- phenixbb - phenix-online.org

LigandFit error
by Priit Eek 14 Aug '11

14 Aug '11

Hi, I'm getting this error when trying to run LigandFit from the GUI: The key gui_output_dir is not in var_type_dict…this means the command-line Wizard needs a conversion in the ligandfit.py script under 'Translating inputs' or else in excluded_inputs or else the Wizard SetVars routine needs this variable set Is this a bug? I am using the 64-bit dev-842 version on OS X 10.7 Lion. Best regards, Priit

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Unexpected Occupancy refiniement for ligands...
by Yuri 13 Aug '11

13 Aug '11

Hey, So I am finishing up a model at 1.5 A and I tried to refine my ligands (3) and waters (468) in addition to altloc residues. The residues refine as expected e.g OccA + OccB = 1.0 and all atoms in A have OccA and all the atoms in B have OccB. My ligands on the other are being refined as the following: HETATM 6867 C1 MLA L 3 32.357 -28.612 7.978 0.93 23.77 C C HETATM 6868 O1A MLA L 3 31.209 -28.949 7.502 0.85 24.79 C O HETATM 6869 O1B MLA L 3 32.454 -28.160 9.141 0.70 22.70 C O HETATM 6870 C2 MLA L 3 33.553 -28.727 7.095 1.00 25.46 C C HETATM 6871 C3 MLA L 3 34.774 -28.070 7.627 0.92 28.45 C C HETATM 6872 O3A MLA L 3 34.830 -27.664 8.808 1.00 30.15 C O HETATM 6873 O3B MLA L 3 35.775 -27.948 6.840 1.00 30.23 C O HETATM 6874 HC21 MLA L 3 33.321 -28.281 6.139 1.00 30.56 C H HETATM 6875 HC22 MLA L 3 33.760 -29.776 6.943 1.00 30.56 C H Each atom is getting an individual occupancy assigned, which physically is impossible :) Any light? Could it be my selection syntax? Corrigendum: I think I sent a bug email last night about an error when writing mtz files in refinement. It was an accident. My naming convention was bad, thats why it crashed. Sorry -- Yuri Pompeu

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R/Rfree discrepancy Phenix vs Refmac
by Sabine Schneider 12 Aug '11

12 Aug '11

Hello, I am refining a structure at 2.1A solved by MR. For curiosity I'm testing things like 'shaking' coordinates, simulated annealing, refinement Refmac vs Phenix and so on, to see what influence that has on stats, maps etc. For instance after MR I did a bit of shaking the coordinates with pdbset (noise 0.1), followed by simulated annealing in Phenix. Phenix states after SA: Start R-work = 0.2671, R-free = 0.2992 Final R-work = 0.2312, R-free = 0.2666 When I use the output pdb of phenix directly in Refmac (with same mtz as input for Phenix) Refmac tells me: Initial R factor 0.2392 R free 0.2887 So I am quite puzzled about the discrepancy. Or can someone tell me if I made an error in reasoning somewhere? Thanks a lot for the help! Sabine

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getting the crystal form
by Bradley Hintze 11 Aug '11

11 Aug '11

I was wondering if there was a easy way to grab the crystal form for a given PDB code? -- Bradley J. Hintze Duke University Graduate Student Department of Biochemistry

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phenix.grow_density documentation
by Joern Krausze 11 Aug '11

11 Aug '11

Dear all, could anybody please provide me with a documentation for phenix.grow_density? I did'nt find one on the Phenix homepage or elsewhere in the depths of the internet. Thanks in advance, Joern ****************************************** Address: Joern Krausze Molecular Structural Biology Helmholtz Centre for Infection Research Inhoffenstrasse 7 38124 Braunschweig Germany Email: joern.krausze(a)helmholtz-hzi.de Phone: +49 (0)531 6181 7023 (office) +49 (0)531 6181 7020 (lab) ****************************************** Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Heiko Gevers, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Ulf Richter, MBA Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

