August 2010 - phenixbb - phenix-online.org

Re: [phenixbb] phenix.ready_set hydrogens not compatable with coot library
by Joseph Noel 24 Aug '10

24 Aug '10

Hi All, Indeed even the latest COOT still relies on the old PDB format and hydrogens fly. Its probably not prudent to use hydrogens in refinement then remove them and add back each time. Kind of defeats the purpose of using them in the first place. Until COOT is updated I found a pretty easy way around things as long as you have access to the internet. Just use the MOLPROBITY site (http://molprobity.biochem.duke.edu/). In addition to it being a fantastic tool for really cleaning up structures, you can quickly upload your refined file from Phenix with hydrogens, then hit the button to downgrade to PDB v23. It creates the appropriate file with renamed hydrogens that work great in COOT. You can then re-upload the COOT rebuilt model and it will "upgrade" naming to the latest PDB version. Download that file and there you go for Phenix refinement. Sounds like a bit but very fast and easy to implement until COOT is upgraded. Joe ___________________________________________________________ Joseph P. Noel, Ph.D. 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 Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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Phenix Structure Soluiton & Refinement webinar
by Angela Criswell 23 Aug '10

23 Aug '10

Dear colleagues, I would like to draw your attention to an upcoming educational webinar to be presented by Paul Adams titled "Structure Solution and Refinement with Phenix" which is scheduled to occur Thursday, August 26th at 10:00 PDT (13:00 PM EST /17:00 UTC/GMT). You can find more information including a registration link at the following site: http://www.rigaku.com/protein/webinars.html Best regards, Angela

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Palestrant, Deborah is out of the office.
by deborah.palestrant＠novartis.com 23 Aug '10

23 Aug '10

I will be out of the office starting 08/23/2010 and will not return until 08/27/2010. I will respond to your message when I return.

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labelit.version bug?
by Ben Eisenbraun 23 Aug '10

23 Aug '10

labelit seems to be working fine, but one of my users pointed this out to me: $ which labelit.version /programs/i386-linux/phenix/1.6.4-486/phenix-1.6.4-486/build/intel-linux-2.6-x86_64/bin/labelit.version $ labelit.version Traceback (most recent call last): File "/programs/i386-linux/phenix/1.6.4-486/phenix-1.6.4-486/labelit/command_line/version.py", line 18, in <module> run() File "/programs/i386-linux/phenix/1.6.4-486/phenix-1.6.4-486/labelit/command_line/version.py", line 7, in run assert (os.path.dirname(build) == os.path.dirname(repos)) AssertionError -ben -- | Ben Eisenbraun | Software Sysadmin | | Structural Biology Grid | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

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phenix.ready_set hydrogens not compatable with coot library
by amadrona＠uci.edu 23 Aug '10

23 Aug '10

hello, After reading many posts on the phenix and coot boards I realize that the hydrogens produced by phenix.ready_set are not compatable with coot. Specifically, coot does not recognize HB3 and HD3 hydrogens. When I do realspace refinement they fly off into space. I have edited HB3 to read HB2 and HB2 to read HB1 and everything works well. I was wondering if there is a fix for this besides editing the pdb each time you run phenix.ready_set. Is there a way to add HB3 hydrogens to the phenix library (CCP4 library)? Thank you -Yarrow

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MD with phenix.refine?
by Ed Pozharski 20 Aug '10

20 Aug '10

Silly question: is there some way to run what would essentially be an MD simulation with phenix.refine? I mean, turn off X-ray-term by setting tardy.target_weights.fix_wxc=0, and then run cartesian dynamics? Ed. -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs

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Ringer: A program to detect molecular motions by systematic X-ray electron-density sampling
by Terry Lang 20 Aug '10

20 Aug '10

The Alber lab at UC Berkeley is pleased to release of the code for Ringer version 1.0 (http://ucxray.berkeley.edu/ringer.htm). Ringer is a program to detect molecular motions by systematic X-ray electron-density sampling. The aim of Ringer is to go beyond static structural snapshots of proteins by uncovering structural ensembles in X-ray electron density. This information can reveal not only which parts of proteins are flexible and which parts are rigid, but it also can define alternate conformations that may be important for function. Alternate conformations of binding sites also may afford additional targets for drug design. The Ringer method is described in Lang et al. /Protein Sci/. 2010 Jul; 19(7):1420-31 <http://www.ncbi.nlm.nih.gov/pubmed/20499387>. An application of Ringer, determining the structural underpinnings of the side chain dynamics critical for the function of the enzyme proline isomerase, was published in Fraser JS et al. /Nature/. 2009 Dec 3;462(7273):669-73 <http://www.ncbi.nlm.nih.gov/pubmed/19956261>. Ringer is freely available to academics. -- PaulaTherese Lang Postdoctoral Scholar Alber Lab, UC Berkeley http://ucxray.berkeley.edu/ringer.htm

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hydrogens in riding model create steric clashes after refinement
by amadrona＠uci.edu 20 Aug '10

20 Aug '10

Hi, I am having a problem with hydrogens causing steric clashes after refinement. I added hydrogens to my pdb using: "phenix.ready_set model.pdb". I was given two sets of coordinates (my model and a pdb for Iron atoms) I included this new model in the next round of refinement but I did not include the pdb for the Iron atoms. I ran refinement with the folowing parmeter file: refinement.main.ordered_solvent = true #refinement.main.ordered_solvent.mode=filter_only refinement.refine.strategy = individual_sites+individual_adp #refinement.refine.adp.individual.isotropic = "chain W" refinement.output.prefix = CIN4_refine refinement.output.serial = 18 refinement.output.write_def_file = True resolution is 1.37A with close to 400,000 unique observations (obs/param is still about 4) Stats: Rwork Rfree bonds angles start: .1444 .1723 .016 1.617 end: .1371 .1657 .010 1.301 I also ran wxu and wxc optimization from the command line. I know that the defualt is "riding-model" so that the hydrogen atoms are not refined. However, I thought that the program would be able to avoid steric clashes. Is there an aditional command I need to turn on to account for this? I am currently fixing every hydrogen that clashes on an individual basis in coot. There are also a handfull of hydrogens that exist out in space that I decided to delete. Thank you very much for your help. -Yarrow

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altloc non-bonded interactions
by Paul Smith 20 Aug '10

20 Aug '10

Is it possible to tell phenix.refine to ignore certain non-bonded interactions? I have a structure at 1.1A with some interesting sulfate molecules that refuse to refine well. I suspect two positions are alternately occupied by sulfate in some cases and two water molecules in others. I would like to refine with both (a sulfate and two waters) with each component at 1/2 occupancy. With alternate conformations of a given sidechain, the two alternate locations automatically ignore one another w.r.t. non-bonded interactions. However, different residues, it would seem, do not. Has anyone encountered a similar situation or do the phenix gurus have any input? As an alternative, can I define an alternate sulfate residue with several missing atoms? Thanks in advance, --Paul

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Re: [phenixbb] stuck with phenix refine
by Ian Munro Slaymaker 19 Aug '10

19 Aug '10

I also have been having a problem with phenix.refine freezing with no error message from the GUI. It usually freezes at the first macro cycle. I am using version 1.6.4-486. -Ian

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