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Age Concern edition of the Computing Commission and Teaching Commission newsletter
by Ralf W. Grosse-Kunstleve 24 Nov '09

24 Nov '09

Posted on behalf of Lachlan Cranswick: The Computing Commission and Teaching Commission has produced a joint November 2009 newsletter on the theme of "Age Concern", which deals with issue concerning "the slow march towards retirement of the major generation of crystallographic programmers", as further explained by David Watkin within the newsletter. http://www.iucr.org/resources/commissions/crystallographic-computing/newsle… or via http://www.iucr.org/resources/commissions/crystallographic-teaching/newslet… --------------------------- This issue's articles include : - the latest background and information from the UK based EPSRC funded Age Concern Project. - history and science within the Caltech based CRYRM single crystal suite; DIMS - Direct methods In Multidimensional Space software; Crunch 1.5 Direct Methods Software; the Glasgow based GX single crystal suite; the Italian based CAOS structure refinement software; Ton Spek's Platon; and a list of programs archived at Armel Le Bail's Crystallography Source Code Museum. - experience in conversion of large crystallographic Fortran-77 to C++; as well as the place of the Quick and Dirty Crystallographic Computer Program - Historical group photographs from some of the Crystallographic Computing and Teaching School of the 1970's. - Archived manuals and source code from the above mentioned software. - Teaching material of Isabella L. Karle, as she presented at the 1978 Erice School on Direct Methods for Solving Crystal Structures - A reprint of the The Analytical Theory of Point Systems (1923) by J. D. Bernal (1901-1971) Further Computing Commission newsletters are intended on theme of Age Concern : capturing the history and the crystallographic science behind past and present Small Molecule, Powder Diffraction, Protein and other crystallographic software. Submissions on this topic are welcome and encouraged. - Lachlan Cranswick ( lachlan.cranswick(a)nrc.gc.ca )

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Confused by the output from Phenix autobuild jobs
by Serah Wangari 24 Nov '09

24 Nov '09

Dear Phenix users, I have run a number of Autobuild jobs using the Phenix GUI and in all cases, I'm not sure what output I should proceed with to the next step. - The first job was for rebuilding a loop section in the model (rebuild-in-place) - As far as I can remember, there was no mtz generated from this job, I had to generate map coefficients with the overall_best pdb and an old mtz using another refinement program. Did I miss something during the job input step, so that no mtz was generated, or how would I proceed in such a case? - The next job involved rebuilding the whole model (rebuild-in-place) - in this case, I took the overall_best pdb, but when I tried to open the overall_best_refine_map_coeffs.mtz in coot, I got this error that coot failed to find F/Phi columns in the mtz file. Then I checked in the TEMPO directory, and I managed to open a random mtz from one of the refinement cycles with coot, but I wasn't confident building into that, so again I had to generate map coefficients using overall_best pdb and an old mtz in another program. - The other job was rebuilding (rebuild-in-place) another model with composite maps generation - Here, in addition to the 12 mtz and pdb files from the 12 omit regions, I got resolve_composite_map.mtz I should assume as the only final output; and no final pdb. Again, this mtz file doesn't have the F/Phi columns as I got the same error as above in coot. I'm not sure how to proceed with this mtz...... I would really appreciate if someone could point me to the right direction or at least direct me to some literature where the output from Phenix autobuild jobs is explained - as I haven't come across such info yet. Thank you in advance, Serah --

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Clean Jobs
by tea.pavkov＠uni-graz.at 24 Nov '09

24 Nov '09

Dear all, I would have a general question - how can I clean the Jobs (in the Job history list and all corresponding directories) in the new GUI? Thank you in advance! Best regards, Tea ----------------------- Dr. Tea Pavkov-Keller KF Uni Graz, ZMB Structural Biology Group Humboldtstr. 50/III 8010 Graz Austria

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Problem installing on Leopard PowerPC G5
by Satpal Virdee 23 Nov '09

23 Nov '09

Hi, I am trying to install the latest 1.5-2 official release on an iMac PowerPC G5 running OSX 10.5.8. During installation I get the error: " Relocating Python framework. . . /usr/bin/install_name_tool: object: libwx_mac-2.8.0.5.0.dylib malformed object (unknown load command 20) Error: see /Users/Sat/Downloads/phenix-installer-1.5-2/build-binary/ mac-ppc-osx/cpemac406-18/log/binary.log for details " Inspection of the binary.log files reveals this: " libfreetype.6.3.10.dylib: /usr/local/phenix-1.5-2/build/mac-ppc-osx/ base/lib/libfreetype.6.3.10.dylib --> /usr/local/phenix-1.5-2/build/mac-ppc-osx/base/lib/libfreetype. 6.3.10.dylib libfreetype.6.dylib libfreetype.6.dylib: /usr/local/phenix-1.5-2/build/mac-ppc-osx/base/ lib/libfreetype.6.dylib --> /usr/local/phenix-1.5-2/build/mac-ppc-osx/base/lib/libfreetype. 6.dylib libfreetype.dylib libfreetype.dylib: /usr/local/phenix-1.5-2/build/mac-ppc-osx/base/lib/ libfreetype.dylib --> /usr/local/phenix-1.5-2/build/mac-ppc-osx/base/lib/libfreetype.dylib libwx_mac-2.8.0.5.0.dylib fix_mac_python: caught error - exiting. " Any help would be most appreciated. Regards, Satpal

