Re: [ccp4bb] Opinion on automation
Hello Teresa, I need to disagree with Graeme over the idea that ccp4i 'hides' what is happening. If you care to you can see all the gorey details of command files, log files etc.. You can run the programs one step at a time and with various modes with ccp4i and iMosflm and learn something of what is going on at each stage but the gui layer at least gives you a much quicker user-friendly way to control them rather than going back to prehistoric scripts. On the other hand pipelines such as xia2 will usually do the job and save you much time. Liz On 17 Feb 2012, at 12:09, Graeme Winter wrote: Dear Theresa, My answer would be - it depends. If you are in the business of learning crystallography, then I would absolutely suggest you start from doing everything by hand. Indeed, if you really want to get stuck in I would suggest starting with the programs you need (mosflm, scala, truncate etc) and scripts so you can get a proper idea what the programs are doing. There is of course CCP4i, but this can hide some of the details which may be instructive to know about. If however you're in the business of getting on with biological research, well I would say that automated tools (be they for data reduction or phasing / model building) are exceedingly useful. If you can find the time, I would always encourage people to do things with automation and by hand, to allow comparison of the results. If nothing else this may give you confidence in the automation software. Best wishes, Graeme On 17 February 2012 11:31, Theresa H. Hsu theresah...@live.com wrote: Dear crystallographers I would like to get some opinion. For someone beginning to learn basic crystallography including indexing, scaling ..., should I start with automated tool like Xia2? Or is manual method for each step better for learning? Thank you. Theresa
Re: [ccp4bb] 3D-fititng which is actually 2D-fititng
Miri, For matching similar small molecules you can try in CCP4mg as described at http://www.ysbl.york.ac.uk/~ccp4mg/ccp4mg_help/superpose.html#interactive_selection the 'user defined' superposition option with 'monomer' mode. This does 2D graph isomorphism for the atoms in one residue. Liz On 26 Feb 2010, at 16:57, Miri Hirshberg wrote: Fri., Feb. 26th 2010 EBI Dear all, I've already replied privately to several people who replied when I first posted th question, but did not set the record-clear for the whole community and I do apologize. What I have is two or more 3D structures, not protein, similar in their 3D but equivalent atoms don't have the same atom-name. I thought that in order to rename equivalent atoms automatically I needed to 3D fit the two structures first. Adel Golovin of PDBeMOTIF fame (http://www.ebi.ac.uk/pdbe-site/pdbemotif ) has pointed out that for the automatic atom renaming process all I needed was 2D-fitting via 2D-graph isomorphism routine which he could provide. Once all structures in a given set have the same atom names, 3D-fitting is doable using numerous software/utilities. Thanks again for the replies, especially to Pavel Afonine (phenix) with whom I had a lengthy exchange. CCP4-board is one of the best... Thanks again Miri
Re: [ccp4bb] SSM superposition of a heterodimer of related chains such that A-B and B-A / SUMMARY
Norbert, Sorry for this late reply. SSM will find multiple alternative matches but most implementations just show you the 'best'. The Superposition tool in CCP4mg uses ssm and has an option to look through the non- optimal matches - hopefully one of these will be the one that you want. Liz On 17 Feb 2010, at 10:35, Norbert Straeter wrote: Dear All, last Friday I posted the following question: I have a heterodimer of two related subunits (A and B). Now I want to superimpose it using a secondary structure matching (SSM) algorithm (e.g. CCP4 superpose or the coot algorithm) such that the superposition matches A onto B and B onto A at the same time. For a perfectly symmetrical closed C2 dimer, it would not make a difference if I just superimposed A onto B, but it is unsymmetrical. I know that this is easy to specify in lsqkab when knowing the matching residue pairs. Does anybody know an SSM program where I can specify the chains to be superimposed (A-B and B-A)? Some replys described how to specify selections in pymol or coot for SSM alignment. To make it more clear, if you specify chains A+B as the moving selection and A+B or B+A as the reference, you will always get the best but trivial superposition of A-A and B-B. It appears as if there is currently no program for SSM superposition for which you can specify the chains to be matched if the structure that needs to be superimposed contains internal symmetry in form of different chains. As a workaround, one can rename chains and residue numbers before and after alignment: OK, here's a possible inelegant solution, till