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runtime error in phenix.refine
by Eugene Valkov 11 Jun '12

11 Jun '12

I'm encountering the following during the second macro-cycle in phenix.refine in latest 1.8-1069 dev build for Linux 64-bit: RuntimeError: Excessive number of cubicles: This may be due to unreasonable parameters: cubicle_edge=5 space_span=(8467.78,8440.85,8372.67) n_cubicles=(1694,1689,1675) max_number_of_bytes=101542821888 Any thoughts/suggestions much appreciated. Thanks, Eugene -- Dr Eugene Valkov Division of Structural Studies MRC Laboratory of Molecular Biology Hills Road, Cambridge, CB2 0QH Email: evalkov(a)mrc-lmb.cam.ac.uk Tel: +44 (0)1223 402261

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How to run normal mode analysis under command mode?
by fn1＠rice.edu 11 Jun '12

11 Jun '12

Hi everyone, I'd like to perturb my model with normal mode analysis. Does phenix have a way to do this? Thanks in advance! Fengyun

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Gordon conference - last chance!
by Anastassis Perrakis 11 Jun '12

11 Jun '12

Dear all, The registration deadline for the Gordon conference on diffraction methods in Structural Biology (15-20 July), is at the end of the week (June 17th). This is you last chance to register and get some of the places left!!! See the program and application information at: http://www.grc.org/programs.aspx?year=2012&program=diffrac Ana and Tassos

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Ordered solvent DOD
by YoungJin 07 Jun '12

07 Jun '12

Hi, When you add waters by ordered solvent option, is it possible putting DOD for neutron data? I added normal waters and changed them to DOD by using ReadySet. But wondering if I want to go further refinement with ordered_solvent on, how can I keep adding DOD rather than HOH. Otherwise, do I have to change again by using REadySet? I also tried to change resid name as DOD but didn't help me. Best, Young-Jin

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R/Rfree can not be reproduced
by 周文昌 03 Jun '12

03 Jun '12

Dear all, I had a weird case in which I can not reproduce the R/Rfree value for the same refinement. "same" means I run my refinement first and then I rerun with "phenix.refine *.eff --overwrite". The R/Rfree values for the two cases are different (0.2942/0.3190 vs 0.2942/0.3085). Should not they be the same always? the command I used: 1st. phenix.refine new-unique.mtz model.pdb xray_data.high_resolution=2.7 fix_rotamers=true strategy=individual_adp+individual_sites+tls ../tls_group_selections.params wxc_scale=0.05 refinement.input.xray_data.labels=FP,SIGFP --overwrite 2nd phenix.refine model_refine_001.eff --overwrite thanks, Wenchang

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Re: [phenixbb] SA omit map
by Huang, Raven H 02 Jun '12

02 Jun '12

Hi all, Was the issue of SA omit map debated last July (involving Tiaard Pining, Pavel, and Folmer) resolved in the newer version of Phenix? Specifically, We'd like to generate the same map for a ligand. It is not for the refinement, but for publication (a reviewer asked us to cover the ligand with the map in a figure). Previously, I used cns to do that (sa_omit_map.inp). But we refined our current structures solely in Phenix. If there is a choice, I'd rather not to move everything to cns and set it up just for the sake of generating a omit map. Thanks, Raven ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Raven H. Huang, Associate Professor Department of Biochemistry Center for Biophysics & Computational Biology University of Illinois at Urbana-Champaign 411 Roger Adams Lab., 600 S. Mathews Ave. Urbana, IL 61801 Phone: 217-333-3967; Fax: 217-244-5858

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partial partial occupancy
by Terry Lang 02 Jun '12

02 Jun '12

Hey Everyone, I have partially occupied ligand that I am trying model. The problem is that the ligand is in at least two conformations PLUS there is a side chain that occludes binding part of the time. In other words, I'm aiming for something like: Residue Conf A occ = 60%, Residue Conf B occ = 40%, Ligand Conf A 30%, Ligand Conf B 10%. Phenix is happy having a single conformation below 100% occupancy but seems to force the total sum of multiple occupancy residues to be 100%. Is there a way to turn that off for the ligand? Thanks Terry -- Paula Therese Lang Postdoctoral Scholar Alber Lab UC Berkeley/QB3

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Occupancy refinement
by Jerome Nwachukwu 01 Jun '12

01 Jun '12

Hi: I have a 2.2Å structure containing a ligand in at least 2 alternate conformations. When the structure is refined via XYZ refinement + occupancy using phenix.refine, both ligand conformers are kicked out of the electron density. Is there a way to prevent this? Thank you, -Jerome Sent from my iPhone

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TLS makes my r-factors shoot through the roof
by Morten Groftehauge 30 May '12

30 May '12

Hi Phenixbb, 3.2A data, 110 Wilson B, I41, twinned. Imperfect inverted repeat dsDNA with 4 protein monomers, NCS not used in refinement. If I don't include TLS I get a nice stable R-factor while RMS goes down. If I include TLS (whether as one group per chain or as chosen by Phenix) this happens: [image: Inline images 1] Density disappears around some of the DNA bases as an obvious difference. If I run Refmac with TLS it just never finishes. While I could just refine without TLS this does make me worried that there is something wrong with my model or my data (besides being terrible). Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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Wilson B and REMARK 3
by Michael Thompson 28 May '12

28 May '12

Hello Everyone, I have a question regarding the Wilson B information reported in REMARK 3 of a pdb file. I am preparing a pdb file for deposition, and I am wondering which is the most appropriate value to report as the Wilson B in REMARK 3? My inclination is to report the Wilson B for the full dataset calculated by XSCALE. This value differs slightly from the Wilson B value calculated by phenix.refine and printed to the refinement log file (XSCALE=27.6 vs. phenix.refine=19.8). I assume this difference is due to phenix.refine using a low-resolution cutoff of ~20A. My concern stems from the fact that REMARK 3 "presents information on refinement program(s) used and the related statistics," so I'm not sure if it's best to include the Wilson B calculated by the refinement software, or the Wilson B for the whole data set. Thanks, Mike -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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