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baton build in coot
by Raja Dey 22 Nov '09

22 Nov '09

Dear Friends, How does CA ZONE > MAIN CHAIN under 'other modeling tools' in coot work? I was trying to rebuild main chain atoms for 3 residues(8,9,10) using CA ZONE > MAIN CHAIN. when I click on one atom in residue 8 and then one atom in residue 10, it failed with a message that says the zone is too short. I increased the zone to 5 residues, still same failed message. Also, is it possible to move an atom in coot? Thanking you in advance for your reply. Raja

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phasing power value in Autosol/Autobuild
by vennila Natesan 19 Nov '09

19 Nov '09

Dear all... I need toknow the phasing power value for my solved structure. Where can i find it out in the output files of autosol and autobuild? I am using phenix1.14.4b and also i need to know the weighted mean phase errors vs resolution. Thanking you.

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I vs F data input
by gerwald jogl 18 Nov '09

18 Nov '09

Hi All, A quick question about diffraction data input. I just noticed that phenix.refine uses Imean/SIGImean and converts these by default in my refinements. Is this the preferred way or would it be better to use F/SIGF (after CCP4)? Thanks, Gerwald

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external ncs reference structures?
by Cathy Lawson 18 Nov '09

18 Nov '09

Dear Phenix developers, We are finishing up refinement of some multiprotein-DNA complex structures at 3-3.5 A resolution and I am wondering if it would be possible with phenix.refine to supply one or more external sets of coordinates from higher-resolution determinations to serve as the ncs references. If so what would be the best way to set this up? thanks, Cathy ********************************** Catherine Lawson, Ph.D. Rutgers University Chemistry & Chemical Biology 610 Taylor Rd Piscataway, NJ 08854 732 445 5494 cathy.lawson(a)rutgers.edu http://roma.rutgers.edu **********************************

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Mac OSX Phenix GUI
by Miguel Ortiz Lombardia 18 Nov '09

18 Nov '09

Hi, This is a question/request to the phenix developers. Are there any plans to make the new phenix GUI to use an X11 python interface instead of the Aqua one? The reason I ask is that we use Mac OSX servers for calculations here and an X11 interface would be a lot more appropriate for this configuration. That way users could export the GUI to their local workstations. As it is implemented now this use of the GUI is impossible on Mac OSX. Before someone makes the suggestion: Remote Desktop simply allows to share the only Aqua desktop that the server can produce, that is, only one user can access the Aqua desktop, whether remotely or locally. We would be happy to test any X11 version you might be willing to develop. Thanks for your great software, which we can use anyway from the command line :-) Best regards, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombardia(a)afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2

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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 16 Nov '09

16 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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Problem reading ".edits" parameter file
by John Pascal 06 Nov '09

06 Nov '09

Hello, On a previous version of PHENIX, 1.4-153, I was able to read in a parameter file with geometry constraints. Upon loading the file, the program asked when to execute the commands, I said at run time, and everything worked fine. Using the same parameter file in PHENIX 1.5-2, I am no longer asked about when to execute the file, and when I proceed to run the refinement, the program quits stating an unexpected character. I can't find anything obviously wrong with the parameter file. Any suggestions? The previous version of PHENIX (the one that worked) is no longer located on my server, so I can't easily return to that version. Thanks. Best Regards, John -- John Pascal, PhD ph 215.503.4596 Assistant Professor fx 215.923.2117 Thomas Jefferson University Biochemistry & Molecular Biology 233 South 10th Street, BLSB 804 Philadelphia, Pennsylvania 19107 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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Phaser question : RMS deviation and FOM
by Peter Grey 06 Nov '09

06 Nov '09

Dear Phenix developers, The expected RMS deviation input to Phaser affects the FOM estimation of phases quality. This in-turn affects the sigmaa weighted maps and most importantly the density modification steps that follow phaser. I would like to ask if, based on the phaser solution and the LLG parameter, one could optimize the RMS estimation or know the real RMS deviation that would result in more true FOM. Thanks, Peter With condolences to the family of Warren DeLano who will be sorely missed

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Analyzing MIR datasets
by Rajagopalan, Senapathy 06 Nov '09

