_coverage, but are outside of the
number of allowed max_choices, will be
considered, up to
max_extra_unique_solutions, if they have
a correlation of no more than
max_cc_extra_unique_solutions with all
other solutions to be tested.
max_choices= 3 Number of choices for solutions to put on screen
max_composite_choices= 8 Number of choices for composite solutions to
consider
max_extra_unique_solutions= 2 Specify the maximum number of solutions to
consider based on their uniqueness as well
as their high scores. Solutions that are
within the range for consideration based on
desired_coverage, but are outside of the
number of allowed max_choices, will be
considered, up to
max_extra_unique_solutions, if they have a
correlation of no more than
max_cc_extra_unique_solutions with all other
solutions to be tested.
max_ha_iterations= 2 Number of iterations of difference Fouriers in
searching for heavy-atom sites
max_range_to_keep= 4.0 The range of solutions to be kept is
range_to_keep * SD of the group of solutions. This
sets the maximum of range_to_keep
min_fom= 0.05 Minimum fom of a solution to keep it at all
min_fom_for_dm= 0.0 Minimum fom of a solution to density modify
(otherwise just copy over phases). This is useful in
cases where the phasing is so weak that density
modification does nothing or makes the phases worse.
min_phased_each_deriv= 1 You can require that the wizard phase at least
this number of solutions from each derivative,
even if they are poor solutions. Usually at least
1 is a good idea so that one derivative does not
dominate the solutions.
minimum_improvement= 0.0 Minimum improvement in score to continue ha
iteration
n_random= 6 Number of random solutions to generate when setting up
scoring table
overall_score_method= *BAYES-CC Z-SCORE You have 2 choices for an
overall scoring method: (1) Sum of individual
Z-scores (Z-SCORE) (3) Bayesian estimate of CC of
map to perfect model (BAYES-CC) You can specify
which scoring criteria to include with
score_type_list (default is SKEW CORR_RMS for
BAYES-CC and CC RFACTOR SKEW FOM for Z-SCORE.
Additionally, if NCS is present, NCS_OVERLAP is
used by default in the Z-SCORE method).
perfect_labels= None Labels for input data columns for hklperfect
Typical value: "FP PHIC FOM"
r_switch= 0.4 R-value criteria for deciding whether to use R-value or
residues built A good value is 0.40
random_scoring= False For testing purposes you can generate random
scores
res_eval= 0.0 Resolution for running resolve evaluation (usually 2.5 A)
score_individual_offset_list= None Offsets for individual scores in
CC-scoring. Each score will be multiplied
by the score_individual_scale_list value,
then score_individual_offset_list value is
added, to estimate the CC**2 value using
this score by itself. The uncertainty in
the CC**2 value is given by
score_individual_sd_list. NOTE: These
scores are not used in calculation of the
overall score. They are for information
only
score_individual_scale_list= None Scale factors for individual scores in
CC-scoring. Each score will be multiplied
by the score_individual_scale_list value,
then score_individual_offset_list value is
added, to estimate the CC**2 value using
this score by itself. The uncertainty in
the CC**2 value is given by
score_individual_sd_list. NOTE: These
scores are not used in calculation of the
overall score. They are for information
only
score_individual_sd_list= None Uncertainties for individual scores in
CC-scoring. Each score will be multiplied by
the score_individual_scale_list value, then
score_individual_offset_list value is added,
to estimate the CC**2 value using this score
by itself. The uncertainty in the CC**2 value
is given by score_individual_sd_list. NOTE:
These scores are not used in calculation of
the overall score. They are for information
only
score_overall_offset= None Overall offset for scores in CC-scoring. The
weighted scores will be summed, then all
multiplied by score_overall_scale, then
score_overall_offset will be added.
score_overall_scale= None Overall scale factor for scores in CC-scoring.
