- phenixbb - phenix-online.org

question about phenix rosetta with two chains
by Elena Seiradake 23 Feb '12

23 Feb '12

Dear Phenixians, I would like to use mr_rosetta to re-build a model with two copies per AU. Although the two copies have the same sequence, they adopt different conformations and one is partially disordered. So I don't want to impose NCS. Could someone please send me an example input file for running mr_rosetta with phenix for multiple chains of the same protein? I think this probably would have to contain "fragment_files_chain_list" and "fragment_files_3_mer_by_chain" etc. (?) I have tried including the above keys in my script, in various ways, but I always get the error: "Sorry, the file path/test_1.pdb representing group 1 has no atoms? This could indicate a problem with sequence alignment in rebuilding" When I run it with just one of the two chains in my pdb (using simple "fragment_file ="), it rebuilds happily. Also, when use both chains and impose NCS=2 it works, but then one of the two chains is forced into the wrong conformation. Any advice on how to change my script would be welcome! Below is part of my simple script, the one that runs ok, using "fragment_file =". seq_file= Seq.dat \ data=test.mtz \ search_models=test.pdb \ already_placed=True \ fragment_files= frag_A_3.gz \ fragment_files= frag_A_9.gz \ rescore_mr.relax=False \ rosetta_models=20 \ ncs_copies= 1\ Cheers Elena

2 1

composite omit map
by Ursula Schulze-Gahmen 22 Feb '12

22 Feb '12

I tried to calculate a composite omit map in autobuild for 3 complexes in the au. The calculation finished without any problems, but the maps look not right. There is density for the molecule, but there is a lot of density in the solvent areas, which I never saw when I calculated regular 2fo-fc maps or fo-fc maps. I also have calculated omit maps in autobuild before for single problem region and never saw anything like this. Any idea what could have gone wrong? Where should I start looking? Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

2 1

autoMR fixed ensemble error
by Alexander Batyuk 22 Feb '12

22 Feb '12

Dear all, I have the following error while trying to put fixed ensemble into AutoMR: Adding Ensemble c1 as fixed solution with: Euler angles: [359.98, 0.0, 0.0] Coords (orthogonal A): [-1.0, 0.476, -1.001] *************ERROR ENDING ******************* **************************************** AutoMR Input failed Python argument types in SOLU.addSOLU_6DIM_ENSE(InputMR_AUTO, str, list, bool, list, float, bool, bool, bool) did not match C++ signature: addSOLU_6DIM_ENSE(phaser::SOLU {lvalue}, std::string, scitbx::vec3<double>, bool, scitbx::vec3<double>, double, bool, bool, bool, bool, scitbx::vec3<double>, double) **************************************** *************ERROR ENDING ******************* What could be the reason for that? I'm running dev-986 on OS X 10.6.8. Stable 1.7.3 gives the same error. Best wishes, Alex -- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun

4 5

Re: [phenixbb] CCN Jan 2012 article : find_alt_origin_sym_mate
by R.D. Oeffner 21 Feb '12

21 Feb '12

Dear Bryan, The factor 0.9 is a purely empirical term. It serves two functions. One is to soften the minimas when atoms coalesce and to also prevent taking the logarithm of a negative number. The closer it gets to zero the more accurately it pinpoints the global minimum when the MLAD score is used for identifying the best superposition betweent two molecules. But if it becomes two small chances are that the landscape of MLAD values will be dotted with many very deep local minima which might lead to wrong results. The square boxes under the min, max symbols are typos to be ignored, sorry. There are currently no plans to publish further details about find_alt_origin_sym_mate. Regards, Robert Oeffner On Wed, Feb 15, 2012 at 4:33 PM, Bryan Lepore <bryanlepore at gmail.com> wrote: > will the find_alt_origin_sym_mate article in CCN Jan. 2012 be > described in any other publications? ... e.g. Acta Cryst., because I am interested in particular : 1. what is the significance of the factor of 0.9 2. is the MLAD a novel formula also, the 'min' and 'max' on p. 6 have small boxes under them [*] as if missing a character - are these integrals? -Bryan [*] tried evince and Adobe Reader on Linux, Adobe Acrobat on OSX 10.5.8 -- Robert Oeffner, Ph.D. Research Associate Department of Haematology, University of Cambridge Cambridge Institute of Medical Research Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY www-structmed.cimr.cam.ac.uk, tel:01223763234, mobile:07712 887162

5 5

error in running autobuild
by intekhab alam 20 Feb '12

20 Feb '12

hi i am working with phenix version 1.7.1-743. after running auto mr i tried to run autobuild but it failed and generated the following message. i am unable to run autobuild now. kindly help. OError : [Errno 5] Input/output error Traceback (most recent call last): File "/usr/local/phenix-1.7.1-743/phenix/wxGUI2/Runtime.py", line 172, in OnUpdate self.propagate_event(event, "OnUpdate") File "/usr/local/phenix-1.7.1-743/phenix/wxGUI2/Runtime.py", line 228, in propagate_event fn(event) File "/usr/local/phenix-1.7.1-743/phenix/wxGUI2/Programs/Phaser/Output.py", line 194, in OnUpdate self.process_callback(callback.message, callback.data) File "/usr/local/phenix-1.7.1-743/phenix/wxGUI2/Programs/Phaser/Output.py", line 209, in process_callback print "CALLBACK: %s %s" % (str(message), str(data)) IOError: [Errno 5] Input/output erro -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

