November 2012 - phenixbb - phenix-online.org

Job history recovery
by Damian Niegowski 20 Nov '12

20 Nov '12

Hello all, I have run into a problem with the Job History tab in the GUI. For one project there is a listing of 16 jobs but when I try going into Job History there is nothing. The .phenix directory for that project is present and all other directories of the individual jobs are there. Is there a way to "restore" the job history from existing parameter files? Regards, Damian Damian Niegowski Ph.D. Institute of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 171 77 STOCKHOLM e-mail: damian.niegowski(a)ki.se phone: 0046 8 524 876 33 fax: 0046 8 736 04 39

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Refining Anomalous Groups
by Brennan Bonnet 20 Nov '12

20 Nov '12

Hi All, I am trying to use phenix.refine to refine partially occupied xenon sites using the Anomalous Groups selection under "Refinement settings". My list of anomalous scatters initially consisted of 22 peaks as located by HySS. Some of these were removed as they originated from S atoms from Met and Cys residues and a few others were removed after previous refinement steps due to having zero occupancy. My remaining sites consist of my xenons (hopefully) and other metals such as Mg or Zn which are mixed in and look like partially occupied xenon sites. My problem is that when I try to define the 11 remaining sites for the "refine anomalous groups" selection the software complains: Invalid combination: F-obs not anomalous, but refinement of 11 f_double_prime values requested (11 scatterers): Please provide anomalous reflection data or fix all f_double_prime values (see refinement.refine.anomalous_scatterer.group input blocks) I can't figure out exactly what I need to change to make it work and can't find a guide anywhere. Do I need to provide additional data or is the syntax for the sites incorrect maybe? Please help! ~Brennan~

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Phaser
by Morten Groftehauge 19 Nov '12

19 Nov '12

Hi guys, I was trying out the new Parallel Phaser (dev-1214) and using a model prepared by Rosetta covering 25% of the total structure (32% identity to the homology model), NCS = 2. 5 models actually but not really relevant since the program spontaneously stopped running after a couple of hours (I love what it's supposed to do though!). My question is about the log however. In the Parallel Phaser log it says: Expected LLG and Resolution Limits ---------------------------------- Expected LLG target: 120.00 Expected LLG achieved: 120.0 Resolution of All Data: 2.38 Resolution limited by eLLG target: 4.83 This resolution WILL NOT be used as the default The expected LLG achieved is greater than 120 (eLLG target) but when I tried to recreate that run in the regular Phaser-MR I get this message in the log Expected LLG and Resolution Limits ---------------------------------- Expected LLG target: 120.00 Expected LLG achieved: 49.7 Resolution of All Data: 2.38 Resolution limited by eLLG target: 2.38 This resolution WILL NOT be used as the default The expected LLG achieved is less than 60 (half eLLG target) FTF rescoring WILL be performed due to low expected LLG signal Deep search will be performed from the start I think the second result looks more realistic (unfortunately) but I still don't understand why the difference? Cheers, Morten PS Seems like there's a memory leak in 1214 and 1207 when I run the Phaser step of MR_Rosetta. Does this sound right? Definitely in 1207 but it seems like it's still there in 1214. -- Morten K Grøftehauge, PhD Pohl Group Durham University

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SASTBX server
by Tanner, John J. 19 Nov '12

19 Nov '12

I apologize if this is an inappropriate post for phenixbb… Has anyone had trouble with the SASTBX server lately? I have been getting this error since Friday when calculating shapes and P(r). Server error! The server encountered an internal error and was unable to complete your request. Error message: Premature end of script headers: cctbx_web.cgi If you think this is a server error, please contact the webmaster<mailto:[email protected]>. Error 500 sastbx.als.lbl.gov<http://sastbx.als.lbl.gov/> Fri Nov 16 07:56:37 2012 Apache/2.2.17 (Unix) PHP/5.3.4

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fwd: West Coast Protein Crystallography Workshop
by Nathaniel Echols 18 Nov '12

18 Nov '12

(There will probably be several people from our group attending this year.) ---------- Forwarded message ---------- From: "Williams, John Charles" <jwilliams(a)coh.org> To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Cc: Date: Sun, 18 Nov 2012 08:15:19 -0800 Subject: West Coast Protein Crystallography Workshop All, Wayne Hendrickson will be the keynote speaker for the West Coast Protein Crystallography Workshop, scheduled for March 17th - March 20th at the Monterey Plaza and Spa. Registration will open up Dec 1st. Hope to see you there! Best, John Williams WCPCW Organizer

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v1.8.1 installation hangs
by Alex Theodossis 18 Nov '12

18 Nov '12

Hi, I'm attempting to install the latest version of phenix on mac 10.5.8, using the command line installer. Installation proceeds well until towards the end, where it hangs on: precompiling .py files I can leave it for up to an hour without any further progress, but upon typing: ctrl+c The installation comes back to life and proceeds to completion. Can anyone advise as to what might be causing this and on how reliable this installation is going to be? Thanks in advance.

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Alternate conformation occupancies sum more than 1
by Mikalai Lapkouski 15 Nov '12

15 Nov '12

Hello, I was refining the 1.2 A structure. After refining occupancies there are several residues with alternate conformers for which the sum of the occupancies is greater than one. For example: GLY A 197 O Occupancy sums to 1.14 MET B 17 CB Occupancy sums to 1.03 TYR B 142 CD1 Occupancy sums to 1.04 TYR B 142 CZ Occupancy sums to 1.01 GLY B 197 O Occupancy sums to 1.23 The density is defined nicely for them, do you know what can be the problem of why the sum could be more than 1? Thank you Mikalai

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Restraints file for a new amino acid residue
by Agnes Thiane Pereira Machado 14 Nov '12

14 Nov '12

Hi We are trying to refine a protein structure with a (covalently) modified residue. The colosest discussion to our problem is: http://www.phenix-online.org/pipermail/phenixbb/2010-August/015629.html We ran: phenix.elbow --residue SSC ourmodel.pdb And read the due cif file at phenix refinement. The residue by itself is OK, but we were not able to perform the peptide bond between C and N. How to complete the .cif file such that it has due restraints for the peptide bond with this modified residue? Agnes

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Off topic: Anomalous signal
by ash.k＠aol.com 14 Nov '12

14 Nov '12

Dear all, I am sorry for this off topic question in the bb. I have good looking but poorly diffracting (3.8-4 A) crystals of SeMet derivative. Mass spec confirmed that Se incorporation is 100% and I got a very good energy scan for Se too. I properly selected the peak, inflection and remote wavelengths for the data collection. But, I do not see anomalous signal in the data collected. Processing in HKL2000 does not show any resolution dependance of Chi square and also xtriage says that the anomalous resolution limit is only up to 8-9A. Is it something usual for the kind of diffraction I am getting or something else is going on? I have 5/200 methionine residues in the sequence. Worst case I can think of is that all the Met side chains are disordered ! Any help would be highly appreciated.. AK

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den_refine on cluster
by Michael Thompson 14 Nov '12

14 Nov '12

Hi All, Apologies if this is a naive question, but I would like to run DEN refinement and I notice the documentation says that it runs optimally on a machine with at least 30 processor cores. Is there any way to run DEN refinement on a SGE cluster as a batch job using something like run_command="qsub" as can be done with autobuild, etc.? 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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