The weighted scores will be summed, then all
multiplied by score_overall_scale, then
score_overall_offset will be added.
score_overall_sd= None Overall SD of CC**2 estimate for scores in
CC-scoring. The weighted scores will be summed, then
all multiplied by score_overall_scale, then
score_overall_offset will be added. This is an
estimate of CC**2, with uncertainty about
score_overall_sd. Then the square root is taken to
estimate CC and SD(CC), where SD(CC) now depends on CC
due to the square root.
score_type_list= SKEW CORR_RMS You can choose what scoring methods to
include in scoring of solutions in AutoSol. (The
choices available are: CC_DENMOD RFACTOR SKEW
NCS_COPIES NCS_IN_GROUP TRUNCATE FLATNESS CORR_RMS
REGIONS CONTRAST FOM ) NOTE: If you are using
Z-SCORE or BAYES-CC scoring, The default is CC_RMS
RFACTOR SKEW FOM (and NCS_OVERLAP if ncs_copies >1).
score_weight_list= None Weights on scores for CC-scoring. Enter the
weight on each score in score_type_list. The weighted
scores will be summed, then all multiplied by
score_overall_scale, then score_overall_offset will
be added.
skip_score_list= NCS_OVERLAP You can evaluate some scores but not use
them. Include the ones you do not want to use in the
final score in skip_score_list.
use_perfect= False You can use the CC between each solution and
hklperfect in scoring. This is only for methods development
purposes.
density_modification
fix_xyz= False You can choose to not refine coordinates, and instead to
fix them to the values found by the heavy-atom search.
fix_xyz_after_denmod= False When sites are found after density
modification you can choose whether you want to
fix the coordinates to the values found in that
map.
hl_in_resolve= False AutoSol normally does not write out HL coefficients
in the resolve.mtz file with density-modified phases. You
can turn them on with hl_in_resolve=True
mask_cycles= 5 Number of mask cycles in density modification (5 is usual
for thorough density modification
mask_type= *histograms probability wang Choose method for obtaining
probability that a point is in the protein vs solvent region.
Default is "histograms". If you have a SAD dataset with a
heavy atom such as Pt or Au then you may wish to choose
"wang" because the histogram method is sensitive to very high
peaks. Options are: histograms: compare local rms of map and
local skew of map to values from a model map and estimate
probabilities. This one is usually the best. probability:
compare local rms of map to distribution for all points in
this map and estimate probabilities. In a few cases this one
is much better than histograms. wang: take points with
highest local rms and define as protein.
minor_cycles= 10 Number of minor cycles in density modification for each
mask cycle (10 is usual for thorough density modification
test_mask_type= True You can choose to have AutoSol test histograms/wang
methods for identifying solvent region based on the
final density modification r-factor.
thorough_denmod= False Choose whether you want to go for quick density
modification (speeds it up and for a terrible map is
sometimes better)
truncate_ha_sites_in_resolve= Auto *Yes No True False You can choose to
truncate the density near heavy-atom sites
at a maximum of 2.5 sigma. This is useful
in cases where the heavy-atom sites are
very strong, and rarely hurts in cases
where they are not. The heavy-atom sites
are specified with "input_ha_file"
use_ncs_in_denmod= True This script normally uses available ncs
information in density modification. Say No to skip
this. See also find_ncs
display
number_of_solutions_to_display= 1 Number of solutions to put on screen
and to write out
solution_to_display= 0 Solution number of the solution to display and
write out ( use 0 to let the wizard display the top
solution)
general
background= True When you specify nproc=nn, you can run the jobs in
background (default if nproc is greater than 1) or
foreground (default if nproc=1). If you set
run_command=qsub (or otherwise submit to a batch queue),
then you should set background=False, so that the batch
queue can keep track of your runs. There is no need to use
background=True in this case because all the runs go as
controlled by your batch system. If you use run_command=csh
(or similar, csh is default) then normally you will use
background=True so that all the jobs run simultaneously.
base_path= None You can specify the base path for files (default is
current working directory)
clean_up= False At the end of the entire run the TEMP directories will
be removed if clean_up is True. The default is No, keep these
directories. If you want to remove them after your run is
finished use a command like "phenix.autobuild run=1
clean_up=True"
coot_name= coot If your version of coot is called something else, then
you can specify that here.
