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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 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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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

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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

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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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