- phenixbb - phenix-online.org

Re: [phenixbb] advice for refinement with anomalous information
by John Rose 27 Aug '10

27 Aug '10

Hi, I am refining my first structure (Cd-SAD) with the Phenix (GUI) and would like to refine anomalous f' and f". When i check the box, a menu appears and I have no idea of how to define the Cd atoms. I looked at the help and FAQ and found this: refinement.refine.anomalous_scatterers { group { selection = name BR f_prime = 0 f_double_prime = 0 refine = *f_prime *f_double_prime So I thought the name should be input as CD in the gui but when I submitted the refinement I got an error. Any help here would be appreciated? Thanks, John Rose

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file type not supported???
by Joseph Noel 24 Aug '10

24 Aug '10

Hi All, I am having a problem that should be totally simple but I am stuck trying to find out what is happening. I use Text Wrangler on my Mac as a text editor of files. I have used it many many times to edit PDB files. It seems now that some PDB files that I have opened and removed a few lines now show up as an unrecognized file type when trying to read them into Phenix or into COOT. However, when I upload them on the Molprobity site they are read fine and processed. However, even the downloaded file from Molprobity gives the same error. I know it must be something simple but stumped and hoping someone else has experienced the same problem and has a quick fix. Thanks! 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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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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