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Phaser output and error messages
by Ian Stokes-Rees 17 Nov '09

17 Nov '09

I'm having some discussion with a colleague about phaser output (we're using Phaser 2.1.4). We haven't been able to find any documentation which can clarify our situation, and I'm hoping someone on the list can help answer these questions. I should mention that I am relatively new to Phaser. 1. PHASER.sol files: Which "SOLU SET" does Phaser consider to be the best? The first or the last? Or the one with the highest LLG, wherever that may be? In our experience of running Phaser over several MTZ files with a range of models the best Phaser solution has always been the first, and this has had the highest LLG. Note: this is with "untuned" Phaser settings for identity, solvent fraction, or number of search models in ASU -- our goal is to do a first run with "generic" settings for these over a larger set of models, then (from TFZ and LLG scores) select a subset for which we will tune Phaser parameters and PDB search model variations. 2. If we are right that the first "SOLU SET" entry is indicative of the potential for the search model to form a good MR candidate, then is it the case that the first entry is the first Phaser solution that is computed? Or is the PHASER.sol file a sorted list output at the end of the run? From my reading of the documentation it is output in order of computation, and *for our purposes* (if my first statement in this question is correct) Phaser can stop after it outputs this first solution. Is there some way to tell Phaser to stop after the first solution is output? I realize that this doesn't sound like it makes sense (how could Phaser know to pick the best solution first, and even if it could, why would it ever continue past this point), however I ask because we have put a 10 minute timeout into our Phaser runs and we have many situations where we get a timeout but PHASER.sol has already been generated and the best LLG solutions are output first. It leaves me wondering why it didn't just stop on its own after outputting the first result instead of being aborted by our (external) timeout that terminates the process? 3. PHASER.sol files: For single domain search models, we usually get output of the form: SOLU SET RFZ=4.5 TFZ=5.2 PAK=0 LLG=14 LLG=14 SOLU 6DIM ENSE model1 EULER 242.049 45.040 326.088 FRAC -0.09425 0.50268 0.42575 however we see three variations: i) No LLG: SOLU SET RFZ=3.1 TFZ=5.0 PAK=0 SOLU 6DIM ENSE model2 EULER 59.983 69.335 319.701 FRAC -1.17131 -0.70030 0.23150 ii) One LLG: SOLU SET RFZ=3.7 TFZ=4.6 PAK=0 LLG=25 SOLU 6DIM ENSE model3 EULER 293.943 128.068 332.147 FRAC 0.06273 0.13175 0.25054 iii) Two LLG entries, but with different values: SOLU SET RFZ=3.8 TFZ=4.1 PAK=0 LLG=21 LLG=20 SOLU 6DIM ENSE model4 EULER 278.058 129.347 33.292 FRAC 0.28446 0.29011 -0.07986 4. Occasionally we get an error that we don't understand: FATAL RUNTIME ERROR: No scattering in pdbfile model1.pdb What does this mean? Is there a problem with the PDB file? We can't see anything obvious in the ones which produce this error. Thanks, Ian -- Ian Stokes-Rees, Research Associate SBGrid, Harvard Medical School http://sbgrid.org

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Request: read definitions from stdin
by Joe Krahn 15 Nov '09

15 Nov '09

I want to be able to run PHENIX in a shell script, where stdin is accepted as a definition input file. It could be simply specified as the usual POSIX syntax where "-" defines stdin in place of an input file. If the front-end is based too heavily on file suffix mappings, you could add a flag "--stdin=SUFFIX" to define reading stdin as if it had the given SUFFIX. It would also be nice to avoid the duplication of output to both stdout and the .log file. Output can always be sent to /dev/null, but it would be nicer to have either a --quiet flag to suppress stdout, or a DEF option to disable the .log output, or both options to let the user decide. Most other computational programs can be run this way, so I assume that other people would find this useful, especially for running PHENIX from scripts. Hopefully, it is also a fairly easy feature to implement. Thanks, Joe Krahn

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R-free rules
by Bryan W. Lepore 13 Nov '09

13 Nov '09

[ phenix.refine v1.5 rel. tag 2 intel linux 2.6 ] if i provide the test set .mtz (flag = "1") in refinement separately from the data .mtz, it looks like reflection_file_converter.py does not flag the work set as "0", if the work set lacks such a flag -- is that right? i.e. when providing the test set, it looks like all observed data must be in the test set, however the work set has flag "0". -bryan (some error output below) Sorry: R-free flags not compatible with F-obs array: missing flag for 22206 F-obs selected for refinement:

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November 15, 2009 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 12 Nov '09