something better comes up Take dimer 1, and put it all into one chain X, keeping numbers for A and adding an offset eg 500 for the B chain. Take dimer 2, and put it all into another chain Y, keeping the numbers for B and adding the same offset to A. Then do a match of chain X with chain Y. (Judith Murray-Rust) Could it help to merge chains A and B first into two longer chains, where C=A+B and D=B+A ? (Matthias Zebisch) Using this strategy, you can probably use your favourite SSM alignment program. I just tested it within coot and it works. Another strategy is the following: One workaround would be to let SSM define the matching residues (should be the same for A-B and B-A) and input those in to lsqkab. (Herman Schreuder) Thanks to all, who provided help to this problem, also to Christian Roth, Gerard Kleywegt (use of explicit and improve commands in lsqman), Yu Wai Chen, Mark A. White, Christina Bourne, Markus Wiederstein (http://topmatch.services.came.sbg.ac.at/), Ed Pozharski and Regina Kettering. Norbert
Re: [ccp4bb] How to sketch a cis double bond (carbon-carbon)
Hi Oliv, I'm sorry, I think you will need to edit the output file from Sketcher _mon_lib.cif - the torsions section ( _chem_comp_tor) will have something like test CONST_1 C1 C2 C3 C4 180.0 0.0 0 the 180 needs changing to 0.0. I think that is all you need to do - no doubt someone will correct me if I'm wrong! Liz On 15 Jun 2009, at 04:35, Oliv Eidam wrote: Hi, Could somebody explain how to sketch cis double bonds with Sketcher? For example a cis-but-2-ene? No matter how I draw the the molecule: When I create a library description I always get the trans double bond. I hope there is way to this through the Sketcher GUI, because I prefer not to edit the angles by hand... Many thanks, Oliv -- Oliv Eidam, Ph.D. Postdoctoral fellow University of California, San Francisco Dept. of Pharmaceutical Chemistry 1700 4th Street, Byers Hall North, Room 501 San Francisco, CA 94158 - Box 2550 Phone: 415-514-4253 Fax : 415-514-4260 Email: eid...@blur.compbio.ucsf.edu
Re: [ccp4bb] Problem with multiple users running ccp4i on one machine
Miguel, CCP4 are intending a major project on the ccp4i database and one of the requirements will certainly be enabling multi-user access to databases. I'm sure we will be looking for your input on other requirements when we have someone in post. Liz On 22 Mar 2009, at 08:11, Miguel Ortiz Lombardia wrote: Dear ccp4i developers, Jumping into this issue a bit late... I have some criticism to make here, please take them friendly, I make them precisely because ccp4i is so useful. I presume there are good reasons behind the new design of CCP4i and its CCP4 DBhandler, but I think you have overlooked the fact that multi-processor, multi-user servers are quite common nowadays. Also, that many end-users don't know/don't need to know what a sqlite database is and will simply let the default preferences turned on, unaware of the consequences. In our lab this has led to people not using the best computer they have available, precisely by reasons similar to those raised by Jun Dong. I know of another case where a user got its database corrupted after getting confused because not being able to see their own projects/directories. I hope that in future versions of ccp4 the multi-users problem will be tackled or, at least, the default option is the old direct-access behaviour (if completely functional). With best regards, Miguel Le 18 mars 09 à 17:46, Ronan Keegan a écrit : Dear Jun Dong, This is a problem with the new mechanism used in CCP4 to store project and job data (the CCP4 DBhandler). The quick fix for now is to turn it off and use the old mechanism for storing the project data. To do this in the CCP4i interface go to System Administration, select Database Configuration and un-check the radio button that sets the option to connect to the database server on start up. Then have all your users restart CCP4i. Kind regards, Ronan Keegan CCP4 Group Jun Dong wrote: Dear CCP4 developers, I just wonder if there will be a fix for this problem. Basically when the first user is running ccp4i on a linux server and then when the second user tries to run ccp4i on the same linux server, the second user will only see the fist user's DirectoriesProjectDir. Best regards, Jun Dong Division of Structural Biology The Wellcome Trust Centre for Human Genetics Oxford University Roosevelt Drive Oxford OX3 7BN Tel: 01865 287558 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Miguel Ortiz Lombardía Architecture et Fonction des Macromolécules Biologiques UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée ) 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-lombar...@afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Re: [ccp4bb] images
