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Re: [phenixbb] refinement of N-glycosylation
by Ling Qin 25 Feb '10

25 Feb '10

Dear Georg, Maybe you need to use quotation marks? I also have n-glycosylation and I in my .eff file there is: } apply_cif_link { data_link = "NAG-ASN" residue_selection_1 = "chain A and resname NAG and resid XXX" residue_selection_2 = "chain A and resname ASN and resid XXX" } Hope this is useful. Please correct me if I am wrong. Ling On Wed, Feb 24, 2010 at 1:13 PM, Georg Mlynek <georg.mlynek(a)univie.ac.at>wrote: > Dear All, > > > > I´m quite new to crystallography and I´m refining a structure with > ASN-NAG-NAG-BMA attached and already got help from Blaine who told me how to > do it, but I´m making a small mistake somewhere and can´t figure out what > I´m doing wrong. Must be just one paranthesis or so, I guess. > > In command line just for testing I put: > > phenix.refine refine_data.mtz refine_1-coot-1FrenumberedGlu.pdb > cif_link.params BMA.cif strategy=individual_sites+individual_adp > main.number_of_macro_cycles=2 --overwrite > > > > where I put in cif_link.params as suggested in the mailing list > http://www.phenix-online.org/pipermail/phenixbb/2009-November/002837.htmlwi… and without paranthesis at the beginning > > > > } > > apply_cif_link { > > data_link = NAG-ASN > > residue_selection_1 = chain A and resname NAG and resid 500 > > residue_selection_2 = chain A and resname ASN and resid 297 > > } > > apply_cif_link { > > data_link = BETA1-4 > > residue_selection_1 = chain A and resname NAG and resid 500 > > residue_selection_2 = chain A and resname NAG and resid 501 > > } > > apply_cif_link { > > data_link = BETA1-4 > > residue_selection_1 = chain A and resname NAG and resid 501 > > residue_selection_2 = chain A and resname BMA and resid 502 > > } > > apply_cif_link { > > data_link = ALPHA1-3 > > residue_selection_1 = chain A and resname BMA and resid 502 > > residue_selection_2 = chain A and resname MAN and resid 503 > > > > and suggested by Blaine with and without paranthesis at the beginning > > > > refinement.pdb_interpretation.apply_cif_link { > > data_link = NAG-ASN > > residue_selection_1 = chain A and resname NAG and resid 500 > > residue_selection_2 = chain A and resname ASN and resid 297 > > } > > refinement.pdb_interpretation.apply_cif_link { > > data_link = BETA1-4 > > residue_selection_1 = chain A and resname NAG and resid 500 > > residue_selection_2 = chain A and resname NAG and resid 501 > > } > > refinement.pdb_interpretation.apply_cif_link { > > data_link = BETA1-4 > > residue_selection_1 = chain A and resname NAG and resid 501 > > residue_selection_2 = chain A and resname BMA and resid 502 > > } > > refinement.pdb_interpretation.apply_cif_link { > > data_link = ALPHA1-3 > > residue_selection_1 = chain A and resname BMA and resid 502 > > residue_selection_2 = chain A and resname MAN and resid 503 > > > > I see in the .geo file that the residues are not bonded, and also in the > .eff file that these lines are not added there, which should be done I > guess, I put the info also direct into the .def file but I get the same > problem? > > > > By the way it shouldn´t matter which name I give to this file as long as > the extension is correct? > > > > Thank you very much and all the best, Georg. > > > > > > > > -----Ursprüngliche Nachricht----- > Von: phenixbb-bounces(a)phenix-online.org [mailto: > phenixbb-bounces(a)phenix-online.org] Im Auftrag von Ursula Schulze-Gahmen > Gesendet: Dienstag, 23. Februar 2010 19:20 > An: phenixbb(a)phenix-online.org > Betreff: [phenixbb] weights optimization, add hydrogens > > > > I am refining a 2.0 A structure in Phenix using mostly the graphical > > interface. The maps are very good and the R factors are low > > (0.208/0.173). But the geometry is not so great with bond deviations of > > 0.208 and Angle deviations of 1.85. What is the best thing to do to try > > to improve the geometry. Should I try to optimize the weights? > > > > The other question is about adding hydrogens to the model. I did add > > them in a previous refinement cycle. After rebuilding the model in coot, > > most of the model still has the hydrogens in the input file for the next > > refinement cycle, but some residues and waters don't have hydrogens. > > When I tried to add hydrogens again to the model, I got an error message > > about atoms being to close. Does Phenix know where to add hydrogens if > > the input model has already hydroegns on many residues? > > > > > > Thanks > > > > Ursula > > > > -- > > Ursula Schulze-Gahmen, PhD. > > QB3, Tjian Lab > > MCB, 16 Barker Hall #3204 > > University of California Berkeley > > Berkeley, CA 94720-3204 > > Phone: (510) 642 8258 > > uschulze-gahmen(a)lbl.gov > > > > > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://phenix-online.org/mailman/listinfo/phenixbb > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > >

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Re: [phenixbb] refinement of N-glycosylation
by Ralf W. Grosse-Kunstleve 24 Feb '10

24 Feb '10

> I?m quite new to crystallography and I?m refining a structure with > ASN-NAG-NAG-BMA attached and already got help from Blaine who told me how to > do it, but I?m making a small mistake somewhere and can?t figure out what > I?m doing wrong. Must be just one paranthesis or so, I guess. > > In command line just for testing I put: > > phenix.refine refine_data.mtz refine_1-coot-1FrenumberedGlu.pdb > cif_link.params BMA.cif strategy=individual_sites+individual_adp > main.number_of_macro_cycles=2 --overwrite Did you get an error message? If not, look in the .eff file for your "apply_cif" definitions. If they don't appear there something went wrong. The file name doesn't matter at all, not even the extension, but it is important that the syntax is correct. To run the syntax check only: iotbx.phil cif_link.params Ralf

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weights optimization, add hydrogens
by Ursula Schulze-Gahmen 24 Feb '10

24 Feb '10

I am refining a 2.0 A structure in Phenix using mostly the graphical interface. The maps are very good and the R factors are low (0.208/0.173). But the geometry is not so great with bond deviations of 0.208 and Angle deviations of 1.85. What is the best thing to do to try to improve the geometry. Should I try to optimize the weights? The other question is about adding hydrogens to the model. I did add them in a previous refinement cycle. After rebuilding the model in coot, most of the model still has the hydrogens in the input file for the next refinement cycle, but some residues and waters don't have hydrogens. When I tried to add hydrogens again to the model, I got an error message about atoms being to close. Does Phenix know where to add hydrogens if the input model has already hydroegns on many residues? Thanks Ursula -- Ursula Schulze-Gahmen, PhD. QB3, Tjian Lab MCB, 16 Barker Hall #3204 University of California Berkeley Berkeley, CA 94720-3204 Phone: (510) 642 8258 uschulze-gahmen(a)lbl.gov

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Phenix.ligandfit is not happy with my labels
by ucbccka 24 Feb '10

24 Feb '10

I am getting an error when trying to run phenix.ligandfit in the version phenix-1.6-289. I am trying to get it to use an mtz generated via refmac <recoils at the chorus of booooo's> and fit the ligand into the difference map. If I run phenix.ligandfit data=phaser_1.1_refmac1.mtz model=phaser_1.1_refmac1.pdb ligand=ATP.pdb It complains about my labels, saying.. ********************************* Sorry, input labels or map type unclear for phaser_1.1_refmac1.mtz For lig_map_type=pre_calculated_map_coeffs supply F and PHI (optionally FOM) (or 2FOFCWT and PH2FOFCWT) For lig_map_type=fo-fc_difference_map supply one column label for FP For lig_map_type=fobs_map supply one column label for FP Please specify which lig_map_type above you would like and also specify the necessary input column labels for your map like one of these samples: input_labels="FP" input_labels="2FOFCWT PH2FOFCWT" input_labels="FP PHIB FOM" ************************************* Looking at the documentation I tried getting PHENIX to tell me what labels it could see by running that autosol query and it kindly told me that my mtz file contained ************************ 'FreeR_flag' 'F_New' 'SIGF_New' 'FC' 'PHIC' 'FC_ALL' 'PHIC_ALL' 'FWT' 'PHWT' 'DELFWT' 'PHDELWT' 'FOM' ************************** so, I ran phenix.ligandfit data=phaser_1.1_refmac1.mtz model=phaser_1.1_refmac1.pdb ligand=ATP.pdb input_labels="DELFWT PHDELWT" and got the original message complaining that my labels are unclear. I even used the GUI, it recognises all the pairs of labels giving me the options to look at each map if I want and then..... complains that my labels are unclear. Clearly my labels are unclear, but I am now unclear how to proceed. If anyone could suggest something please then I would be most appreciative. Clearly. cheers