06 Nov '09

Hi All, I am a new user to Phenix and am trying to process MIR datasets from a parameter file typing 'phenix.autosol mir.eff' and keep running into the error message saying: _______________ Possible choices: /Users/sena/data/crystallography/raw1025/Processing/iafinal_d212121.mtz:I,SIGI,merged /Users/sena/data/crystallography/raw1025/Processing/iafinal_d212121.mtz:IPR,SIGIPR,merged Please use scaling.input.xray_data.obs_labels to specify an unambiguous substring of the target label. Unable to get range of aniso B from xtriage output Multiple equally suitable arrays of observed xray data found. ******************************************************************************** Failed to carry out AutoSol_scale_and_analyze_mir: Sorry, there is something wrong with the file /Users/sena/data/crystallography/raw1025/Processing/iafinal_d212121.mtz ... xtriage cannot analyze it? ******************************************************************************** ___________________ The 'mir.eff' file contains: ------------------ # autosol { seq_file = sequence.dat #scaling.input.xray_data.obs_labels='I SIGI' # xray_data_labels = FP, SIGFP # autosol.input.xray_data.labels=FP labels='I SIGI' crystal_info { space_group = p212121 unit_cell = 49.020 73.140 187.350 90.000 90.000 90.00 } native { data = iafinal_d212121.mtz } deriv { data = s10final_d212121.mtz atom_type = I sites = 2 inano = noinano *inano anoonly } deriv { data = s13final_d212121.mtz atom_type = I sites = 1 inano = noinano *inano anoonly } deriv { data = s23final_d212121.mtz atom_type = I sites = 1 inano = noinano *inano anoonly } } ----------------- I guess the error comes because the program is not able to make a choice as to which columns to take from the mtz file. But no matter what 'label' syntax I use or where I use it, it doesn't seem to help. Obviously, I am missing something here. So could someone please help me with this. Also, I tried the same thing using the phenix wizard and it still gives me the same error. Thanks Sena Methodist. Leading Medicine. Recognized by U.S.News & World Report as an "Honor Roll" hospital Ranked No. 8 on FORTUNE magazine's list of the "100 Best Companies to Work For" in 2009 Designated as a Magnet hospital for excellence in nursing Visit us at methodisthealth.com Follow us at twitter.com/MethodistHosp ***CONFIDENTIALITY NOTICE*** This e-mail is the property of The Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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molecular replacement - restricting rotation around a specified orientation
by Christine Gee 06 Nov '09

06 Nov '09

Dear Phenix developers, We have a protein with two sub domains (N-lobe and C-lobe) we are trying to solve by MR. The C-terminal sub domain solves fine (TFZ 11.1), but the N-terminal lobe is not being placed correctly. I read in the online documentation that you can specify a limited rotation range around the orientation you would expect for the N-lobe based on the C-lobe orientation. My question is, how do specify what orientation to start with? I know I need some Euler numbers, but are they just the same ones that the C-lobe writes out with and I use an N- lobe that is basically the other half of the C-lobe pdb (ie the X,Y,Z co-ordinates are consistent with each other at the beginning of the search)? Or do I need to position the N-lobe with the solution C-lobe and write it out for use in the search model, and then how do I specify the Euler? Also we were going to try and use normal mode perturbation to generate an ensemble and I was wondering if there is more documentation somewhere on how to do that? Regards Christine

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about Turbo Frodo
by Zhongli Cui 06 Nov '09

06 Nov '09

Dear all, I have ever used Turbo Frodo as the modelling software in protein crystallography. It is a very convinient software to learn. But it seems that the lience email of turbo is out of work. Does anyone know if Turbo is still maintained by AFMB and the new email for lience? Thanks Zhongli ---------------- Cui Zhongli Professor, Ph.D Dept. of Microbiology College of Life Sciences Nanjing Agricultural University 1 Weigang, Nanjing, 210095 Jiangsu Province P.R. China. Mail: czl(a)njau.edu.cn Tel: 86-25-84396753 Mob: (0)13951080529

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Running Phenix 1.5.2 with Martin Horvath
by Raghav Kalia 04 Nov '09

04 Nov '09

I recently downloaded and installed phenix 1.5-2. I can launch the GUI by double clicking on the phenix icon. However, I cannot get to run phenix.refine on the command line. How does one set paths so that phenix.refine will be recognized in a terminal window? Raghav Kalia

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Re: [phenixbb] phenixbb Digest, Vol 48, Issue 4
by Leo Sazanov 04 Nov '09