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Large size display system
by jens j birktoft 11 Aug '11

11 Aug '11

Sorry if this topic is bit off-list We are looking for some advice regarding a presentation system that permit the display in high definition of interactive molecular graphic sessions (incl. PHENIX,COOT, PyMOL. CHIMERA etc ) to our research group (10-12 people). Ideally we would like a 32"-36" LCD monitor coupled to a computer equipped with the proper graphics card for the large display as well as 24" monitor . Any suggestions would be appreciated Cheers Jens *+++++++++++++++++++++++++++++++++++++++++++++++++++++++* * * *Jens J. Birktoft, Department of Chemistry, New York University e-mail: birktoft(a)nyu.edu <jens.knold(a)gmail.com> slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025 Phone: 212-749-5057* *+++++++++++++++++++++++++++++++++++++++++++++++++++++++* * * *Jens J. Birktoft e-mail: jens.knold(a)gmail.com slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025 Phone: 212-749-5057 *

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Re: [phenixbb] rosetta fragment files -- corrected command
by Thomas C. Terwilliger 11 Aug '11

11 Aug '11

Hi again David, Sorry, corrected command below. Can you try the version of the script I put in phenix: phenix.adjust_robetta_resid fragments_in fragments_adjusted <start_resno> Let me know if that doesn't do it! All the best, Tom T >> Hi, >> >> I'm also trying to use rosetta with a protein that has more than 650 aminoacids. I have found the answer on last June to the similar question about the fragment files but I couldn't make the script to change the aminoacids numbers work so far >> http://www.phenix-online.org/pipermail/phenixbb/2011-June/017268.html >> >> However I think the script got out of format and I can't make it work. I have python installed however I'm a total beginner on python. >> >> Is it possible that I could have the scrip file so I don't lose the proper format? >> Also, should I replace something inside (like put the file name somewhere) so it works? >> >> Thanks in advance >> >> David Neves >> Institut de Biologie Structurale >> Grenoble France >> >>

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rosetta fragment files
by David NEVES 11 Aug '11

11 Aug '11

Hi, I'm also trying to use rosetta with a protein that has more than 650 aminoacids. I have found the answer on last June to the similar question about the fragment files but I couldn't make the script to change the aminoacids numbers work so far http://www.phenix-online.org/pipermail/phenixbb/2011-June/017268.html However I think the script got out of format and I can't make it work. I have python installed however I'm a total beginner on python. Is it possible that I could have the scrip file so I don't lose the proper format? Also, should I replace something inside (like put the file name somewhere) so it works? Thanks in advance David Neves Institut de Biologie Structurale Grenoble France

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autobuild mtz file
by intekhab alam 08 Aug '11

08 Aug '11

Hi there i run autobuild in phenix and have my model and mtz file. when i open my mtz file in coot using the option open mtz, a window pops " column label assignment" How can i convert this mtz file that can open in coot which has both 2fo-fc as well as fo-fc maps. -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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Intensity-Weighted Reciprocal Lattice
by Michael Thompson 05 Aug '11

05 Aug '11

Hello ccp4 & phenix BB members, I would like to view the intensity-weighted reciprocal lattice for several data sets that I have collected. (The data have been indexed, integrated and scaled with Denzo and Scalepack.) I was wondering if anyone could offer some advice on what might be the best and/or most practical way to do this? I know that there are several programs out there that can generate sections (i.e. 0,k,l) of the reciprocal lattice, such as LABELIT and xrayplot. Are there any other options for doing this, perhaps within ccp4 and/or phenix? I once saw someone give a presentation and they had a little video that showed a three dimensional section of the reciprocal lattice rocking back and forth, which was really cool. I liked this because I felt like it gave a much more holistic representation as opposed to viewing a bunch of individual sections. I don't know if there is an easy way to do this, or if this person somehow managed to create this 3D depiction from a series of sections. Any tips or recommendations would be appreciated. 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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