- phenixbb - phenix-online.org

refine occupancies for MET/MSE double conformations
by Anastassis Perrakis 12 Nov '08

12 Nov '08

Hi there - I was pleased to read in the manual: if no selections are provided (refine.occupancies.individual=None and refine.occupancies.group=None) then phenix.refine by default will refine individual occupancies for atoms that have partial occupancy values in input PDB file (except zeros) and it will perform group constrained occupancy refinement for all atoms in alternative conformations. Occupancies of all other atoms will be fixed. If selections are provided (refine.occupancies.individual=atom_selection or refine.occupancies.group=atom_selection) then the selected atoms will be added to the list of atoms defined above (atoms with partial occupancies or those in alternative conformations). See this document for examples of atom_selection syntax. However, I want to refine my MET residues in double conformations, one as MET (AMET) and the other one as MSE (BMSE) with each 0.5 occupancy to start with. When I try that I get: == ----------Initial model statistics (before refinement)---------- ... |-Occupancies statistics------------------------------------------------------| Sorry: There are atoms with negative occupancies. Check input PDB file. === The PDB file has 0.5 and 1.0 occupancies only. I am also using: == refinement.refine.strategy=tls+individual_sites+individual_adp +group_anomalous refinement.refine.adp.tls="chain A" refinement.refine.adp.tls="chain B" refinement.main.number_of_macro_cycles=4 refinement.simulated_annealing.start_temperature=5000 refinement.refine.adp.individual.anisotropic =" chain C" refinement .input .xray_data .labels=I_Mystery(+),SIGI_Mystery(+),I_Mystery(-),SIGI_Mystery(-),merged refinement.refine.anomalous_scatterers { group { selection = "name ZN " f_prime = -0.3 f_double_prime = 2.5 refine = *f_prime *f_double_prime } group { selection = "name SE " f_prime = -5.2 f_double_prime = 3.8 refine = *f_prime *f_double_prime } } == Any hints on how to proceed ? Should I define groups for the occupancy refinement explicitely and not rely to automatic assignment? And if so how? How do people treat this partial Se-Met issue ? We solved the structure with SeSAD ... if I out MSE I get pretty large negative density peaks on the Se ... if I put MET I get positive peaks ;-) And there are good reasons to believe in partial Se- substitution in this case. Thanks in advance, Tassos

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cis peptide
by Jianghai Zhu 09 Nov '08

09 Nov '08

Hi, Does phenix.refine restrain cis peptide? How do I know if the refined pdb file contain any cis peptide? Thanks. -- Jianghai

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User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 05 Nov '08

05 Nov '08

Dear Users, Through the Collaborative Crystallography Pilot Program (CC) at the Advanced Light Source, scientists can send protein crystals to Berkeley Center for Structural biology (BCSB) staff researchers for data collection and analysis. The CC Pilot Program can provide a number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; * Reduced travel costs. Thumbnail Description: ====================== The Collaborative Crystallography program will be piloted on beamlines 5.0.1 and 5.0.2 for one year; if successful it will be implemented on a permanent basis. CC proposals will go through the regular ALS General User proposal review process for beamtime allocation. Proposals will be reviewed and ranked by the Proposal Study Panel, and beamtime will be allocated accordingly. BCSB staff will schedule the projects to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography ============= How To Apply: To submit a proposal, go to: http://www-als.lbl.gov/als/quickguide/independinvest.html Click on "protein crystallography" to begin proposal. For question 3 select "Collaborative PX 501/502." For question 9, please describe a specific research project with a clear end point. In order to request CC time for January/February 2009 allocation period, proposals must be submitted by November 15, 2008. The deadline for CC proposals for the time period March/April 2009 will be January 15, 2009. Regards, Banumathi Sankaran

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weight optimization
by Raja Dey 03 Nov '08

03 Nov '08

Hi, I was trying to optimize weights as follows, but it came out with the error given below. Can anyone tell me what's wrong? I used phenix.refine ../p65_nat.mtz ../p65_136.1.pdb optimize_wxc=true optimize_wxu=true output.prefix=136.1 ----------xray term weight optimization (wxc)---------- Traceback (most recent call last): File "/usr/local/phenix-1.3b-rc6/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/command_line.py", line 82, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/driver.py", line 1143, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/strategies.py", line 449, in refinement_machine log = log) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 256, in __init__ self.wxc_optimization() File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 511, in wxc_optimization wxc = self.holder.wxc AttributeError: weight instance has no attribute 'holder' Thanks... Raja

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DNA sugar pucker
by Laura Murray 26 Oct '08

