October 2013 - phenixbb - phenix-online.org

labelit distl_minimum_number_spots_for_indexing
by Christian Roth 22 Sep '15

22 Sep '15

Dear Phenix-Team I installed the latest nightly build 1.8-1069. I tried to index some diffraction images and to overwrite the minimum usable spots for indesing I tried the suggested command. However If I try this command, it seems that it does not exist. At least in the list of the possible distl commands it does not show up. Do I have to install some additional stuff or change some preferences to get this command? Best Regards Christian

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Appropriate number of reflections for FreeR
by Joseph Noel 03 Nov '13

03 Nov '13

Hi All. I think I have asked this before but forgot. Old age. What is the appropriate number / percentage of reflections to flag for a statistically appropriate Free-R calculation? If I am correct, the reflection file editor in Phenix chooses by default either 10% of the measured reflections or 2000 whichever comes first. ______________________________________________________________________________________ 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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Phenix.Rosetta_refine on Ubuntu 12.04 LTS
by Jan Gebauer 01 Nov '13

01 Nov '13

Dear all, I'm trying to get rosetta_refine working on ubuntu 12.04 LTS. This was the (latest) way I tried it: 1) Downloaded phenix-dev-1523 binary & installed it via installer in /usr/local/science/phenix4rosetta/phenix-dev-1523 2) Downloaded rosetta 2031wk42 and extracted it in /usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle 3) Inserted into phenix_env.sh export ROSETTA_BIN=/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/source/bin export PHENIX_ROSETTA_PATH=/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/ export ROSETTA_BIN=/usr/local/science/phenix4rosetta/rosetta_2013wk42_bundle/main/database 4) sources phenix_env.sh 5) build the interface via rosetta.build_phenix_interface nproc=4 6) exceute the refinement via phenix.rosetta_refine phasermodel.pdb data.mtz nproc=4 The programm runs fine, up to the point where it should generate models via rosetta, it then stops and crashes. I have attached some logfiles Has anyone managed to run rosetta_refine on Ubuntu? Which phenix and rosetta versions did you use? Ist there anything wrong on my above mentioned build protocol? I'm thankful for any help. Regards, Jan Gebauer -- 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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warning: do not upgrade Mac OS yet!
by Nathaniel Echols 31 Oct '13

31 Oct '13

There is some kind of strange issue with wxPython on the new Mac OS ("Mavericks"), which for at least the 1.8.4 version prevents Phenix application windows (but not the main GUI) from opening. It is also printing out an extraordinary number of warning messages about fonts to the console. I'm hoping there is a simple solution (which seems likely, since 1.8.2 is mostly okay despite using the same version of wxPython), but until we figure out what is causing this, I recommend leaving your Macs unmolested if you want to use the Phenix GUI. Updates to follow if-and-when I fix this. thanks, Nat

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Using phenix_rosetta_refine
by Jan Gebauer 30 Oct '13

30 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 28 Oct '13

28 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 28 Oct '13

28 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 27 Oct '13

27 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 26 Oct '13

26 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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