04 Nov '09

Thanks, restore results works fine for what I need now. phenixbb-request(a)phenix-online.org wrote: > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > Today's Topics: > > 1. Re: re-run jobs in GUI (Nathaniel Echols) > 2. Elbow ligand building (Joe Krahn) > 3. Re: Elbow ligand building (Nigel W Moriarty) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 4 Nov 2009 08:34:24 -0800 > From: Nathaniel Echols <NEchols(a)lbl.gov> > Subject: Re: [phenixbb] re-run jobs in GUI > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Message-ID: <529970F2-E319-4152-B4F1-E46184755554(a)lbl.gov> > Content-Type: text/plain; charset=us-ascii; format=flowed; delsp=yes > > On Nov 4, 2009, at 8:08 AM, Leo Sazanov wrote: > >> Hi, in a new GUI how can one re-run previous jobs (to make some >> modifications to them)? >> > > Open the main GUI (the command 'phenix', or click the home button on > the toolbar of any other program), click the "job history" toolbar > button, select a job from the list, and click "restore results". This > should restore both the results tab or window, and the configuration. > There is also a "restore last job [for the current project]" button on > the toolbar. Any inconsistencies here are definitely a bug, but it > was working for most programs in 1.5-2. (The main exception is the > reflection file editor, but that will also save/restore results in the > next available nightly build.) > > >> If I just try to open parameter (.eff) file from the main file menu in >> Autobuild, the file does not show up, even though it exists. >> Just adding it to the list of input files works, but the information >> is >> not passed on into GUI? >> > > > It's a little complicated right now. If you want to apply the > contents of a parameter file, this is best done at startup - e.g. drag > and drop the file onto the launch icon, or use it as a command line > argument ('phenix.autobuild params.eff'). For phenix.refine, you can > also save default parameters (Preferences->Refinement, or project > settings, or from the utilities menu) and it will start with them pre- > loaded. Once the program window is drawn, however, it's clumsier - > files *should* be passed down to the command-line module (if not, also > a bug), but they won't immediately be applied to the GUI, because of > the way it tracks parameters internally. > > I can't promise that every pre-existing configuration file will be > processed cleanly by the GUI - it's difficult to anticipate what users > will try to do. If you encounter cases where the parameters are > misinterpreted, let me know. > > -------------------- > Nathaniel Echols > Lawrence Berkeley Lab > 510-486-5136 > NEchols(a)lbl.gov > > > > > > > > ------------------------------ > > Message: 2 > Date: Wed, 04 Nov 2009 12:35:01 -0500 > From: Joe Krahn <krahn(a)niehs.nih.gov> > Subject: [phenixbb] Elbow ligand building > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Message-ID: <4AF1BB45.20707(a)niehs.nih.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > I am having some problems building ligand parameters with elbow. > > I have an accurate reference structure, but elbow seems to "regularize" > the coordinates in a way the distorts the structure. Is there a way to > disable this? > > With --opt, QM optimization should hopefully remove distortions, but it > is not doing a very good job for this molecule. So, I decided to > optimize using Gaussian, and a better basis set. > > It seems that the Gaussian interface is still fairly simple, and it > seems that you have to edit the Gaussian.csh template. So, I did that, > but got the "Gaussian does not seem to be installed" message. > Unfortunately, elbow runs the Gaussian script with output to /dev/null, > so there is no way to see any error messages. Maybe that should be done > only when the --quiet flag is given. > > I edited the Python source to let errors go to the tty, and found that > the problem is in the way the script is invoked using "csh -c %s.csh". > That only works if "." is in your $PATH, which is often the case. It > also invokes an extra instance of csh, because it is invoked as a system > command. The correct way to run a shell script is to leave out the '-c'. > Elbow makes the script executable, so an even better approach is to just > leave out "csh", and do "os.system('./%s.csh' % project)". Then, the > script can be in sh/bash/etc. Maybe the was the intent of using '-c'? > > Thanks, > Joe Krahn > > > ------------------------------ > > Message: 3 > Date: Wed, 04 Nov 2009 10:09:47 -0800 > From: Nigel W Moriarty <NWMoriarty(a)lbl.gov> > Subject: Re: [phenixbb] Elbow ligand building > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Message-ID: <4AF1C36B.3010500(a)lbl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Joe > > On 11/4/09 9:35 AM, Joe Krahn wrote: > >> I have an accurate reference structure, but elbow seems to "regularize" >> the coordinates in a way the distorts the structure. Is there a way to >> disable this? >> >> > eLBOW will always run a simple optimisation unless you specify the final > geometry you like using > > phenix.elbow --final-geometry accurate.pdb > > Naturally, you are smart to use a better input format thus > > phenix.elbow filename.sdf --final-geometry accurate.pdb > >> With --opt, QM optimization should hopefully remove distortions, but it >> is not doing a very good job for this molecule. So, I decided to >> optimize using Gaussian, and a better basis set. >> >> > Good thinking. > >> It seems that the Gaussian interface is still fairly simple, and it >> seems that you have to edit the Gaussian.csh template. So, I did that, >> but got the "Gaussian does not seem to be installed" message. >> Unfortunately, elbow runs the Gaussian script with output to /dev/null, >> so there is no way to see any error messages. Maybe that should be done >> only when the --quiet flag is given. >> >> > Maybe I'll implement this with a --verbose flag. > >> I edited the Python source to let errors go to the tty, and found that >> the problem is in the way the script is invoked using "csh -c %s.csh". >> That only works if "." is in your $PATH, which is often the case. It >> also invokes an extra instance of csh, because it is invoked as a system >> command. The correct way to run a shell script is to leave out the '-c'. >> Elbow makes the script executable, so an even better approach is to just >> leave out "csh", and do "os.system('./%s.csh' % project)". Then, the >> script can be in sh/bash/etc. Maybe the was the intent of using '-c'? >> > This is old code from before PHENIX had a smart module for running > commands. I'll update to code. > > Nigel > > -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915

1 0

Elbow ligand building
by Joe Krahn 04 Nov '09

04 Nov '09

I am having some problems building ligand parameters with elbow. I have an accurate reference structure, but elbow seems to "regularize" the coordinates in a way the distorts the structure. Is there a way to disable this? With --opt, QM optimization should hopefully remove distortions, but it is not doing a very good job for this molecule. So, I decided to optimize using Gaussian, and a better basis set. It seems that the Gaussian interface is still fairly simple, and it seems that you have to edit the Gaussian.csh template. So, I did that, but got the "Gaussian does not seem to be installed" message. Unfortunately, elbow runs the Gaussian script with output to /dev/null, so there is no way to see any error messages. Maybe that should be done only when the --quiet flag is given. I edited the Python source to let errors go to the tty, and found that the problem is in the way the script is invoked using "csh -c %s.csh". That only works if "." is in your $PATH, which is often the case. It also invokes an extra instance of csh, because it is invoked as a system command. The correct way to run a shell script is to leave out the '-c'. Elbow makes the script executable, so an even better approach is to just leave out "csh", and do "os.system('./%s.csh' % project)". Then, the script can be in sh/bash/etc. Maybe the was the intent of using '-c'? Thanks, Joe Krahn

