- phenixbb - phenix-online.org

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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Simulated anneal
by Qiang Chen 14 Nov '12

14 Nov '12

Hi all, I have a 3.05Å structure. I refine it to Rwork=25.2 Rfree=28.81. I use Molprobity to check the structure. The clash score is 100th and Molprobity score is 99th. I was suggested to run simulated anneal to help reduce Rwork and Rfree. I tried Cartesian and Torsion and different seed. The best result I got is: torsion anneal, start_temp=2500,final_temp=300, random_seed=4250146. The Rwork:25.8, Rfree=31.2. I checked the new model and found that some places in a domain were not correctly traced. The density for that domain is not good and have several flexible loops. My question is: does simulated anneal always work and reduce Rwork/Rfree? At the final stage of refinement, does it necessary to use simulated anneal again? Thanks! yamei The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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phenix.pdbtools - renumber specific chains
by Antony Oliver 13 Nov '12

13 Nov '12

Apologies if this has been covered before - but can someone point me to a way of renumbering only specific chains (i.e. F, G, H etc). I have tried using phenix.pdbtools with either selection = "chain F or chain G or chain H" or keep "chain A or chain B or chain C or chain D" - but in both cases phenix renumbers every single residue! With thanks, Antony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oliver(a)sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512

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Setting up MR_Rosetta
by Julio Lenin 08 Nov '12

08 Nov '12

Hello guys, I am currently trying to setup MR_Rosetta but I am running into some trouble. When I run the tutorial for Defensin HNP-3 from the GUI I always get an error during the ... process (see image at this dropbox link). I know that my path for phenix and rosetta are correct since I can run the phenix_regression.wizards.test_command_line_rosetta_quick and phenix_regression.wizards.test_command_line_rosetta_quick test_rosetta_rebuild. If I try to trace down the error, I can only get the same info that I got from the GUI error message (vide supra). As additional info, here are somme details of my setup: MacBookPro 4,1 running OS 10.6.8 Core2Duo 2.5 Ghz 6 Gb RAM Rosetta 3.2 compiled with flags bin mode=release Phenix 1.8.1-1168 And my input settings for the GUI run (dropbox) Now, this might just be confusing but there was one command line test that my setup failed: phenix_regression.wizards.test_command_line_rosetta test_mr_rosetta The error is kinda cryptic (see dropbox copy of the error) but it seem to be a discrepancy in the scoring results not a missing program or any other kind of misconfiguration. Of course, I might be wrong. Any advice? Best regards. -- Lenin Domínguez-Ramírez "And for all the current and rather silly emphasis on structural biology,understanding enzymes means understanding catalysis and catalysis is concerned with kinetics, not structure: as Jeremy Knowles aptly remarked, studying the photograph of a racehorse cannot tell you how fast it can run." Cornish-Bowden, 1995 Lenin Domínguez-Ramírez, PhD "What are we to think of an organism that loses practically all of its cellular water at ordinary temperatures and pressures and ceases to metabolize, but upon being rehydrated resumes all of the characteristics it previously exhibited?...we should be reluctant to call such an organism dead (unless we are willing to entertain the possibility of its resurrection) because it resumes an active life upon simple restoration of water."

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