Dear CCP4BB, For further research of a particular structure wouldn't hints on expressing, purifying and crystalizing the protein often be more useful than images or amplitudes? Liz On 18 Mar 2009, at 17:00, Ethan Merritt wrote: On Wednesday 18 March 2009 09:41:59 Garib Murshudov wrote: Dear all Before going into and trying to find a technical solution to the problem it would be good if decide if we need images. As far as I know if we face with a problem to solve and we know that it is necessary to solve then we find technical solution to the problem (either from other fields or we find our own solution with some elements of reinvention of new MX wheels). Do we need images to store? What kind of information we can extract from images that we cannot from amplitudes, intensities (even unmerged)? Does anybody have a convincing argument for favour of images? Overlooked superlattice? Incorrect point group assignment? Failure to recognize a non-merohedral twin? Thermal diffuse scatter? Subsequent improvements in integration programs? Ethan regards Garib On 18 Mar 2009, at 16:32, Herbert J. Bernstein wrote: Actually the radiologists who manage CT and PET scans of brains do have a solution, called DICOM, see http://medical.nema.org/. If we work together as a community we should be able to do as well as the rocket scientists and the brain surgeons' radiologists, perhaps even better. -- Herbert = Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 y...@dowling.edu = On Wed, 18 Mar 2009, Jacob Keller wrote: Apparently it DOES take a rocket scientist to solve this problem. Maybe the brain surgeons also have a solution? JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** - Original Message - From: Klaas Decanniere klaas.decanni...@vub.ac.be To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, March 18, 2009 5:36 AM Subject: Re: [ccp4bb] images Herbert J. Bernstein wrote: Other sciences have struggled with this and seem to have found an answer. Have e.g. a look at http://heasarc.nasa.gov/docs/heasarc/fits.html kind regards, Klaas This is a good time to start a major crystallogrpahic image archiving effort. Money may well be available now that will not be avialable six month from now, and we have good, if not perfect, solutions available for many, if not all, of the technical issues involved. Is it really wise to let this opportunity pass us by? The deposition of images would be possible providing some consistent imagecif format was agreed. This would of course be of great use to developers for certain pathological cases, but not I suspect much value to the user community - I down load structure factors all the time for test purposes but I probably would not bother to go through the data processing, and unless there were extensive notes associated with each set of images I suspect it would be hard to reproduce sensible results. -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
Re: [ccp4bb] ccp4mg and speed
Jan, CCP4mg uses the same MTZ-map code as COOT - one thing that will make a difference in time is the resolution of the map. Overwise I'm not sure that ther is much that you can do - on the other hand the developers are busy converting CCP4mg to use Qt rather than Tcl/Tk for the GUI and this has significantly improved performance. We hope to have a trial version of the program out soon (without all the functionality) and a new release in autumn. Liz Jan Abendroth wrote: Hi all, ... tried on the ccp4mg bb before ... ccp4mg is such a nice program, yet it is so slow in my hands. An average sized map calculated from a mtz file takes about 30s to display, while coot displays both 2FoFc and FoFc maps in about 5s. Is there anything I can do to speed things up? I use: - ccp4mg-1.1.1-Linux-Fedora-Core - coot-Linux-i386-fedora-6 - python2.4 - Fedora Core release 6 Thanks a lot for any hints. Jan
Re: [ccp4bb] Graphics software to show epitope foot-print
Hi Anders and CCP4bb Would something like http://www.ysbl.york.ac.uk/~ccp4mg/index_info_5.html (done with CCP4mg) be useful? In that image the molecule surface is coloured by electrostatics (but could be any other property) and the contact area to a ligand is indicated by dots on the surface. Liz On Wednesday 14 May 2008 08:34, ANSV (Anders Svensson) wrote: Dear colleagues, I am looking for a graphics software program that can make the following, easily. Make a surface representation of a macromolecule. That surface should be coloured according to some property. On, or close to, that surface the outer rim of a binding epitope from a second molecule should be indicated by a line or string, a foot-print representation, without altering the original colouring of the surface. Unfortunately I can not find out any program that can make it easily, or have not understood all features of the programs. Can anyone help? Kind regards Anders Svensson __ Anders Svensson Novo Nordisk A/S Denmark
Re: [ccp4bb] Any programs other than GRASP have a surface scribing function?