2 1

re-run jobs in GUI
by Leo Sazanov 04 Nov '09

04 Nov '09

Hi, in a new GUI how can one re-run previous jobs (to make some modifications to them)? If I just try to open parameter (.eff) file from the main file menu in Autobuild, the file does not show up, even though it exists. Just adding it to the list of input files works, but the information is not passed on into GUI? -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915

2 1

low resolution, high B, low R
by gerwald jogl 03 Nov '09

03 Nov '09

Hi All, I am working on a 4.2 A structure and feel somewhat uneasy about my refinement results. First, my R/Rfree at the moment is 0.18/0.25. The refinement is not complete and weights are not optimized, so the gap may get smaller. It's just that at 4.2 A, I don't quite expect such low R factors... There is nothing funny with the data, no messing around, no conversions - straightforward data set and a basic rigid body, individual_sites+group_adps, simulated annealing, no tls yet, no ncs. I am aware that one possible answer is that phenix is just really good... The other issue is about B factors. Phenix will happily refine B factors to values of 300 if there is no density in the region and that brings up the question about how to deal with disordered regions in general. Are there any current opinions out there about what would constitute 'reasonable' B factors? Conversely, when would a B factor indicate that it is better to remove the residue from the model instead of leaving it and calling it disordered. Also, this is after group_adp at 4.2 A - should I maybe take this as an indication that this is asking too much from the data and go back to a single adp per chain and tls? All comments are appreciated. Thanks! Gerwald

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Re: [phenixbb] phenixbb Digest, Vol 48, Issue 2
by Xuewu Zhang 03 Nov '09

03 Nov '09

You are right. It started in the 2nd macro cycle. I should have been a little more patient. Sorry about it. Thanks, Xuewu On Tue, Nov 3, 2009 at 2:00 PM, <phenixbb-request(a)phenix-online.org> wrote: > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > Today's Topics: > > 1. Re: optimization of wxc and wxu (Xuewu Zhang) > 2. Re: optimization of wxc and wxu (Pavel Afonine) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 3 Nov 2009 08:28:58 -0600 > From: Xuewu Zhang <xuewu.zhang(a)gmail.com> > Subject: Re: [phenixbb] optimization of wxc and wxu > To: phenixbb(a)phenix-online.org > Message-ID: > <926abad50911030628h31d09c53m59c2c84f1d024596(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi phenix developers/gurus, > > I am using the latest night build of phenix on OS X snow leopard. I found > that phenix ignores these lines in my custom refinement file: > > refinement.target_weights.optimize_wxc="True" > refinement.target_weights.optimize_wxu="True" > > Manually setting up the scale factors however works. I am not sure whether > this is a bug or a platform related issue. > > Thanks, > Xuewu Zhang >

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Re: [phenixbb] optimization of wxc and wxu
by Xuewu Zhang 03 Nov '09

03 Nov '09

Hi phenix developers/gurus, I am using the latest night build of phenix on OS X snow leopard. I found that phenix ignores these lines in my custom refinement file: refinement.target_weights.optimize_wxc="True" refinement.target_weights.optimize_wxu="True" Manually setting up the scale factors however works. I am not sure whether this is a bug or a platform related issue. Thanks, Xuewu Zhang

2 1

GUI and X servers
by Leo Sazanov 02 Nov '09

02 Nov '09

Hi, I am accessing our linux server (where phenix sits) via Exceed X server from Windows machine, and everything used to work fine until recent (I think from v.1-5-2) versions of phenix. Now if I launch new GUI, mouse position is not recognised anymore not only by phenix, but then also by other programs - so if I click on something, something else completely gets activated. I did not change any Exceed settings, so the problem seems to be due to phenix. Also, same thing happens with Xming server. If I access from Mac machine, everything seems to be OK. Has anybody seen it and what could be the reason for that? Thanks! -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915

3 3

Error message when starting phenix gui
by Folmer Fredslund 30 Oct '09

30 Oct '09

Dear all Should I be concerned about this error message when starting phenix 1.5-2?: Gtk-Message: Failed to load module "canberra-gtk-module": libcanberra-gtk-module.so: cannot open shared object file: No such file or directory Best regards, Folmer Fredslund

3 4

Converting .mtz to xplor or having phenix output to xplor file
by Sam Stampfer 28 Oct '09

28 Oct '09

Hi, This isn't exactly phenix-related but someone might know an easy solution. I'm trying to open an electron density map in pymol. It won't open .mtz files and the .xplor files I generated from ccp4i don't seem to work either. I need to have my density as a .xplor file in order for pymol to open it (I think). How would I generate a .xplor file from .mtz? Or, alternately, how can I set phenix to output a .xplor file? I've had it output to a cns file instead of .mtz but that didn't help me get it in .xplor format. Thanks! -Sam

5 6

external program interference : libwx_gtk2ud-2.8.so.0 not found on ubuntu 64 bit
by hari jayaram 27 Oct '09