data_quality= *moderate strong weak The defaults are set for you
depending on the anticipated data quality. You can choose
"moderate" if you are unsure.
debug= False You can have the wizard stop with error messages about the
code if you use debug. NOTE: you cannot use Pause with debug.
expt_type= *Auto mad sir sad Experiment type (MAD SIR SAD) NOTE: Please
treat MIR experiments as a set of SIR experiments. NOTE: The
default for this keyword is Auto which means "carry out
normal process to guess this keyword". If you have a single
file, then it is assumed to be SAD. If you specify
native.data and deriv.data it is SIR, if you specify
peak.data and infl.data it is MAD. If the Wizard does not
guess correctly, you can set it with this keyword.
extra_verbose= False Facts and possible commands will be printed every
cycle if Yes
i_ran_seed= 588459 Random seed (positive integer) for model-building
and simulated annealing refinement
max_wait_time= 100.0 You can specify the length of time (seconds) to
wait when testing the run_command. If you have a cluster
where jobs do not start right away you may need a longer
time to wait.
nbatch= 1 You can specify the number of processors to use (nproc) and
the number of batches to divide the data into for parallel jobs.
Normally you will set nproc to the number of processors
available and leave nbatch alone. If you leave nbatch as None it
will be set automatically, with a value depending on the Wizard.
This is recommended. The value of nbatch can affect the results
that you get, as the jobs are not split into exact replicates,
but are rather run with different random numbers. If you want to
get the same results, keep the same value of nbatch.
nproc= 1 You can specify the number of processors to use (nproc) and the
number of batches to divide the data into for parallel jobs.
Normally you will set nproc to the number of processors available
and leave nbatch alone. If you leave nbatch as None it will be
set automatically, with a value depending on the Wizard. This is
recommended. The value of nbatch can affect the results that you
get, as the jobs are not split into exact replicates, but are
rather run with different random numbers. If you want to get the
same results, keep the same value of nbatch.
resolve_size= _giant _huge _extra_huge *None Size for solve/resolve
("","_giant","_huge","_extra_huge")
run_command= csh When you specify nproc=nn, you can run the subprocesses
as jobs in background with csh (default) or submit them to
a queue with the command of your choice (i.e., qsub ). If
you have a multi-processor machine, use csh. If you have a
cluster, use qsub or the equivalent command for your
system. NOTE: If you set run_command=qsub (or otherwise
submit to a batch queue), then you should set
background=False, so that the batch queue can keep track of
your runs. There is no need to use background=True in this
case because all the runs go as controlled by your batch
system. If you use run_command=csh (or similar, csh is
default) then normally you will use background=True so that
all the jobs run simultaneously.
skip_xtriage= False You can bypass xtriage if you want. This will
prevent you from applying anisotropy corrections, however.
temp_dir= None Define a temporary directory (it must exist)
thoroughness= *quick thorough You can try to run quickly and see if you
can get a solution ("quick") or more thoroughly to get the
best possible solution ("thorough").
title= Run 1 AutoSol Sun Dec 7 17:46:23 2008 Enter any text you like to
help identify what you did in this run
top_output_dir= None This is used in subprocess calls of wizards and to
tell the Wizard where to look for the STOPWIZARD file.
verbose= False Command files and other verbose output will be printed
heavy_atom_search
acceptable_cc_hyss= 0.2 Hyss will be run at up to n_add_res_max+1
resolutions starting with res_hyss and adding
increments of add_res_max/n_add_res_max. If the best
CC value is greater than acceptable_cc_hyss then no
more resolutions are tried.
add_res_max= 2.0 Hyss will be run at up to n_add_res_max+1 resolutions
starting with res_hyss and adding increments of
add_res_max/n_add_res_max. If the best CC value is greater
than acceptable_cc_hyss then no more resolutions are tried.
best_of_n_hyss= 1 Hyss will be run up to best_of_n_hyss_always times at
a given resolution. If the best CC value is greater than
good_cc_hyss and the number of sites found is at least
min_fraction_of_sites_found times the number expected
and Hyss was tried at least best_of_n_hyss times, then
the search is ended.