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Technology Specialist Position, Lawrence Berkeley National Laboratory
by Paul Adams 23 Feb '10

23 Feb '10

We are seeking a structural biologist technology specialist to research, document, and communicate new technologies to the scientific community. This project is part of the NIH-funded Protein Structure Initiative (PSI) Knowledgebase. The position requires interactions with other groups in the Knowledgebase, members of the Protein Data Bank, researchers at NIH-funded PSI centers, scientific journals, and the broader biological research community. The successful candidate will work under the direction of the Principal Investigator for this project. Primary duties and responsibilities are promoting new PSI- developed technologies to the broader scientific community, and maintaining and further developing a web portal describing these technologies. The successful candidate will need to be able to produce attractive online content, and have good scientific writing /proof reading skills. There is also a large community outreach element to the role, including presentations at meetings, the answering of questions via email, and the possibility of establishing an online forum. Additional tasks may include setting up a SVN software repository, and other online tools which will be of assistance to the structural biology community. Qualifications: B.S., M.S., Ph.D. or equivalent in a scientific discipline, preferably structural biology, biology, or chemistry. Demonstrated experience of scientific research using either computation or instrumentation. Solid interpersonal skills and the ability to work in a team environment are critical. Ability to communicate with a broad range of researchers. Excellent spoken and written English skills are essential. Familiarity with scripting languages such as Python. Experience with maintaining web sites. To apply: visit http://cjo.lbl.gov/ and search for the keyword PSI or the job number 24114. Please see http://cjo.lbl.gov/app_instr.html for details of how to apply. NOTE: This is a one year Term appointment with the possibility of renewal under the same terms and conditions, contingent upon continued funding and availability of work. -- Paul Adams Acting Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Patty Jimenez [ PAJimenez(a)lbl.gov ] [ 1-510-486-7963 ] --

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metal ion
by chene＠umbi.umd.edu 19 Feb '10

19 Feb '10

Dear Phenix users, My question may have been asked before. I am refining a structure containing calcium ions. I am wondering if the program considers it to be divalent Ca++ or neutral calcium atom. It seems that the ion and neutral atom have different atomic scattering factors. Thanks Chen Chen Chen, PhD, Research Associate Center for Advanced Research in Biotechnology (CARB), University of Maryland Biotechnology Institute (UMBI), 9600 Gudelsky Drive, Rockville, MD 20850 240-314-6122

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Re: [phenixbb] riding model and deposition
by Alex Theodossis 18 Feb '10

18 Feb '10

Dear Pavel, thank you for your comments. Alex

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omit map with twinning?
by Kelly Daughtry 18 Feb '10

18 Feb '10

Hello all, The omit_map in the new gui (version 1.5) is great, but I can not include a twin law when calculating the omit map, thus the result is very messy unclear maps. I do not know if 1.6 has the solution or not, I am still lobbying our computer guy to upgrade to it... Is there a way from the command line i can include the twin law in autobuild so I can calculate the omit map, or can I just add it into the eff file? My other solution has been to use the create maps function with my data and pdb with ligand removed. This works, giving me a nice Fo-DFc map, but it would be nice to be able to show a true omit map for the ligand, as is customary in most structure papers I have run across. Thanks in advance for any help you can provide! Kelly ******************************************************* Kelly Daughtry PhD Candidate Department of Physiology and Biophysics Boston University School of Medicine 590 Commonwealth Ave R 390 Boston MA, 02215 (P) 617-358-5548 *******************************************************

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riding model and deposition
by Alex Theodossis 18 Feb '10

