[ccp4bb] buccaneer crashes
Dear CCP4 folks, I am trying to run Buccaneer to build a substantial part of my structure: I have a model for one protein domain, but not for the other, though there is clear density for it in a MR-Buster map. I'm using CCP4 6.1.13 on a Mac-Pro under OS X 10.5.8 with a CCP4Interface 2.0.6 This is the error message: "The program run with command: python -u /sw/share/xtal/ccp4-6.1.13/ bin/buccaneer_pipeline -stdin has failed with error message Traceback (most recent call last): File "/sw/share/xtal/ccp4-6.1.13/bin/buccaneer_pipeline", line 3, in from CCP4pipeline import Control ImportError: No module named CCP4pipeline" What is going on? What can one do? Cheers, Anita
[ccp4bb] problem of conventions
Dear all, I would like to share my experiencde with a rather unexpected problem of indexing conventions. Perhaps I can save people some time I have a crystal in the more unusual P21212 space-group (No 18). Its unit cell lengths are b>a>c (please note). I systematically use XDS for data integration, since so far it was able to handle even the most horrible-looking spots. Now XDS indexed my data in space-group 18, but with the axes order anot exist. I did not realise this until I had spent a couple of weeks with beautiful peaks in rotation functions, but hopeless results in translation functions. It wasn't until I looked more closely into the definition of the screw axes that I realised the problem. POINTLESS does not allow a reindexing of reflexions within the same space-group, but fortunately REINDEX did the trick at the level of intensities, because I like to use SCALA for careful scaling of my data. So, basically, beyond just warning people who might encounter similar problems, I was wo,dering if XDS could perhaps reindex reflexions according to Int. Table conventions once the screw axes of a crystal system have been identified? With best wishes, Anita Anita Lewit-Bentley Unité d'Immunologie Structurale CNRS URA 2185 Département de Biologie Structurale & Chimie Institut Pasteur 25 rue du Dr. Roux 75724 Paris cedex 15 FRANCE Tel: 33- (0)1 45 68 88 95 FAX: 33-(0)1 40 61 30 74 email: ale...@pasteur.fr
Re: [ccp4bb] Atom labels in PDB file for Refmac
Thanks to all who answered - and so fast! - MET residues should become MSE (i.e. Se-MET instead of S-Met) - ' SD ' atom name should become 'SE ' - remove the columns 77-80 I had changed S to SE and that's fine Simply using an editor I changed the pdb file - and it works!! Thanks again, Anita
[ccp4bb] Atom labels in PDB file for Refmac
Dear all, This question may have been asked before, but I cannot find an answer in the recent ccp4bb archives - sorry! I am using an SeMet-protein data set as my native protein, since it diffracted to high resolution and should give all the information I need. I would therefore like to introduce the Se atom within the Met residue, so as to provide a correct description of the molecule. What format/syntax should I use for Refmac to recognise it? SED (with SE in he last column) does not work, nor does just simple SE left- shifted. Thanks for any hint! Anita Anita Lewit-Bentley Unité d'Immunologie Structurale CNRS URA 2185 Département de Biologie Structurale & Chimie Institut Pasteur 25 rue du Dr. Roux 75724 Paris cedex 15 FRANCE Tel: 33- (0)1 45 68 88 95 FAX: 33-(0)1 40 61 30 74 email: [EMAIL PROTECTED]
[ccp4bb] more REFMAC problems
Dear all, just to add to the list of problems mentioned by several people: I have been using the LSQ (least-squares) option in REFMAC (using a command file, as this option is not available vie the GUI interface) just to tidy up my structure. This works fine (with all recent REFMAC versions) - but the output mtz file does not carry any structure factors!! (again for all recent versions). One has to go through some complicated acrobatics to recover the structure factors corresponding to one's refined structure Another problem I encountered concerns the output of Coot: the output coordinate file carries over the header from the input file, without any modifications to it. Thus if at the start of a refinement one has, say, cis-peptide bonds, they remain in the pdb file even after one has corrected them in Coot - and then REFMAC does odd things to them! In the end, one has to edit the pdb file output by Coot before running Refmac - not very automatic. Best wishes for Christmas and the New Year, anyway! Anita Anita Lewit-Bentley Unité d'Immunologie Structurale CNRS URA 2185 Département de Biologie Structurale & Chimie Institut Pasteur 25 rue du Dr. Roux 75724 Paris cedex 15 FRANCE Tel: 33- (0)1 45 68 88 95 FAX: 33-(0)1 40 61 30 74 email: ale...@pasteur.fr