best_of_n_hyss_always= 10 Hyss will be run up to best_of_n_hyss_always
times at a given resolution. If the best CC value
is greater than good_cc_hyss and the number of
sites found is at least
min_fraction_of_sites_found times the number
expected and Hyss was tried at least
best_of_n_hyss times, then the search is ended.
good_cc_hyss= 0.3 Hyss will be run up to best_of_n_hyss_always times at
a given resolution. If the best CC value is greater than
good_cc_hyss and the number of sites found is at least
min_fraction_of_sites_found times the number expected and
Hyss was tried at least best_of_n_hyss times, then the
search is ended.
hyss_enable_early_termination= True You can specify whether to stop HYSS
as soon as it finds a convincing solution
(Yes, default) or to keep trying...
hyss_general_positions_only= True Select Yes if you want HYSS only to
consider general positions and ignore sites
on special positions. This is appropriate
for SeMet or S-Met solutions, not so
appropriate for heavy-atom soaks
hyss_min_distance= 3.5 Enter the minimum distance between heavy-atom
sites to keep them in HYSS
hyss_n_fragments= 3 Enter the number of fragments in HYSS
hyss_n_patterson_vectors= 33 Enter the number of Patterson vectors to
consider in HYSS
hyss_random_seed= 792341 Enter an integer as random seed for HYSS
mad_ha_n= None Number of heavy atoms (anomalously-scattering atoms) in
the au
mad_ha_type= Se Enter the anomalously-scattering or heavy atom type. For
example, Se or Au. NOTE: if you want Phaser to add
additional heavy-atoms of other types, you can specify them
with mad_ha_add_list.
max_single_sites= 5 In sites_from_denmod a core set of sites that are
strong is identified. If the hand of the solution is
known then additional sites are added all at once up
to the expected number of sites. Otherwise sites are
added one at a time, up to a maximum number of tries
of max_single_sites
min_fraction_of_sites_found= 1.0 Hyss will be run up to
best_of_n_hyss_always times at a given
resolution. If the best CC value is greater
than good_cc_hyss and the number of sites
found is at least
min_fraction_of_sites_found times the
number expected and Hyss was tried at least
best_of_n_hyss times, then the search is
ended.
min_hyss_cc= 0.05 Minimum CC of a heavy-atom solution in HYSS to keep it
at all
n_add_res_max= 2 Hyss will be run at up to n_add_res_max+1 resolutions
starting with res_hyss and adding increments of
add_res_max/n_add_res_max. If the best CC value is
greater than acceptable_cc_hyss then no more resolutions
are tried.
input_files
cif_def_file_list= None You can enter any number of CIF definition
files. These are normally used to tell phenix.refine
about the geometry of a ligand or unusual residue.
You usually will use these in combination with "PDB
file with metals/ligands" (keyword
"input_lig_file_list" ) which allows you to attach
the contents of any PDB file you like to your model
just before it gets refined. You can use
phenix.elbow to generate these if you do not have a
CIF file and one is requested by phenix.refine
group_labels_list= None For command-line and script running of AutoSol,
you may wish to use keywords to specify which set of
data columns to be used from an MTZ or other file
type with multiple datasets. (From the GUI, it is
easy because you are prompted with the column
labels). You can do this by specifying a string that
identifies which dataset to include. All allowed
values of this identification string will be written
out any time AutoSol is run on this dataset like
this: NOTE: To specify a particular set of data you
can specify one of the following (this example is for
MAD data, specifying data for peak wavelength): ...:
peak.labels='F SIGF DANO SIGDANO' peak.labels='F(+)
SIGF(+) F(-) SIGF(-)' You can then use one of the
above commands on the command-line to identify the
dataset of interest. If you want to use a script
instead, you can specify N files in your
input_data_file_list, and then specify N values for
group_labels_list like this: group_labels_list
'F,SIGF,DANO,SIGDANO' 'F(+),SIGF(+),F(-),SIGF(-)'
This will take 'F,SIGF,DANO,SIGDANO' as the data for
datafile 1 and 'F(+),SIGF(+),F(-),SIGF(-)' for
datafile 2 You can identify one dataset from each
input file in this way. If you want more than one,
then please use phenix.reflection_file_converter to
split your input file, or else use the GUI version of
AutoSol in which you can select any subset of the
data that you wish.
input_file_list= None Input data files: Any standard format is fine. If
all files are Scalepack premerged or all are Scalepack
unmerged original index then they will be used as is.
