- phenixbb - phenix-online.org

Using phenix_rosetta_refine
by Jan Gebauer 29 Oct '13

29 Oct '13

Dear all, I tried to install phenix.rosetta_refine for a recently solved structure, which only diffracts up to 3.5-4.0 Angstrom (anisotropic). However, I was unable to get the programs correctly set up. I first tried to compile phenix 1.8.4-1496 from source according to this documentation : http://www.phenix-online.org/version_docs/dev-1500/rosetta_refine.htm. The build process failed during GTK2 building, without an obvious explanation (error code 1, no missing libraries ...) I then realised that the developer version are potentially more suitable, as they seem to be prepared for this. I installed the binary from 1523 and tried to start the building process from there with rosetta.build_phenix_interface nproc=X Unfortunatelly Rosetta 3.5 seems to have a different folder structure. There is no main subfolder, instead there are "rosetta_sources", "rosetta_tools" and so one. After a fast "cp rosetta_sources main/source/" it worked a bit but still exited with: scons: *** Error converting option: extras Invalid value(s) for option: python File ..... /setup.py, line 72, in setup_build_options I have the following questions: 1) Am I right to assume that I do NOT have to recompile the dev 1523 (1520 states "Python shared library for linux) on Linux? 2) Which rosetta version do I have to use? Does 3.5 work? There is no 3.6 on rosettacommons... (or is it hidden?) Regards, Jan -- Dr. Jan Gebauer AG Prof. Baumann Institut für Biochemie / Uni-Köln Otto-Fischer-Str. 12-14 / 50674 Köln Fon: +49 (221) 470 3212 Fax: +49 (221) 470 5066 http://px.uni-koeln.de/

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Need help with atom selection for anisotropic refinement
by Dr. Mark Mayer 27 Oct '13

27 Oct '13

Hi, I'm trying to do a mixed individual isotropic anisotropic refinement b factor refinement and can't get my atom selections to be accepted by phenix.refine. For the atoms I want to do isotropic refinement I used optional (element H or element D or resname HOH or chain E or chain F or chain A or chain B) for the anisotropic selection I used chain A and chain B and not (element H or element D or resname HOH or chain E or chain F or chain A resseq 5:11 or chain A resseq 66:72 or chain A resseq 117:138 or chain A resseq 152:184 or chain A resseq 196:210 or chain A resseq 249:251 or chain B resseq 3:6 or chain B resseq 66:72 or chain B resseq 166:210 or chain B resseq 249:251) I've tried various combuinations, but so far all have given the error message: Selection string results in empty selection. Thanks for your help Mark --

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Alternative Conformation, Restraints
by Moritz Machelett 27 Oct '13

27 Oct '13

Hello everyone, I am in the final rounds of refining my protein at high resolution and currently trying to model an alternative conformation of a Chl /a/-phytol chain. I inserted a second phytol chain with coot - worked out well so far (alternate chain identifiers A and B for both phytol chains). After using phenix.refine, however, the occupancy of the second phytol chain was refined to 0. When splitting the whole Chl molecule the occupancy refines to sensible values (0.34 and 0.66). We would prefer to only model the phytol chain in alternate conformation as the macrocycle superpose perfectly. Any suggestions regarding the occupancy problem? Another issue concerns restraints. We tried to turn of specific nonbonded restraints and found a phenixbb message from 2007: http://www.phenix-online.org/pipermail/phenixbb/2007-September/011734.html Are there any news/updates on this matter? Any help appreciated! Thanks, Moritz -- Moritz M. Machelett Ruhr University Bochum Protein Crystallography, Department of Biophysics, ND04/396 44780 Bochum Tel: +49-(0)234/32-25754

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fem map
by nih\mayerm 27 Oct '13

27 Oct '13

Hi, I'm trying to make a fem amp using phenix-1.8.4-1496 using my refined structure and mtz with map coefficients as input: phenix.development.fem 3222_Glu_refine_78.mtz 3222_Glu_refine_78.pdb coot 0.7.0-1 fails to generate a map when fem.mtz is opened, either in auto or manual mode mtzdmp for fem.mtz gives: Col Sort Min Max Num % Mean Mean Resolution Type Column num order Missing complete abs. Low High label 1 NONE -37 35 0 100.00 -5.0 14.2 61.69 1.21 H H 2 NONE 0 101 0 100.00 38.0 38.0 61.69 1.21 H K 3 NONE 0 44 0 100.00 16.8 16.8 61.69 1.21 H L 4 NONE 0.0 1796.7 25825 84.81 84.67 84.67 31.87 1.21 F 2mFoDFc 5 NONE -180.0 180.0 25825 84.81 1.07 90.28 31.87 1.21 P PHI2mFoDFc 6 NONE 0.0 2750.2 0 100.00 144.76 144.76 61.69 1.21 F 2mFoDFc_FilSharp 7 NONE -180.0 180.0 0 100.00 1.26 90.34 61.69 1.21 P PHI2mFoDFc_FilSharp 8 NONE 0.2 24426.8 0 100.00 235.27 235.27 61.69 1.21 F KICK 9 NONE -180.0 180.0 0 100.00 0.02 89.63 61.69 1.21 P PHIKICK 10 NONE 0.2 9283.0 0 100.00 132.01 132.01 61.69 1.21 F FEM 11 NONE -180.0 180.0 0 100.00 0.23 90.34 61.69 1.21 P PHIFEM

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Using experimental phases in refinement
by Joseph Noel 26 Oct '13