3 2

FFT map coefficients only for certain chains
by Zhang yu 19 Feb '12

19 Feb '12

Dear Phenixers, Is that possible to generate map coefficients only for certain chains? For example, I have two chains, A and B, and I would like to output a map file only contains coefficients for chain A. The "isomesh" command in Pymol could generate similar images. But my purpose is not for presentation, I need a map file only contains coefficient for certain chains. In the interface of "FFT" tool in Phenix or CCP4, there is an option to include a PDB file and define atom selections. It describe that "If a PDB is supplied, the output map will cover the model plus a buffer on all sides. The atom selection parameters can be used to specify a smaller region" . If I define the selection as chain A when I run the FFT, the output map still covers a rectangular block containing chain A, instead of regions only surrounding chain A. Thanks. Yu Zhang

3 4

CCN Jan 2012 article : find_alt_origin_sym_mate
by Bryan Lepore 17 Feb '12

17 Feb '12

will the find_alt_origin_sym_mate article in CCN Jan. 2012 be described in any other publications? -Bryan

2 2

MRage
by Graeme Winter 17 Feb '12

17 Feb '12

Hi Folks, Following from the newsletter article I am trying to test out phaser.MRage. I have a well solved case which I know is in the pdb and a sequence file: phaser.MRage hklin=data.mtz composition.component.sequence=sequence.pir symmetry_exploration=pointgroup mode=full search.services=ncbi composition.count=3 however it generates a second component then complains it knows nothing about this: Sorry: Molecular weight needed for component 2. Any suggestions how to get around this? Many thanks, Graeme [gw56@ws050 rage]$ phaser.MRage hklin=data.mtz composition.component.sequence=sequence.pir symmetry_exploration=pointgroup mode=full search.services=ncbi composition.count=3 ############################################################################### # MRage version 0.1.0 # ############################################################################### All configuration options: -------------------------- hklin = data.mtz labin = None resolution_cutoff = 2.5 crystal_symmetry { unit_cell = None space_group = None } mode = quick *full symmetry_exploration = *pointgroup enantiomorph dataset output { root = "mrage" max_solutions_to_write = 0 gui_base_dir = None save_aniso_data = False job_title = None } composition { count = 3 component { sequence = sequence.pir stoichiometry = 1 ensemble { coordinates { pdb = None identity = None } } model_collection { trim = False coordinates { pdb = None identity = None } } template { pdb = None alignment = None } homology { file_name = None max_hits = 3 } search { services = local ncbi max_hits = 3 } } component { sequence = None stoichiometry = 1 ensemble { coordinates { pdb = None identity = None } } model_collection { trim = False coordinates { pdb = None identity = None } } template { pdb = None alignment = None } homology { file_name = None max_hits = 3 } search { services = local *ncbi max_hits = 3 } } } queue { technology = lsf threading sge *multiprocessing pbs cpus = 1 submission_command = None qslot_cpus = 1 } packing_pool = 20 rotation_peaks_cutoff = 0.75 post_refinement_cutoff = 0.75 final_selection_cutoff = 0.75 b_factor_refinement = True significant_peak_threshold = 7.0 sculptor_protocols = 11 10 13 12 1 3 2 5 4 7 6 9 8 *all minimal template_equivalence = False exclude_pdb_ids = None simple_run { enable = False component_sequence = None template_model = None blast_services = local ncbi max_blast_hits = 3 } Sorry: Molecular weight needed for component 2.

2 2

AutoSol with 4.2A dataset for a protein/DNA complex
by Wei Shi 16 Feb '12

16 Feb '12

Hi everyone, I have got a 4.2A SeMet MAD dataset for a protein-DNA complex. And, the native dataset for this protein-DNA complex is ~3.2A. The space group for the native and SeMet crystals seem to be different. I am not sure whether it’s possible to solve the structure with the current data I have, and wondering whether any of you have experience with working with this low-resolution data and any suggestion for me. I processed the data with XDS in space group P31, and used *.cns.hkl file from XDSCONV as an input for AutoSol and also include the sequence for protein only. The protein dimer has 418 residues and DNA is 32bp. I run Autosol with the default setting. Below is statistics I got. It seems that I didn’t get anything promising. Any comment or suggestion about what to try next? Thank you so much! Statistics: Top solution: 2 Sites: 11. Space group: P32. FOM: 0.550. BAYES-CC: 8.10. Residues: 465 Side-chains: 0. Chains: 60. Model CC: 0.67 R-work: 0.4100 R-free: 0.4569. Under Heavy-atom search and phasing: Space group # of refined sites FOM Overall score R-factor Map skew Corr. of local RMS density Solution1 P31 11 0.530 8.10+/-11.80 0.4184 -0.12 0.66 Solution2 P32 11 0.550 8.10+/-11.80 0.3881 -0.10 0.66 Best, Wei

4 4

Comprehension of Orotidine 5'-Monophosphate Decarboxylase
by Kevin Jin 15 Feb '12

15 Feb '12

Dear all, I wrote a story for Orotidine 5'-Monophosphate Decarboxylase. http://www.jinkai.org/Enzymology.html Best, Kevin

1 0