In all other cases all files are converted next to
Scalepack premerged.
input_ha_file= None If the flag "truncate_ha_sites_in_resolve" is set
then density at sites specified with input_ha_file is
truncated to improve the density modification procedure.
input_phase_file= None MTZ data file with FC PHIC or equivalent to use
for finding heavy-atom sites with difference Fourier
methods.
input_refinement_file= None Data file to use for refinement. The data in
this file should not be corrected for anisotropy.
It will be combined with experimental phase
information for refinement. If you leave this
blank, then the output of phasing will be used in
refinement (see below). If no anisotropy
correction is applied to the data you do not need
to specify a datafile for refinement. If an
anisotropy correction is applied to the data
files, then you must enter a datafile for
refinement if you want to refine your model. (See
"correct_aniso" for specifying whether an
anisotropy correction is applied. In most cases
it is not.) If an anisotropy correction is
applied and no refinement datafile is supplied,
then no refinement will be carried out in the
model-building step. You can choose any of your
datafiles to be the refinement file, or a native
that is not part of the datasets for structure
solution. If there are more than one dataset you
will be asked each time for a refinement file,
but only the last one will be used. Any
standard format is fine; normally only F and sigF
will be used. Bijvoet pairs and duplicates will
be averaged. If an mtz file is provided then a
free R flag can be read in as well. If you do
not provide a refinement file then the structure
factors from the phasing step will be used in
refinement. This is normally satisfactory for SAD
data and MIR data. For MAD data you may wish to
supply a refinement file because the structure
factors from phasing are a combination of data
from different wavelengths of data. It is better
if you choose your best wavelength of data for
refinement.
input_refinement_labels= None Labels for input refinement file columns
(FP SIGFP FreeR_flag)
input_seq_file= Auto Enter name of file with 1-letter code of protein
sequence NOTES: 1. lines starting with > are ignored
and separate chains 2. FASTA format is fine 3. If
there are multiple copies of a chain, just enter one
copy. 4. If you enter a PDB file for rebuilding and it
has the sequence you want, then the sequence file is not
necessary. NOTE: You can also enter the name of a PDB
file that contains SEQRES records, and the sequence from
the SEQRES records will be read, written to
seq_from_seqres_records.dat, and used as your input
sequence. NOTE: for AutoBuild you can specify
start_chains_list on the first line of your sequence
file: >> start_chains_list 23 11 5 NOTE: default
for this keyword is Auto, which means "carry out normal
process to guess this keyword". This means if you
specify "after_autosol" in AutoBuild, AutoBuild will
automatically take the value from AutoSol. If you do not
want this to happen, you can specify None which means
"No file"
refine_eff_file_list= None You can enter any number of refinement
parameter files. These are normally used to tell
phenix.refine defaults to apply, as well as
creating specialized definitions such as unusual
amino acid residues and linkages. These
parameters override the normal phenix.refine
defaults. They themselves can be overridden by
parameters set by the Wizard and by you,
controlling the Wizard. NOTE: Any parameters set
by AutoBuild directly (such as
number_of_macro_cycles, high_resolution, etc...)
will not be taken from this parameters file. This
is useful only for adding extra parameters not
normally set by AutoBuild.
model_building
add_sidechains= True Add side chains on to main-chain in Textal
model-building. This requires a sequence file
build= True Build model after density modification?