[ccp4bb] TLS refinement in Refmac gets stuck
Dear ccp4 folks, I am refining a structure in several crystal forms, with several molecules in the asymmetric unit. The structure is rather flexible, so I am using TLS refinement, having first submitted the coordinates to the TLSMD server (http://skuld.bmsc.washington.edu/~tlsmd/). The TLS refinement worked OK with REFMAC 5.2.0019 (CCP4 6.0.2) for 3 molecules in the asu, but not for crystal forms with 6 molecules/asu (it just got hung). For the latter crystal forms I have switched to CCP4 6.1.0 with REFMAC 5.5.0066, where it worked fine for two crystals - and now plays up for the third crystal! It is not exactly crashing, so I don't know what is going on. This is the last part of the logfile: "Problem xyz 1230 5.6147661 -5.1691742 2.8234024 -1.55429840E-02 9.35771316E-02 0.17803398 0.23723726 -0.13626081 5.39243035E-02 -0.14011805 -1.55429840E-02 0.11864197 0.40574944 0.71992165 0.57164854 -0.39361250 *** * Information from CCP4Interface script *** Writing final coordinates (XYZOUT) to /Users/anita/work/Integ/ SOLEIL_09_08/3MSe_NTLS9_8_6_refmac1.pdb *** *** * Information from CCP4Interface script *** Writing final phases (HKLOUT) to /Users/anita/work/Integ/ SOLEIL_09_08/3M_Se_TLS_refmac1.mtz *** *** * Information from CCP4Interface script *** Writing final TLS (TLSOUT) to /Users/anita/work/Integ/ SOLEIL_09_08/3MSe_NTLS9_8_6_refmac1.tls *** " Unfortunately, there are NO files written out! There is no real error message either, the CCP4i interface says the job has finished normally. I have already tried to vary the number of TLS fragments, with no better result. The older Refmac just gets hung Any help will be appreciated! Thanks, Anita Anita Lewit-Bentley Unité d'Immunologie Structurale CNRS URA 2185 Département de Biologie Structurale & Chimie Institut Pasteur 25 rue du Dr. Roux 75724 Paris cedex 15 FRANCE Tel: 33- (0)1 45 68 88 95 FAX: 33-(0)1 40 61 30 74 email: ale...@pasteur.fr
Re: [ccp4bb] TLS refinement in Refmac gets stuck
Hi Ian, A bug was reported with that version of Refmac, though I've no idea if that would cause your problem: you should upgrade to the latest version from the York website. Done - and here is what happens: 1) the latest CCP4 package (6.1.1) runs the same version of Refmac (5.5.0066) and, predictably, crashes the same way; 2) on the Refmac webside there are much more recent versions of Refmac, not yet incorporated into the CCP4 package. Versions 72 and higher have a bug fix for TLS refinement. 3) included version 5.5.0086 (the precompiled version for Mac - intel) in CCP4 6.1 - and that runs fine except that it exits with a "bus error, child killed" I HATE seeing a child killed but anyway, the output pdb and mtz files exist in the "scratch" directory with a .tmp extension, but otherwise perfectly useable. So I can scrape along if I remember to copy the .tmp files accross to my working directory. Better than nothing! Thanks for your hint. Cheers, Anita -Original Message- From: owner-ccp...@jiscmail.ac.uk [mailto:owner- ccp...@jiscmail.ac.uk] On Behalf Of Anita Lewit-Bentley Sent: 23 February 2009 15:31 To: CCP4BB@JISCMAIL.AC.UK Subject: TLS refinement in Refmac gets stuck Dear ccp4 folks, I am refining a structure in several crystal forms, with several molecules in the asymmetric unit. The structure is rather flexible, so I am using TLS refinement, having first submitted the coordinates to the TLSMD server (http://skuld.bmsc.washington.edu/~tlsmd/ <http://skuld.bmsc.washington.edu/~tlsmd/jobs/TLSMD7413_IBXkmSis/ANALYSIS/ index.html> ). The TLS refinement worked OK with REFMAC 5.2.0019 (CCP4 6.0.2) for 3 molecules in the asu, but not for crystal forms with 6 molecules/ asu (it just got hung). For the latter crystal forms I have switched to CCP4 6.1.0 with REFMAC 5.5.0066, where it worked fine for two crystals - and now plays up for the third crystal! It is not exactly crashing, so I don't know what is going on. This is the last part of the logfile: "Problem xyz 1230 5.6147661 -5.1691742 2.8234024 - 1.55429840E-02 9.35771316E-02 0.17803398 0.23723726 -0.13626081 5.39243035E-02 -0.14011805 -1.55429840E-02 0.11864197 0.40574944 0.71992165 0.57164854 -0.39361250 ** * * Information from CCP4Interface script ** * Writing final coordinates (XYZOUT) to /Users/anita/work/Integ/SOLEIL_09_08/3MSe_NTLS9_8_6_refmac1.pdb ** * ** * * Information from CCP4Interface script ** * Writing final phases (HKLOUT) to /Users/anita/work/Integ/SOLEIL_09_08/3M_Se_TLS_refmac1.mtz ** * ** * * Information from CCP4Interface script ** * Writing final TLS (TLSOUT) to /Users/anita/work/Integ/SOLEIL_09_08/3MSe_NTLS9_8_6_refmac1.tls ** * " Unfortunately, there are NO files written out! There is no real error message either, the CCP4i interface says the job has finished normally. I have already tried to vary the number of TLS fragments, with no better result. The older Refmac just gets hung Any help will be appreciated! Thanks, Anita Anita Lewit-Bentley Unité d'Immunologie Structurale CNRS URA 2185 Département de Biologie Structurale & Chimie Institut Pasteur 25 rue du Dr. Roux 75724 Paris cedex 15 FRANCE Tel: 33- (0)1 45 68 88 95 FAX: 33-(0)1 40 61 30 74 email: ale...@pasteur.fr Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing i.tic...@astex-therapeutics.com and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the ind
[ccp4bb] LSQKAB error
Dear all, I am trying to compare several related structures using LSQKAB. In order to refine the superpositions, I'd like to use the option "radius", to see the relative postion of certain residues within a given distance from a common point. The programme reads the commands OK: " ALL ATOMS MORE THAN 30.000 ANGSTROMS FROM REFERENCE POINT 46.520 37.890 40.280 EXCLUDED" as well as the fixed input coordinate file: " Logical name: XYZIN2 File name: wtC_on_MnA_SSM.pdb PDB file is being opened on unit 1 for INPUT." No sign of any other file being opened/read, but the following error message is output instead: " LSQKAB: ERROR: in XYZADVANCE file has not been opened LSQKAB: ERROR: in XYZADVANCE file has not been opened " and the job stops. This happens for both ccp4 versions 6.0.2 and 6.1.1. Is there a working version of the programme somewhere? If not, what other programme could do the same thing (in a simple way...)? Thanks for any suggestions! Anita Anita Lewit-Bentley Unité d'Immunologie Structurale CNRS URA 2185 Département de Biologie Structurale & Chimie Institut Pasteur 25 rue du Dr. Roux 75724 Paris cedex 15 FRANCE Tel: 33- (0)1 45 68 88 95 FAX: 33-(0)1 40 61 30 74 email: ale...@pasteur.fr
Re: [ccp4bb] LSQKAB error
Dear Norman, That did the trick! And was easy to do... Thanks a lot, Anita Dear Anita You could try adding the following additional line of input: rotate matrix 1 0 0 0 1 0 0 0 1 This multiplies the data in XYZINM by the identity matrix (so that the data should be unchanged) but has the side effect of forcing the program to read in the XYZINF input file. Norman From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Anita Lewit-Bentley Sent: 16 March 2009 14:59 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] LSQKAB error Dear all, I am trying to compare several related structures using LSQKAB. In order to refine the superpositions, I'd like to use the option "radius", to see the relative postion of certain residues within a given distance from a common point. The programme reads the commands OK: " ALL ATOMS MORE THAN 30.000 ANGSTROMS FROM REFERENCE POINT 46.520 37.890 40.280 EXCLUDED" as well as the fixed input coordinate file: " Logical name: XYZIN2 File name: wtC_on_MnA_SSM.pdb PDB file is being opened on unit 1 for INPUT." No sign of any other file being opened/read, but the following error message is output instead: " LSQKAB: ERROR: in XYZADVANCE file has not been opened LSQKAB: ERROR: in XYZADVANCE file has not been opened " and the job stops. This happens for both ccp4 versions 6.0.2 and 6.1.1. Is there a working version of the programme somewhere? If not, what other programme could do the same thing (in a simple way...)? Thanks for any suggestions! Anita Anita Lewit-Bentley Unité d'Immunologie Structurale CNRS URA 2185 Département de Biologie Structurale & Chimie Institut Pasteur 25 rue du Dr. Roux 75724 Paris cedex 15 FRANCE Tel: 33- (0)1 45 68 88 95 FAX: 33-(0)1 40 61 30 74 email: ale...@pasteur.fr
[ccp4bb] packing diagrammes
Dear all, does anyone know of a programme that would allow the graphical representation of the packing of protein molecules in a crystal? Ideally one would like to represent the protein as an elipsoid (or similar relatively simple shape) corresponding to its volume, over a few unit cells so as to visualise the continuity of solvent channels etc. Thanks for any leads! Anita Anita Lewit-Bentley Unité d'Immunologie Structurale CNRS URA 2185 Département de Biologie Structurale & Chimie Institut Pasteur 25 rue du Dr. Roux 75724 Paris cedex 15 FRANCE Tel: 33- (0)1 45 68 88 95 FAX: 33-(0)1 40 61 30 74 email: ale...@pasteur.fr