26 Oct '13

Hi Folks, I am wondering if anyone can recommend some good reference(s) of structure refinements that employed experimental phases. We are attempting to collect experimental phases for a series of structures for which we have refined the structure already. I assume we can easily use initial model phases (space group doesn't change) to locate anomalous scatters and calculate experimental phases from the elucidation of the heavy atom arrangement. Most of the structures range from 1.7 to 2.4 A resolution. Would also appreciate any advice on the most efficient and accurate set of steps to accomplish this. If anyone thinks that this will not add much to the refinement of these structures would also appreciate some critiques. The protein in question crystallizes with 68% solvent content and one monomer per assymetric unit. We are employing ensemble refinement as the protein in question displays local conformational changes depending on the type of ligand(s) bound and also pH and similar but distinct crystallization conditions. We are carrying this out on ~400 mutants to do a very large scale comparison. Sorry for the long email but since we want to try and understand even minor conformational changes I thought phased-refinement would be much more powerful then refining just against the Fs. Thanks again in advance, Joe ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

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protein-ligand complex structure
by Wei Shi 25 Oct '13

25 Oct '13

Hi all, I am working on a structure of protein-ligand complex. Four ligands are placed for the dimer protein and the density for the two ligands of the first monomer is better than the density for the other two ligands of the second monomer. Ligand is moved to fit density better in Coot (and for two ligands of the first monomer, they fits the density almost perfectly), but after a refinement in phenix (default settings + NCS restraints + Secondary structural restraints + Optimize X-ray/stereochemistry weight +Optimize X-ray/ADP weight), some part of the ligand which fits density good before moved out of the density again...Besides, it always shows green density in Coot for the ligand region even in places where the ligand is in density... Any suggestions or ideas about how to fit the ligand better and why the density for ligands of the second monomer is worse than that for the first monomer and why the ligands would move out of density after refinement? Is it because the protein model is not good enough to get the ligand density good? There is a conformational change upon ligand binding, and I rebuilt some part of the protein manually, and the density for a region of about 30 residues is not very good, and I tried to mutate those to alanies and refine, but it didn't help me see the density better... Any suggestions or ideas on how to improve this protein-complex structural model? Thank you so much! The statistics for the current best model is as follows, and the resolution of the dataset is 2.8Å. start final ------------------------------ ---------------- R-work: 0.3359 0.2993 R-free: 0.3619 0.3558 RMS(angles): 1.03 1.55 RMS(bonds): 0.006 0.007 MolProbity validation Ramachandran outliers: 4.7% (Goal: < 0.2%) Ramachandran favored: 85.3% (Goal: > 98%) Rotamer outliers: 4.5% (Goal: 1%) C-beta outliers: 0 (Goal: 0) Clashscore: 7.43 Overall score: 2.56 Thank you so much! Best, Wei

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Diffraction pattern from structure factors
by Bala Venkatakrishnan 25 Oct '13

25 Oct '13

Hi Are there programs available to generate a diffraction pattern from structure factors? Purely for learning purposes. -- Bala -- Balasubramanian Venkatakrishnan, Ph.D. Post-doctoral Fellow Molecular and Cellular Biochemistry Dept. 212 S Hawthorne Dr Simon Hall Room 213 Bloomington, IN 47405-7003 Indiana University Tel.:(812) 856-1874

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DEN refinement using CC instead of Rfree
by Morten Grøftehauge 25 Oct '13

25 Oct '13

Hi guys, Is there any way to do a DEN refinement run where it looks for the best map-model CC instead of the best Rfree? Even more useful would be map-model CC of selected residues... Or can I run DEN refinement on only part of the structure? That should in theory be faster. And since the Rfree values for the correct parts of the structure would be then fixed then I should get rid of the problem of Phenix selecting the refinement weights that result in the structure most like the input structure. Does that make sense? Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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job numbers
by SD Y 24 Oct '13

24 Oct '13

Hi, I am using latest version of Phenix. Since last week, I noticed that that two jobs having same number (not always). So, I cant open the recent job in GUI, though I could see results in folder. Is there any fix for this? ThanksSDY

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autobuild mistake
by Heather L Condurso 23 Oct '13

23 Oct '13

So I was running autobuild on the command line with: phenix.autobuild data=data.mtz model=model.pdb rebuild_in_place=False acceptable_r=0.2 I have a model from another data set that is missing some loops and new data sets which I would like to use autobuild to see if the model can be extended. I am using 1.8.4-1496 on a mac with osx 10.6.8. I was an idiot and when looking in the directory to check out one of the RUN_FILE_#.log files, I accidentally clicked on the RUN_FILE executable which started another AutoBuild subprocess. Since then all the other subprocesses had finished, but overall run stalled at: Splitting work into 4 jobs and running with 1 processors using sh background=False in ./AutoBuild_run_6_/TEMP0 Final job will be run with sh with background=True Starting job 1...Log will be: ./AutoBuild_run_6_/TEMP0/RUN_FILE_8.log Starting job 2...Log will be: ./AutoBuild_run_6_/TEMP0/RUN_FILE_9.log Starting job 3...Log will be: ./AutoBuild_run_6_/TEMP0/RUN_FILE_10.log Starting job 4...Log will be: ./AutoBuild_run_6_/TEMP0/RUN_FILE_11.log And the combine and extend didn't happen. I saw a post about combining models from autobuild but it was for rebuild_in_place=True and the post mentioned that the models needed to have identical sequences for it to work. Is there a way to save my mistake without starting over? The run I had restarted had yielded Rs=999.9 so If there is a way to maybe combine just 3 of the 4 that may be helpful as well. Thanks, Heather Condurso condurso(a)bc.edu

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