build_type= RESOLVE_AND_TEXTAL *RESOLVE TEXTAL You can choose to build
models with RESOLVE and TEXTAL or either one, and how many
different models to build with RESOLVE. The more you build,
the more likely to get a complete model. Note that
rebuild_in_place can only be carried out with RESOLVE
model-building
capra= True CAPRA is used to place CA atoms
cc_helix_min= None Minimum CC of helical density to map at low
resolution when using helices_strands_only
cc_strand_min= None Minimum CC of strand density to map when using
helices_strands_only
d_max_textal= 1000.0 This low-resolution limit is only used for Textal
model-building
d_min_textal= 2.8 Textal has an optimal high-resolution limit of 2.8 A
This limit is only used for Textal model-building
fit_loops= True You can fit loops automatically if sequence alignment
has been done.
group_ca_length= 4 In resolve building you can specify how short a
fragment to keep. Normally 4 or 5 residues should be
the minimum.
group_length= 2 In resolve building you can specify how many fragments
must be joined to make a connected group that is kept.
Normally 2 fragments should be the minimum.
helices_strands_only= False You can choose to use a quick model-building
method that only builds secondary structure. At
low resolution this may be both quicker and more
accurate than trying to build the entire structure
If you are running the AutoSol Wizard, normally
you should choose 'Yes' and use the quick
model-building. Then when your structure is solved
by AutoSol, go on to AutoBuild and build a more
complete model (this time normally using
helices_strands_only=False).
helices_strands_start= True You can choose to use a quick model-building
method that builds secondary structure as a way
to get started...then model completion is done as
usual. (Contrast with helices_strands_only which
only does secondary structure)
input_compare_file= None If you are rebuilding a model or already think
you know what the model should be, you can include a
comparison file in rebuilding. The model is not used
for anything except to write out information on
coordinate differences in the output log files.
NOTE: this feature does not always work correctly.
loop_cc_min= 0.4 You can specify the minimum correlation of density from
a loop with the map.
n_cycle_build= 3 Choose number of cycles (3). This does not apply if
TEXTAL is selected for build_type
n_random_frag= 0 In resolve building you can randomize each fragment
slightly so as to generate more possibilities for tracing
based on extending it.
n_random_loop= 3 Number of randomized tries from each end for building
loops If 0, then one try. If N, then N additional tries
with randomization based on rms_random_loop.
ncycle_refine= 3 Choose number of refinement cycles (3)
number_of_builds= 2 Number of different solutions to build models for
number_of_models= 3 This parameter lets you choose how many initial
models to build with RESOLVE within a single build
cycle. This parameter is now superseded by
number_of_parallel_models, which sets the number of
models (but now entire build cycles) to carry out in
parallel. A zero means set it automatically. That is
what you normally should use. The number_of_models is
by default set to 1 and number_of_parallel_models is
set to the value of nbatch (typically 4).
offsets_list= 53 7 23 You can specify an offset for the orientation of
the helix and strand templates in building. This is used
in generating different starting models.
quick_build= False Choose whether you want to go for quick
model-building (speeds it up, and for poor maps, is
sometimes better)
rebuild_side_chains= False You can choose to replace side chains (with
extend_only) before rebuilding the model (not
normally used)
refine= False This script normally refines the model during building.
Say No to skip refinement
resolution_build= 0.0 Enter the high-resolution limit for
model-building. If 0.0, the value of resolution is
used as a default.
resolve_command_list= None Commands for resolve. One per line in the
form: keyword value value can be optional
Examples: coarse_grid resolution 200 2.0 hklin
test.mtz NOTE: for command-line usage you need to
enclose the whole set of commands in double quotes
(") and each individual command in single quotes
(') like this: resolve_command_list="'no_build'
'b_overall 23' "
retrace_before_build= False You can choose to retrace your model n_mini
times and use a map based on these retraced models
to start off model-building. This is the default
for rebuilding models if you are not using
rebuild_in_place. You can also specify
n_iter_rebuild, the number of cycles of
retrace-density-modify-build before starting the
main build.
rms_random_frag= None Rms random position change added to residues on
ends of fragments when extending them If you enter a
negative number, defaults will be used.