26 Oct '08

Hi. I'm one of the Richardsons' people. I have more experience with RNA, but have looked at DNA some as well. 1. On C2'-endo and C3'-exo being equivalent: no, not quite equivalent, but related. If you do have C1', C4', and O4' in the plane, then "popping" C2' out on one side or C3' out on the other is relatively similar (sort of) and there's a recognized "twist" conformation where you've got them both out of plane a bit. However, you can really get C3' mostly in-plane with the other three and have a conformation that's distinctly a C2' endo pucker rather than looking like it could be either one. If you're building ideal B-form DNA, it would be better to use a real C2'-endo pucker than the twist, and certainly better than using the C3'-exo. 2. I'm afraid I don't know the appropriate format for use with PHENIX, but there are pucker-specific parameters available on the Nucleic Acid Database site: http://ndbserver.rutgers.edu -- specifically, here: http://ndbserver.rutgers.edu/standards/parameter.html -- these are set up for XPLOR, but the values should help. At any rate, these files distinguish the dihedrals for C2'-endo and C3'-endo sugar puckers. (The set for higher resolution also provides slightly different bond lengths and angles for them, since the ring strains are a bit different.) And I don't think they make a habit of turning up C3'-exo. Laura Murray

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sugar puckering in an ideal B-DNA
by chern 26 Oct '08

26 Oct '08

Hi all, does anybody know why coot and sybil (and may be others that I don't know about) generate an ideal dna with C3*-exo puckers instead of C2*-endo, as text books say. maia

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phenix.refine output map format
by Paul Emsley 25 Oct '08

25 Oct '08

Dear Phenixers, Is is possible for phenix.refine to output a ccp4 map? If so, how? Thanks, Paul.

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elbow
by chern 24 Oct '08

24 Oct '08

Dear all, could I use eLBOW to create a .cif file for a B-DNA to restrain sugar puckers? Maia

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sugar puckering in DNA
by Maia Cherney 24 Oct '08

24 Oct '08

Hi Yu Seon. I would appreciate it very much if you send me your added restraints to the cif file. Maia YS. Chung wrote: > Hi Maia, > I had the same problem when I was refining with phenix. I ended up > looking at the torsions that were used in 3DNA (the program I used to > analyze the puckerings) and manually added the restraints to the .cif > files used in phenix. I can send you an example if you'd like. The > puckerings improved a lot when I used the modified .cif files. > Yu Seon > > On Fri, 24 Oct 2008 10:43:44 -0600 > "chern" <chern(a)ualberta.ca> wrote: > >> Sorry, I gave a wrong subject name in my previous e-mails. Should've >> been sugar puckering in DNA. >> I am wondering why the default .cif file for DNA does not include all >> >> information about sugar puckers. >> I do not have some fancy nucleotides. They are regular. >> >> Maia >> >> ----- Original Message ----- From: "Ralf W. Grosse-Kunstleve" >> <rwgk(a)cci.lbl.gov> >> To: <phenixbb(a)phenix-online.org> >> Sent: Friday, October 24, 2008 10:03 AM >> Subject: Re: [phenixbb] elbow >> >> >> >>>> The answer is yes but there may be better options. Ralf is the >>>> >> best >> >>>> person to answer this question but one option is to start with the >>>> >> .cif >> >>>> file in the monomer library. >>>> >>> This is more a chemistry question than a formatting question. >>> Since I'm not deeply familiar with the DNA chemistry, I was >>> >> pointing >> >>> Maia to phenixbb in hopes that someone may already have figured out >>> the list of torsion angle restraints to fix sugar puckers. >>> >>> What Maia really wants is: >>> >>> >>>> could you please send me a specific example of how to modify a cif >>>> >> file >> >>>> to specify the sugar puckers in DNA (I want them C2'-endo). >>>> >>> Has anyone on this list done this already? >>> >>> Ralf >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>> >>> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> > >

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Re: [phenixbb] phenix.autobuild
by Matthew Chu 24 Oct '08

24 Oct '08

Thank you for the detailed information Tom, my autobuild job is actually running properly! Just some more minors questions: 1. AutoBuild Wizard will use phenix.elbow to generate geometries for any ligands that are not recognized, but how can I find out which ligands that can actually be recognized by phenix? Or to be save, we better run elbow to generate the libraries for every single ligands? 2. eLBOW can automatically add hydrogens to the input molecules if there are less than a quarter of the possible hydrogens, however this command doesn't work: phenix.elbow input_file.pdb --add-hydrogens=True, and I can't find this option under the elbow manual? And actually I would like to remove those hydrogens so it should be "add-hydrogens=false"? I am now using phenix-1.3-rc2. Thanks again! Matt -- ---------------------------------------------------------------------------- Matthew LH Chu PhD Student School of Pharmacy and Pharmaceutical Sciences University of Manchester ----------------------------------------------------------------------------

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