27 Oct '09

I just downloaded and installed phenix 1.5.2 . I want to run phenix with the GUI on my 64 ubuntu 8.04 box When I run phenix I get the following error: hari@charlie:~$ phenix Traceback (most recent call last): File "/usr/local/phenix-1.5-2/phenix/wxGUI2/command_line/main.py", line 13, in <module> run(sys.argv[1:]) File "/usr/local/phenix-1.5-2/phenix/wxGUI2/command_line/main.py", line 7, in run from wxGUI2 import App File "/usr/local/phenix-1.5-2/phenix/wxGUI2/__init__.py", line 109, in <module> import wx File "/rawdata12/wx-widgets-read-only/wxPython/wx/__init__.py", line 45, in <module> from wx._core import * File "/rawdata12/wx-widgets-read-only/wxPython/wx/_core.py", line 4, in <module> import _core_ ImportError: libwx_gtk2ud-2.8.so.0: cannot open shared object file: No such file or directory I know that I should not be getting this error because I have wxwidgets and wxpython installed and I have wx working on this machine for other apps. Consequently I do have a libwx_gtk2ud-2.8.so.0 on my LD_LIBRARY_PATH. I tried with and without a libwx_gtk2ud-2.8.so.0 in my LD_LIBRARY_PATH and I still got the same error. Any ideas why phenix GUI does not start? Thanks Hari hari@charlie:~$ which phenix /usr/local/phenix-1.5-2/build/intel-linux-2.6-x86_64/bin/phenix hari@charlie:~$ echo $LD_LIBRARY_PATH /home/hari/ccp4-6.0.99e/lib::/home/hari/ccp4-6.0.99e/extralib

2 3

Command to call/read external file when running phenix.refine from
by Ashley Pike 23 Oct '09

23 Oct '09

Hi, I am running phenix.refine(v.1.5.2) from the command line using a batch file containing all my customised options ie. phenix.refine my_parameters. From this batch file (my_parameters) I also want to include additional geometric and NCS restraints. Rather than have them clutter things up, I want to call/invoke them from an external file instead. I had been told that this is possible using the command 'include file <filename>' but it seems that this is not doing what I had hoped. When run in this way phenix.refine doesn't complain but is not using the restraints. Needless to say everything is fine when I actually include the information directly in the batch file. Any hints what I am doing wrong? Cheers, Ashley

5 6

1.5.2 and validation
by Mark Collins 23 Oct '09

23 Oct '09

Hi I just installed 1.5.2 and tried it out for a few hours this afternoon. Is it possible to run the phenix programs from the command line without being forced to launch the shiney new gui? I have 3 structures I had considered finished by R/Rfree and Molprobity. I was playing around with polygons (great way to quickly assess the structure) and found that 2 of the 3 strucutres are "bad" with very low RMSDs for bonds, angles, chirality, dihedrals and planarity. All were refined with phenix 1.3, but they are all fairly small ~80-90 residues. So do I need to go back and revisit these, advice much appreciated? Also I found that I can edit the validate_0.eff (from phenix/project_data/ ) and run the file from the command line. But is there a way to actually change keys_to_show and fiters for polygon in the gui? Also it seems that the *twinned crashed the validation when run this way (bug reported). Thanks Mark

2 1

The new GUI is really nice!
by Laurie Betts 23 Oct '09

23 Oct '09

I think I initially sent this to the wrong address, sorry. Just wanted to say: I just downloaded the new version of PHENIX (1.5-2) on my Mac; I had a lot of trouble with previous versions using the GUI (but really like the command line driven flexibility), but now playing around with the new one, I think I will become hooked. Thank you all VERY much from all of us phenix-o-philes. Laurie Betts

1 0

new GUI is really nice
by Laurie Betts 23 Oct '09

23 Oct '09

I just downloaded the new version of PHENIX (1.5-2) on my Mac; I had a lot of trouble previously using the GUI (but really like the command line driven flexibility), but now playing around with the new one, I think I will become hooked. Thank you all VERY much from all of us phenix-o-philes. Laurie