rms_random_loop= None Rms random position change added to residues on
ends of loops in tries for building loops If you enter
a negative number, defaults will be used.
semet= False You can specify that the dataset that is used for
refinement is a selenomethionine dataset, and that the model
should be the SeMet version of the protein, with all SD of MET
replaced with Se of MSE.
solve_command_list= None Commands for solve. One per line in the form:
keyword value value can be optional Examples:
verbose resolution 200 2.0
start_chains_list= None You can specify the starting residue number for
each of the unique chains in your structure. If you
use a sequence file then the unique chains are
extracted and the order must match the order of your
starting residue numbers. For example, if your
sequence file has chains A and B (identical) and
chains C and D (identical to each other, but
different than A and B) then you can enter 2 numbers,
the starting residues for chains A and C. NOTE: you
need to specify an input sequence file for
start_chains_list to be applied.
thorough_loop_fit= True Try many conformations and accept them even if
the fit is not perfect? If you say Yes the parameters
for thorough loop fitting are: n_random_loop=100
rms_random_loop=0.3 rho_min_main=0.5 while if you say
No those for quick loop fitting are: n_random_loop=20
rms_random_loop=0.3 rho_min_main=1.0
trace_as_lig= False You can specify that in building steps the ends of
chains are to be extended using the LigandFit algorithm.
This is default for nucleic acid model-building.
use_any_side= False You can choose to have resolve model-building place
the best-fitting side chain at each position, even if the
sequence is not matched to the map.
use_met_in_align= Auto *Yes No True False You can use the heavy-atom
positions in input_ha_file as markers for Met SD
positions.
ncs
find_ncs= Auto *Yes No True False This script normally deduces ncs
information from the NCS in chains of models that are built
during iterative model-building. The update is done each cycle
in which an improved model is obtained. Say No to skip this.
See also "input_ncs_file" which can be used to specify NCS at
the start of the process. If find_ncs="No" then only this
starting NCS will be used and it will not be updated. You can
use find_ncs "No" to specify exactly what residues will be
used in NCS refinement and exactly what NCS operators to use
in density modification. You can use the function
$PHENIX/phenix/phenix/command_line/simple_ncs_from_pdb.py to
help you set up an input_ncs_file that has your specifications
in it.
ncs_copies= None Number of copies of the molecule in the au (note: only
one type of molecule allowed at present)
ncs_refine_coord_sigma_from_rmsd= False You can choose to use the
current NCS rmsd as the value of the
sigma for NCS restraints. See also
ncs_refine_coord_sigma_from_rmsd_ratio
ncs_refine_coord_sigma_from_rmsd_ratio= 1.0 You can choose to multiply
the current NCS rmsd by this
value before using it as the
sigma for NCS restraints See
also
ncs_refine_coord_sigma_from_rmsd
optimize_ncs= True This script normally deduces ncs information from the
NCS in chains of models that are built during iterative
model-building. Optimize NCS adds a step to try and make
the molecule formed by NCS as compact as possible, without
losing any point-group symmetry.
refine_with_ncs= True This script can allow phenix.refine to
automatically identify NCS and use it in refinement.
NOTE: ncs refinement and placing waters automatically
are mutually exclusive at present.
phasing
do_madbst= True Choose whether you want to skip FA calculation (speeds
it up)
f_doubleprime_list= None Enter f" for the heavy-atom for this dataset
f_prime_list= None Enter f' for the heavy-atom for this dataset
fixscattfactors= True For SOLVE phasing and MAD data you can choose
whether scattering factors are to be fixed by choosing
'Yes' to fix them or 'No' to refine them. Normally
choose 'Yes' (fix) if the data are weak and 'No'
(refine) if the data are strong.
ha_sites_file= None Input sites file... with xyz in fractional
coordinates or a PDB file with coordinates NOTE: This
file is optional if you specify a partial model file
have_hand= False Normally you will not know the hand of the heavy-atom
substructure, so have_hand=False. H | |||||||