12 Nov '09

Dear Users, The deadline for October/November/December 2009 Collaborative Crystallography proposals will be *November 15, 2009. * ------------------------------------------------------------------------ Through the Collaborative Crystallography Program (CC) at the Advanced Light Source (ALS), scientists can send protein crystals to Berkeley Center for Structural Biology (BCSB) staff researchers for data collection and analysis. The CC Program can provide a number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; and * Reduced travel costs. To apply, please submit a proposal through the ALS General User proposal review process for beamtime allocation. Proposals are reviewed and ranked by the Proposal Study Panel, and beamtime is allocated accordingly. BCSB staff schedule the CC projects on Beamlines 5.0.1 and 5.0.2 to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography ----------------------------------------------------------------------------------------- How To Apply: To learn more, go to: http://www-als.lbl.gov/als/quickguide/independinvest.html To submit a proposal, go to: http://alsusweb.lbl.gov/. Scroll down to "*Structural Biology beamlines (includes protein SAXS)*" and click on "New Proposal." Enter your proposal information, with attention to the following details: * For question 3/First choice, select "5.0.1 (Monochromatic);" for question 3/Second choice, select "5.0.2 (MAD)." * Check box (yes) in response to question "Do you want collaborative crystallography (beamline 5.0.1 or 5.0.2 only) * In question 9, please describe a specific research project with a clear end point. In order to request CC time for October/November/December 2009 allocation period, proposals must be submitted by *November 15, 2009.* The deadline for CC proposals for the time period March/April 2010 will be January 15, 2010. Regards, Banumathi Sankaran

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sulfate on a 2 fold axis
by David Cobessi 12 Nov '09

12 Nov '09

Hi, I am finishing to refine a structure using Phenix. A sulfate ion is located on a 2 fold axis. When I refine the structure with Refmac, the geometry of the ion is well conserved, while when I use Phenix the geometry is destroyed and the sulfate ion is like a cross!! Any idea to keep the good geometry of this ion in Phenix during the refinement? Thanks in advance, David -- David Cobessi Institut de Biologie Structurale 41, Rue Jules Horowitz 38027 Grenoble Cedex-1, France Tel:33(0)438789613 33(0)608164340 Fax:33(0)438785122

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phenix.cif_as_mtz
by Bryan W. Lepore 12 Nov '09

12 Nov '09

[ v. 1.5 release tag 2 intex-linux-2.6 redhat-e4.8 ] `phenix.cif_as_mtz file.cif --symmetry=FILE.pdb --show-log --show-details-if-error` .. reports "No data extracted from input cif file.", nothing else. command works w/ other .cif/.pdb's, CRYST1 lines, etc. look comparable between them,... not sure where to look next. thanks for any suggestsions. -bryan

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Nino Campobasso is out of the office.
by Nino.2.Campobasso＠gsk.com 11 Nov '09

11 Nov '09

I will be out of the office starting 11-Nov-2009 and will not return until 12-Nov-2009.

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Failed to make map after phenix.refine
by Zhou, Tongqing (NIH/VRC) [E] 11 Nov '09

11 Nov '09

Hi, All I am having problem with the new 1.5.2. After few rounds of refinement, the program failed to write out maps. It ended with: "Sorry: Duplicate mtz_label_amplitudes:FOFCWT" Here is the portion in my param file which worked fine before: electron_density_maps { map_format = *xplor map_coefficients_format = mtz *phs suppress = None map { mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" likelihood_weighted = True obs_factor = 2 calc_factor = 1 } map { mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" likelihood_weighted = True obs_factor = 1 calc_factor = 1 } } Thanks in advance for your help. Tongqing

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C-ter amidation of peptide
by Nate Nicely 10 Nov '09

10 Nov '09

Dear all, How best to handle a C-terminally amidated peptide in phenix? I defined the atom as 'N' and the resname as 'NH2' following a structure I found that also bears a C-terminally amidated peptide. However phenix.refine seems not to be making the linkage between the amide and the preceding residue. Putting the structure into phenix.elbow returns, "No unknown residues." Thanks, Nate N.

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Glycan refinement
by Zhou, Tongqing (NIH/VRC) [E] 10 Nov '09

10 Nov '09

Dear All, I am refining a structure with a N-linked glycosylation site. There is density that goes beyond the first NAG, at least to MAN3. I know in Phenix there is data_link = NAG-ASN for the ASN-NAG connection, but I don't know how to do the "apply_cif_link' for the extensions such NAG-NAG, NAG-MAN, MAN-MAN...., any suggestions are appreciated. Thanks, Tongqing Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4607B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 594-8710 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ****************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ******************************************************************

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