1 0

Re: [phenixbb] AutoMR and capsids
by SIPPEL,KATHERINE H 22 Oct '09

22 Oct '09

Dear Randy, > If you're sure that there are 3 full copies (and that you > couldn't, say, have six half-copies sitting on crystallographic > 2-folds), the best would be to search for full capsids. Now, for > each copy there are 60 different ways that the capsid could be > oriented, but the version of Phaser distributed with the latest > Phenix release should recognize the internal symmetry -- let us > know if it doesn't! I'm pretty sure its not actually full copies. The unit cell is 262.9, 262.9, 609.1 with an R32 space group. I'm downloading the latest release at the moment. > If it turns out that a capsid is sitting on a symmetry axis, > Phaser will probably reject it because of an outrageous number of > clashes. In that case, you should turn off the clash test, just > look for one copy, and then examine the overlapped solution to > see which part of the capsid is crystallographically unique. Thanks for the tips on the ASU, I wouldn't have thought of that. > Hi Katherine, > Back when I did this with HBV I had one capsid per > crystallographic AsU and I >used Amore (pre-phaser or phenix). I > searched with the icosohedral ASU >looking for 60 copies, and was > surprised how easily the solution fell out. If >you use this > strategy, you really just need one icos ASU per capsid and you > >can then expand the rest using standard icos symmetry. > I think the answer will be do what's easiest, and if it's 99% ID > it should >fall out pretty easily anyway. Bear in mind that > depending on what you've >done to these capsids the icos ASU's > may have slightly re-oriented (in my case >I had added a drug > that kept the icos ASU identical but had tilted the whole >thing > relative to the plane of the capsid). This may also guide your > strategy. > Good luck, > Christina Our standard protocol is Amore with CNS. When Amore failed I thought I might try something different. I have really enjoyed Phenix for my small proteins and thought that I might take advantage of that lovely NCS feature in phenix.refine. I just wasn't sure how to proceed within the AutoMR program. Obviously in the end I will go with what works. > PS- Isn't Mavis around in Florida somewhere, or are you even in > her lab? She >and Rob are a great resource.... I do work for Rob and Mavis and they are a fabulous resource. Best bosses ever (and no they won't see this, its just the truth). Thanks for the help, Katherine > On Oct 22 2009, SIPPEL,KATHERINE H wrote: > >> Dear all, >> >> I am currently trying to use AutoMR to do molecular replacement >> on an icosahedral virus capsid. It is a T=1 capsid so there are >> 60 copies of the monomer per capsid and based on the Matthews >> coefficient there are ~3 capsids in the unit cell. The search >> model is 99% identical (thank God) but I am unsure how to >> approach this. >> >> Do I used the 60-mer as the model and search for three copies? >> Do I use a monomer for the model and search for 180 copies? >> Should I break the model down to smaller pieces (i.e. a 30-mer >> and copies=6, or 12-mer and copies=15)? >> >> I would appreciate any help I can get on this one. >> >> Thanks, >> >> Katherine >> >> -- >> SIPPEL,KATHERINE H >> Ph. D. candidate >> Department of Biochemistry and Molecular Biology >> College of Medicine >> University of Florida >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > > -- SIPPEL,KATHERINE H Ph. D. candidate McKenna Lab Department of Biochemistry and Molecular Biology College of Medicine University of Florida

1 0

Another questions: water for adp and partial occupancy
by Young-Jin Cho 22 Oct '09

22 Oct '09

Hi, I thought we should put water molecules as isotropic and full occupancies. However, I saw different cases. So I am wondering the reasons for putting waters as anisotropic and with partial occupancies in an active sites. Does any one have this kind of experience or can you explain the advantage or disadvante of this types of strategy? Thanks in advance, Young-Jin Cho

2 1

AutoMR and capsids
by SIPPEL,KATHERINE H 22 Oct '09

22 Oct '09

Dear all, I am currently trying to use AutoMR to do molecular replacement on an icosahedral virus capsid. It is a T=1 capsid so there are 60 copies of the monomer per capsid and based on the Matthews coefficient there are ~3 capsids in the unit cell. The search model is 99% identical (thank God) but I am unsure how to approach this. Do I used the 60-mer as the model and search for three copies? Do I use a monomer for the model and search for 180 copies? Should I break the model down to smaller pieces (i.e. a 30-mer and copies=6, or 12-mer and copies=15)? I would appreciate any help I can get on this one. Thanks, Katherine -- SIPPEL,KATHERINE H Ph. D. candidate Department of Biochemistry and Molecular Biology College of Medicine University of Florida

3 2

Partially occupied SO4 and waters
by Chris Waddling 21 Oct '09

21 Oct '09

I have a partially occupied sulfate ion that is refining to 55% along with one of two arginine side chains. Associated with the second conformation of the arginine, there is positive density for three partially occupied waters. In Shelxl, I can use the PART identifier to specify that the sulfate ion and the waters are not present simultaneously and are associated with their respective Arg side chain conformation. Is there a way to do this in Phenix? Thanks, Chris -- Dr. Christopher A. Waddling, Ph.D. University of California at San Francisco

