- phenixbb - phenix-online.org

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 ----------------------------------------------------------------------------

3 3

NAG-ASN link geometry
by nihmayerm 23 Oct '08

23 Oct '08

We are refining a 2.7 A structure with multiple ASN-NAG links using phenix-1.3-final. The torsion angle between the Asn amide and the sugar is quite variable, while from the chemistry of this link we would expect a value close to 180°, as reported in the PDB survey by Imberty & Perez (Protein Engineering 8:669-709). A quick look at some entries in the PDB revealed close to textbook geometry for the NAG-ASN link in structures around 1Å resolution (e.g. 1UWC) and gets much worse in some lower resolution structures, including those refined with PHENIX. The NAG-ASN link used by PHENIX does not contain a torsion angle definition, and I would like to ask (i) if its appropriate to use one in refinement, and if so (2) could people share their cif file for this link. Thanks - MLM

1 0

optimize weights error
by Sean Johnson 23 Oct '08

23 Oct '08

I just tried optimizing weights in phenix.refine using optimize_wxc=true and optimize_wxu=true in the command line. I got the following error: ----------xray term weight optimization (wxc)---------- Traceback (most recent call last): File "/usr/local/phenix-1.3b-rc5/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-rc5/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-rc5/phenix/phenix/refinement/driver.py", line 1150, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/phenix-1.3b-rc5/phenix/phenix/refinement/strategies.py", line 446, in refinement_machine log = log) File "/usr/local/phenix-1.3b-rc5/phenix/phenix/refinement/weight_xray_chem.py", line 252, in __init__ self.wxc_optimization() File "/usr/local/phenix-1.3b-rc5/phenix/phenix/refinement/weight_xray_chem.py", line 507, in wxc_optimization wxc = self.holder.wxc AttributeError: weight instance has no attribute 'holder' Any suggestions? Thanks, Sean -- Sean Johnson, PhD R. Gaurth Hansen Assistant Professor Utah State University Department of Chemistry and Biochemistry 0300 Old Main Hill Logan, UT 84322-0300 (435) 797-2089 (435) 797-3390 (fax) sean.johnson(a)usu.edu

2 2

phenix.autobuild
by Matthew Chu 22 Oct '08

22 Oct '08

Dear all, I tried to rebuild my structure from a refined model (by refmac) by phenix.autobuild. I am not sure if it runs properly since this is my first time to run this module....it took like almost a day to just finish the run_1 (there should be five runs by default?), which means it will take me another 4 days to finish the whole thing. My protein has around 350 residues and in the refined model, I have omitted some loops (about 80 residues) because I cannot see the electron density of those regions. I have put the seq.dat file with the full sequence (~350 residues) and the commands "place_water=Yes" and "s_annealing=True". The resolution is 2.4 A. Should it be taken so long to run? Thanks in advance! Kind regards, Matt -- ---------------------------------------------------------------------------- Matthew LH Chu PhD Student School of Pharmacy and Pharmaceutical Sciences University of Manchester ----------------------------------------------------------------------------

2 1

phenix.pdbtools question
by Simon Kolstoe 21 Oct '08

21 Oct '08

Dear phenix list, I am wanting to model a poly-proline structure. I created the file in PyMOL, saved it as a pdb, and then tried to regularize it with: phenix.pdbtools polypro.pdb --geometry_regularization However the program reported (snipped to the last few lines): ATOM 63 CD PRO 6 -3.290 3.487 -2.968 1.00 0.00 C ATOM 69 2HD PRO 6 -2.824 2.626 -3.453 1.00 0.00 H Distance model: 1.09209 (ideal: 0.97) ATOM 63 CD PRO 6 -3.290 3.487 -2.968 1.00 0.00 C ATOM 70 3HD PRO 6 -4.165 3.171 -2.396 1.00 0.00 H Distance model: 1.44721 (ideal: 1.473) ATOM 57 N PRO 6 -2.321 4.145 -2.118 1.00 0.00 N ATOM 63 CD PRO 6 -3.290 3.487 -2.968 1.00 0.00 C Distance model: 1.53855 (ideal: 1.525) ATOM 58 CA PRO 6 -1.810 5.407 -2.632 1.00 0.00 C ATOM 59 C PRO 6 -2.332 6.603 -1.817 1.00 0.00 C Distance model: 1.23088 (ideal: 1.231) ATOM 59 C PRO 6 -2.332 6.603 -1.817 1.00 0.00 C ATOM 60 O PRO 6 -3.080 6.424 -0.856 1.00 0.00 O Sorry: Number of bonds with excessive lengths: 74 I thought the whole purpose of geometry regularization was to get rid of excessive lengths, not just tell me they are there!! How do I get the program to really regularize my geometry? Thanks, Simon

3 3

phenix.reduce (v1.3) changes
by Mark Collins 21 Oct '08

21 Oct '08

Hi Did the --ALLALT command change. I thought the --help gave the flag description as "builds hydrogens for all conformations" but no it says "process adjustments for all conformations" And by default (-ONLYA) so I only have conf A with hydrogens using the --ALLALT flag. Long and short of it I think something is up? Thanks Mark

1 0

postdoc position in LBNL
by Peter Zwart 20 Oct '08

20 Oct '08

Dear All, We would like to bring the following postdoctoral research position to your attention. Within Lawrence Berkeley Laboratory, we have an opening for a postdoc to work on the development of new software for the analysis of small angle X-ray scattering (SAXS) data. The availability of user friendly, robust software analysis tools for SAXS data is of growing importance as the biological community is increasingly using SAXS as a standard method to analyze complex biological systems. We are developing a new set of tools, including a software library, for SAXS data analysis. The successful candidate will have the opportunity to work with experienced software developers in the field of biophysics and interact with users and beamline staff on SAXS beamline 7.3.3 at the Advanced Light Source (ALS) in Berkeley California. Interested candidates can contact me (Peter Zwart, PHZwart(a)lbl.gov) for more details, or visit the LBL job site at: http://jobs.lbl.gov/ Sincerely, Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

1 0

Twin refinement with anomalous pairs
by Francis E Reyes 20 Oct '08

20 Oct '08

All How does phenix.refine handle the twin refinement target when refining against F+/F-? I'm specifically asking for the proper assignment of F +/F- for twin related reflections (e.g. 10.1107/S0907444902021704). My data is currently in P41 with friedel pairs as output by scala. Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

3 2

Re: [phenixbb] sa_omit-map
by mathieu Coincon 18 Oct '08

18 Oct '08

Hi, omit-map works fine for me but I have two items on my wish list. 1) Can we compute a difference-map (mFo-DFc map instead of 2mFo-DFc map) ? 2) Is it possible to play with the size of the area omitted around the selection ? Thanks again. A true phenix-fan -------------- Mathieu Coincon PhD Student Universite de Montreal Biochemistry 514-343-6111 #5352

2 1

phenix.refine: including modifications
by Patrick Loll 17 Oct '08

17 Oct '08

Hi all, I'm starting to use phenix.refine and have some questions about defining modifications during refinement: I want to refine a structure that includes several alpha-D-mannose residues. I see that mon_lib_list.cif contains, under the "LIST OF RECOGNIZED MODIFIED MONOMERS," the following line: MAN-a-D MAN-b-D SUG-a-D MAN alpha_D_mannose D-pyranose Question: Where/how do I invoke this modification? I.e., how do I tell the refinement program that a particular sugar is an alpha, and not a beta, mannose? Clearly I can't label the residue MAN-a-D in the PDB file, as this would step on the chain identifier. I'm guessing that I label each sugar MAN in the PDB file, and then insert some instructions about applying the modification in the CIF file that I supply to the refinement program. However, I'm not able to find an example of the appropriate syntax. Thanks, Pat Loll ------------------------------------------------------------------------ --------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.loll(a)drexelmed.edu

4 5