[ccp4bb] packing diagrammes
Dear all, thanks to everybody who offered their experience and hints. The most convenient way of preparing a packing diagramme, at least for me, was via PyMol as suggested by Michael Klein (see below). One can do something similar with the CCP4 graphics package, but for some reason the protocol suggested by the manual slows down the computer too much to be practical. Anyway, the challenge is out there: a programme for preparing a packing diagramme with the protein represented by a reasonable approximation of its real shape. It would make a good teaching tool as well. Thanks again, Anita I have made a few figures like the one you describe. I calculate the center of mass of the domain using ccp4 program pdbset with the command COM #! /bin/csh -f ### Take output from O into a form suitable for refinement pdbset xyzin domain.pdb xyzout junk.pdb << eof-1 #cell132.02 115.21 96.20 90.00 90.00 90.00 NCODE 1 # New cell in junk.pdb, it is recommended that a spgrp is also given #spacegroup P212121 COM eof-1 # then run pdbset.csh > pdbset.log the center of mass is then listed in the pdbset.log I then make a fake atom out of the center of mass X,Y,Z coordinates using a pdb style format, name the atom O or whaterver. I then use pymol to display the atom as a sphere. Example: ATOM 2 O TYR A 59 4.198 22.414 35.783 1.00 24.65 AO replace 4.198 22.414 35.783 with the center of mass coordinates from pdbset.. In pymol use command: show spheres, set sphere_scale=1.5 change the number to adjust the size if the spheres do not show up try to ray the image.. if you want to show the symmetry of the atom/spere in pymol symexp s,nameofyourobject,(all),50 change the number to adjust how big the symm operators are.. sorry if it seems complex, it really is'nt too bad and will work! HTH, michael -- Michael G. Klein Ph.D. Project Research Scientist Structural Genomics DOE Joint Genome Institute 2800 Mitchell Drive Walnut Creek, CA 94598 Phone: (925) 927-2556 mgkl...@lbl.gov
[ccp4bb] Arp/wArp error
Dear all, I have a nice MAD map produced by Sharp and would like to trace a chain into it using Arp/wArp. When I input the mtz file via the CCP4i interface, I get the following message: "Cannot extract ARP/wARP asymmetric unit limits The job will fail if run" Well it DOES fail when run! My space group is C2 (given as C121 in the mtz file header), the mtz file is a standard structure factor file generated by CAD (adding Sharp phases to native data which are at a higher resolutino than the MAD data) and I just don't see what is going wrong. I am using CCP4 6.1.2 and Arp 7.0.1, with the CCP4Interface version 2.0.5 running on Mac OSX version 10.5.8. Any advice will be extremely welcome! Anita Anita Lewit-Bentley Unité d'Immunologie Structurale CNRS URA 2185 Département de Biologie Structurale & Chimie Institut Pasteur 25 rue du Dr. Roux 75724 Paris cedex 15 FRANCE Tel: 33- (0)1 45 68 88 95 FAX: 33-(0)1 40 61 30 74 email: ale...@pasteur.fr
Re: [ccp4bb] Arp/wArp error
Dear Jan, that is an annoying thing with Arp/wARP - it sometimes does not recognise some space groups, esp. the monoclinic ones with eg can be called C2 or C121 etc. Run the mtz file again through CAD, use SG 5 or C2. That should work. and it does! Thanks a lot. Let's hope these annoying obstacles can get removed from the path of - otherwise really happy - CCP4 users! Thanks again, Anita Bonne chance Jan On Tue, Dec 1, 2009 at 8:41 AM, Anita Lewit-Bentley wrote: Dear all, I have a nice MAD map produced by Sharp and would like to trace a chain into it using Arp/wArp. When I input the mtz file via the CCP4i interface, I get the following message: "Cannot extract ARP/wARP asymmetric unit limits The job will fail if run" Well it DOES fail when run! My space group is C2 (given as C121 in the mtz file header), the mtz file is a standard structure factor file generated by CAD (adding Sharp phases to native data which are at a higher resolutino than the MAD data) and I just don't see what is going wrong. I am using CCP4 6.1.2 and Arp 7.0.1, with the CCP4Interface version 2.0.5 running on Mac OSX version 10.5.8. Any advice will be extremely welcome! Anita Anita Lewit-Bentley Unité d'Immunologie Structurale CNRS URA 2185 Département de Biologie Structurale & Chimie Institut Pasteur 25 rue du Dr. Roux 75724 Paris cedex 15 FRANCE Tel: 33- (0)1 45 68 88 95 FAX: 33-(0)1 40 61 30 74 email: ale...@pasteur.fr -- -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island, WA, USA work: JAbendroth_at_decode.com home: Jan.Abendroth_at_gmail.com