3 2

Re: [phenixbb] Molprobity percentile statistic
by hari jayaram 20 Oct '09

20 Oct '09

Thanks Nat and Pavel for your emails, Thanks for the suggestion of using phenix.polygon. The comparative analysis of my structure relative to others at my resolution was what I was after. And thats the reason I liked the molprobity statistics expressed as percentile since it helped me realize how far I have to go relative to other structures at the PDB. If its not too difficult can I cast my vote to report it inside the phenix GUI. Its just that running the full analysis inside of phenix is significantly faster than running it on the duke webservers. In molprobity If I remember correctly the overall score is some weighted average, and the molprobity paper also cautions against taking it too literally. Also If I remember the molprobity percentiles are absolute and not only composed of structures at similar resolutions . Regardless thanks for the hint about phenix.polygon . I just looked at my phenix.polygon report and I am afraid its a little asymmetric. Hari On Mon, Oct 19, 2009 at 9:58 PM, hari jayaram <harijay(a)gmail.com> wrote: > Thanks Nat and Pavel for your emails, > Thanks for the suggestion of using phenix.polygon. The comparative > analysis of my structure relative to others at my resolution was what > I was after. > > And thats the reason I liked the molprobity statistics expressed as > percentile since it helped me realize how far I have to go relative to > other structures at the PDB. If its not too difficult can I cast my > vote to report it inside the phenix GUI. Its just that running the > full analysis inside of phenix is significantly faster than running it > on the duke webservers. > > In molprobity If I remember correctly the overall score is some > weighted average, and the molprobity paper also cautions against > taking it too literally. Also If I remember the molprobity percentiles > are absolute and not only composed of structures at similar > resolutions . > > Regardless thanks for the hint about phenix.polygon . > I am attaching a snapshot of my polygon ..I an afraid its a little > asymmetric. > > Hari > > On Mon, Oct 19, 2009 at 7:48 PM, Pavel Afonine <PAfonine(a)lbl.gov> wrote: >> Hi Hari, >> >> if you run phenix.model_vs_data you will get those numbers (namely: >> Ramachandran outliers, clashscores, CB-deviations; although you will not >> get "Molprobity score" simply because I don't know what it is and so I >> didn't add it): >> >> phenix.model_vs_data model.pdb data.mtz >> >> Nat: every time time you run model_vs_data for whatever purpose (getting >> fmodel, etc...) you get an object that contains all these numbers. >> >> Pavel. >> >> >> On 10/19/09 3:32 PM, hari jayaram wrote: >>> Hi i just started using the phenix GUI front-end to Molprobity . Its >>> really nice the way it plugs into coot and displays all the statistics >>> etc. >>> Is there any place that it also reports the percentile clashscore and >>> percentile Molprobity score for overall model quality a la the >>> webserver at molprobity.biochem.duke.edu >>> >>> Thanks >>> Hari >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> >

2 1

Molprobity percentile statistic
by hari jayaram 19 Oct '09

19 Oct '09

Hi i just started using the phenix GUI front-end to Molprobity . Its really nice the way it plugs into coot and displays all the statistics etc. Is there any place that it also reports the percentile clashscore and percentile Molprobity score for overall model quality a la the webserver at molprobity.biochem.duke.edu Thanks Hari

3 2

Re: [phenixbb] pseudo-merohedral twinning or pseudo-symmetry?
by Gino Cingolani 17 Oct '09

17 Oct '09

Laurie, I had a similar problem. Scaling statistics in P212121 were OK, and - of course - no twinning was detected ... but nothing made sense during refinement. Looking at the data more carefully I found that if one rescales in P21, the b-angle was stably refined to 90.20 with ~30% better Rsym than in orthorhombic. When running xtriage on the P21 data, I found the data were indeed "pseudomerohedrally-twinned" with twinning fraction ~0.38. Good luck! Gino

3 2

pseudo-merohedral twinning or pseudo-symmetry?
by Laurie Betts 16 Oct '09

16 Oct '09

Hi - We have a data set that seems to process well in primitive orthorhombic. a=80, b=87, c=114. The data has overall Rsymm around 10% to 2.6 Angstrom, where I/sigI > 2, and Chi-squared is around 1.4. Phenix.xtriage shows some pathology in intensity statistics such that the L-test indicates <|L|> = 0.414 and <L^2> = 0.241, with the L-test Z score = 7.334. The Wilson ratio for acentric refls is 1.774. According the xtriage, There were no "pseudomerohedral" twin laws found, and the comments at the end say "As there are no twin laws possible given the crystal symmetry, there could be a number of reasons......" Is it more likely that this is a case of pseudo-symmetry, or would one not expect the intensity statistics to have the values they do in that case. Also, is the absence of twin laws defined by the fact that proper merohedral twinning is not possible for P222 space groups? Still confused, Laurie Betts

2 1

autobuild
by Colin Levy 16 Oct '09

16 Oct '09

Hi, can autobuild be setup to use kicked maps when starting from a molecular replacement model? Thanks Colin

2 1

Re: [phenixbb] grouped occupancy definitions
by Dr. Mark Mayer 15 Oct '09

15 Oct '09

Hi Pavel, I'm digging in docs and list serv but could not find out, and figured you probably know faster. I need to make an occ.params file for some groups of non adjacent side chains which interact with each other, and associated waters. 1) How do I select ACs 2) How do I constrain water occupancies so that their Q + that of coupled protein atomes does not exceed 1. If I match the AC flags for the waters and side chains will this take care of it. e.g. if residues 2 and 21 have coupled ACs and waters 101 and 102 move in when residue 21 is in one of its ACs how would I define below? refinement { refine { occupancies { constrained_group { selection = chain A and resseq 2 selection = chain A and resseq 21 selection = chain W and resseq 101 selection = chain W and resseq 102 } } Thanks !!! -- +++++++++++++++++++++++++++++++++++++++++++++++++++++++ Mark Mayer Ph.D.

2 2

low resolution refinement question
by Peter Grey 15 Oct '09

15 Oct '09

Dear Phenix users, I refine a large complex with three monomers in ASU at very low resolution - 4.5A - and would like to ask two questions. - Could you give some tips about refinement at this resolution other than rigid body refinement - Can TLS and grouped B-factors work at this poor resolution ? - I would really prefer that rigid body refinement will strictly obey the NCS that was found in the molecular replacement solution. I understand constrained NCS does not exist yet in phenix but is there something approximate that can be used in rigid body refinement ? I tried the conventional restrained NCS and the result was just like without restrains. Thank you for your time , Peter.

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