James, CCP4mg will allow you select a set of atoms and draw a surface over them in whatever colour scheme that you choose. The tutorial explaining this is at http://www.ysbl.york.ac.uk/~ccp4mg/ccp4mg_help/tutorial/surfaces.html Cheers Liz James Thompson wrote: Dear CCP4'ers, Any Windows/Linux/OS X programs have a surface scribing function similar to that found in GRASP, to quickly draw the border of a surface selection (or subset) and calculate or display local features of the molecular surface? I have no access to SGIs now. I have a memory of similar function elsewhere but am not finding the ability within GRASP2, DINO, CHIMERA, etc. Perhaps I'm thinking of Setor which was also IRIX, and perhaps this memory is suspect... Other selection methods for a molecular surface require more of my time to define the subset. Many thanks, Jim James R. Thompson Assistant Professor of Biophysics Mayo Clinic College of Medicine Department of Physiology and Biomedical Engineering Mayo Proteomics Research Center Office 507-538-3891 Fax 507-538-3954 E-mail [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]
Re: [ccp4bb] questions about hydrophobic core
Sebastiano, I can suggests one approach to finding core residues.. CCP4mg will calculate the total asa buried per residue and residues can be selected by the criteria of their buried area. One way to define the protein core would be to select residues with, say, 5.0A*2 asa. You can easily see what has been selected in the molecular graphics and try varying the criteria if necessary. If you need to do this for many structures we could write a script. Liz On Tuesday 19 June 2007 09:55, Sebastiano Pasqualato wrote: Hi all, a few days ago I sent a post in which I was asking if anybody knew a program to automatically define the hydrophobic core of a protein, given the pdb. Unfortunately I got no answers, and indeed a more thorough googling around revealed that such a program might not exist. So it seems I have to define my hydrophobic core residues by hand... So now my question would be: how to define the hydrophobic core residues? I would tend to say that those that bury more than ## % (say 70%, 80% ??) of their otherwise solvent accessible surface area could be defined as such, but how can I get such a per residue percentage? (NB: this is not the asa buried upon interaction, so I don't know how to get the asa of the free amino acid) Alternatively, are there other simple and defined rules to state which are the hydrophobic core residues? Any help appreciated, thanks in advance, ciao s -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 Milano Italy tel +39 02 9437 5094 fax +39 02 574 303 310
Re: [ccp4bb] ccp4mg can't start
Tim Yanming, Our first suggestion is to try the latest version (1.0) - a few startup issues were fixed between the two versions. Normally I would encourage you to use the python version distributed with ccp4mg. The C++/Python interface was built against a particular version of Python and probably will not work with others. Liz Tim Grune wrote: Hi Yanming, it looks like ccp4mg looks for python in a specific path within the ccp4mg. Edit the script ccp4mg (you find out where it is with 'which ccp4mg'). Look at the very end of that file for where python is called (probably with some arguments). Make sure it says only 'python', not anything like '/usr/local/ccp4/ccp4mg-0.12.1/bin/..//pythondist/bin/python'. Then ccp4mg will use the python of your system. This works for me and ccp4mg does not need its own python installation. Maybe the ccp4mg-developers may want to comment on whether this is a bad idea and may have a negative influence on ccp4mg's performance? Tim -Original Message- From: Yanming Zhang [EMAIL PROTECTED] To: Tim Grune [EMAIL PROTECTED] Date: Wed, 16 May 2007 01:47:08 -0400 (EDT) Subject: Re: [ccp4bb] ccp4mg can't start Dear Tim, Thanks for your help. python 2.4.2 is the version. Following is the output of ccp4mg -dbx: GNU gdb Red Hat Linux (6.3.0.0-1.132.EL4rh) Copyright 2004 Free Software Foundation, Inc. GDB is free software, covered by the GNU General Public License, and you are welcome to change it and/or distribute copies of it under certain conditions. Type show copying to see the conditions. There is absolutely no warranty for GDB. Type show warranty for details. This GDB was configured as i386-redhat-linux-gnu.../usr/local/ccp4/ccp4mg-0.12.1/bin/..//pythondist/bin/python: No such file or directory. (gdb) Starting program: /usr/local/ccp4/ccp4mg-0.12.1/bin/..//python/ui/ui.py -debug opengl command No executable file specified. Use the file or exec-file command. (gdb) No stack. (gdb) No symbol table is loaded. Use the file command Any suggestion? Thanks On Wed, 16 May 2007, Tim Grune wrote: Hi Yanming, which version of python is running on your system(python -V)? Maybe it is too old? Otherwise, does 'ccp4mg -dbx' produce any more output? On Wednesday 16 May 2007 11:20, you wrote: Dear Tim, I checked the two files, Both are empty. Linux distribution: 2.6.9-42.ELsm Thanks Yanming On Wed, 16 May 2007, Tim Grune wrote: Could you send the contents of the files /home/yzhang/.CCP4MG/ccp4mg_stdout.txt and /home/yzhang/.CCP4MG/ccp4mg_stderr.txt What Linux distribution are you using? Tim On Wednesday 16 May 2007 10:31, Yanming Zhang wrote: Dear All, lately I have a fantacy toward ccp4mg. But either from ccp4i or typing 'ccp4mg' directly from the prompt(Linux), I got the following error message: Loading fonts.. ...DONE Starting graphics thread.. ...DONE Parsing command line.. ...DONE Redirecting output to /home/yzhang/.CCP4MG/ccp4mg_stdout.txt Redirecting errors to /home/yzhang/.CCP4MG/ccp4mg_stderr.txt Started at Fri May 16 09:16:59 2003 /usr/local/ccp4/ccp4mg-0.12.1/bin/ccp4mg: line 281: 10773 Killed python $CCP4_MG/python/ui/ui.py $* Any quick remedy? Thanks Yanming -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia
