October 2008 - phenixbb - phenix-online.org

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",… [View More]

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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 … [View More]

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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 … [View More]

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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

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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 … [View More]

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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

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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

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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 … [View More]

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Hydrogen occupancy issue?
by Mischa Machius 17 Oct '08

17 Oct '08

Hi - I have a problem regarding occupancies of hydrogens in residues with alternate conformations. Specifically, when a residue exists in alternate conformations, the H hydrogen of the following residue (the one attached to the N) also exists in the same number of alternate locations. The occupancies of these hydrogens do not add up to 1.00 like the occupancies of the hydrogens for the preceding residue do. In fact, these occupancies are all 1.00. Is that a bug, a feature, or did I … [View More]

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Weighted phase combination in phenix.refine?
by Francis E Reyes 17 Oct '08

17 Oct '08

Hi all I have experimental phases and a preliminary model. Will phenix.refine do phase combination while weighting the experimental phase and model phases (which also has NCS) ? By default? 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

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