18 Feb '10

Dear phenixbb, I have refined a 1.3A structure using individual anisotropic B-factors (Rfactor, 15.5%; Rfree, 17.7%). Additional use of the riding model during refinement has improvement the R values (Rf, 14.5%; Rfree, 16.6%), although bond length and angle outliers did increase (anyone know why that would be?). I have decided to deposit the model obtained using the riding model, but am unsure whether to include the hydrogen coordinates in the deposition. The Phenix.refine documentation advises that they are left in, as they are needed to reproduce the refinement statistics. However, reviewing the high resolution structures in the PDB I found that: 1. In the case of structures refined using REFMAC or SHELX, the riding model does not seem to be included, although its use during refinement is mentioned in the pdb header. 2. In the case of structures refined using PHENIX, use of the riding model is sometimes indicated in the header, but hydrogen coordinates only appear to be included in the pdb in the case of structures refined to a resolution better than 1.3A. As far as I can understand the purpose of the riding model is to provide additional restraints for refinement, so as long as its use is made evident in the pdb header (and maybe the methods section of the publication) that should be enough. Inclusion of hydrogens in the model, when you can't see them seems inappropriate. Nevertheless, I would appreciate a more authoritative perspective on this issue. Thank you in advance, Alex Theodossis

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refinement error with ligand
by Christian Roth 17 Feb '10

17 Feb '10

Dear all, I started a refinement of one of my structures using the GUI of phenix (Version 1.6). I used the options of adding hydrogens and dis a suimulated annealing. I used the output file and corrected it manually using Coot. I incorporated a few Ethylenglycol Monomers which might have bound. I merged everything wrote the file out and loaded this pdb in the GUI. I got an error which might be du to the fact that I didnt specify a CIF file for the ligand. I started ready set from the GUI to check the pdb and used REEL to create a CIF File. I added the CIF-File to the File list and tried to start again phenix.refine using the hydrogen option but no sim. annealing. However I got always the following error log: # Date 2010-02-17 Time 12:00:35 CET +0100 (1266404435.31 s) #phil __OFF__ Command line arguments: "/homes/roth/clcf/049b32mlsyncref/phenix/phenix/project_data/refine_15.eff" "-- overwrite" HOST = bbzws339 HOSTTYPE = i486-linux VENDOR = intel USER = roth PID = 29983 ------------------------------------------------------------------------------- PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography Version: 1.6 Release tag: 289 Platform: intel-linux-2.6 linux User: roth ------------------------------------------------------------------------------- phenix.refine: Macromolecular Structure Refinement Monomer Library directory: "/software/linuxsoft/phenix-1.6-289/chem_data/mon_lib" Total number of atoms: 16881 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1575 Classifications: {'peptide': 94} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 87} and so on for other chains Chain: "R" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'EDO': 1} Unexpected atoms: {'EDO,HO1': 1, 'EDO,HO2': 1} Classifications: {'undetermined': 1} Number of atoms with unknown nonbonded energy type symbols: 16 "HETATM16821 HO2 EDO K 1 .*. H " "HETATM16826 HO1 EDO K 1 .*. H " "HETATM16828 HO2 EDO L 1 .*. H " "HETATM16834 HO1 EDO L 1 .*. H " "HETATM16836 HO2 EDO M 1 .*. H " "HETATM16840 HO1 EDO M 1 .*. H " "HETATM16842 HO2 EDO N 1 .*. H " "HETATM16848 HO1 EDO N 1 .*. H " "HETATM16850 HO2 EDO O 1 .*. H " "HETATM16857 HO1 EDO O 1 .*. H " ... (remaining 6 not shown) I looked in the pdb for this atoms, but I cannot find them. When I use a cif file created directly by phenix elbow using command line and when I did not use the update hydrogen button the refinement works. But the new residues as well as the EDO molecules have no hydrogens in riding positions. Do I have to remove all hydrogens and attach them again for every cycle? One Refinement runs for more then 5 hours regardless I use sim annealing or not. This seems to be very long for me. Maybe I want too many optimization steps? Could anyone explain me what goes wrong here. I am no so much experienced with phenix and now I run out of ideas. Thanks in advance Christian

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