Re: [ccp4bb] SUMMARY: scala and xds data
Just to point out that Scala does not refine cell parameters: I believe XDS does Phil On 24 Apr 2010, at 18:57, Peter Grey wrote: Hi Ingo, Scala might be beneficial after xds when several datasets need to be scaled together. Scala will refine cell parameters to fit best all the datasets together where as xscale uses as cell parameters those of the first dataset. If you use xscale you have to be prudent in your choice of the first dataset. Peter. On Sat, Apr 24, 2010 at 7:31 PM, Ingo Korndoerfer korndoer...@crelux.comwrote: as it turns out: the bad news (for me) 1. something went wrong in my data processing. point taken. yes. i was so hypnotized by the strange error message, that i did not realize this. the good news 2. pointless and scala run just fine (everybody can relax), and the strange messages are more an esthetic problem, that phil evans said he will fix in the next pointless release. had i looked at the pointless output i would have seen, of course, that my data are complete nonsense. embarassing ... thanks to phil for taking time to look over this, and thanks to the others who also replied and asked why i even scale xds data with scala rather than xscale. there are reasons for this, but the interesting news for me was, that it might be that xscale possibly delivers better data from xds than scala does, which, of course, now, i will have to look into ... time will tell ... greetings ingo -- Peter
Re: [ccp4bb] SUMMARY: scala and xds data
Hi Phil, Indeed it does, both during integration (INTEGRATE, only if you ask for it with the proper keyword) and in the post-refinement step (CORRECT). Normally this should be quite sufficient. I haven't seen a single case where this was not sufficient. Fred. Message du 25/04/10 09:55 De : Phil Evans A : CCP4BB@JISCMAIL.AC.UK Copie à : Objet : Re: [ccp4bb] SUMMARY: scala and xds data Just to point out that Scala does not refine cell parameters: I believe XDS does Phil
Re: [ccp4bb] YATQ (yet another twinning question) - may involve pirates
Hi, ARP/wARP as of version 7.1 generates instructions for Refmac to carry out twin refinement during protein model building. Refmac version 5.5.16 or higher is required. ARP/wARP is not yet making active use of NCS for tracing protein chains. This development is almost accomplished and will be out in the next release. Best regards, Victor Garib Murshudov wrote: I hope Kevin will respond soon. I think he has done (or is planning to do) to twinning and ncs in his pipeline of model building. I think something like that may already be in new ARP/wARP (Victor and Tasos will correct me if I am wrong) regards Garib
Re: [ccp4bb] SUMMARY: scala and xds data
Dear Fred and Phil, However there is no refinement of these parameters in XSCALE so if you need to scale together several crystals (e.g. very small crystals that show severe radiation damage after a few degrees) you end up with a sub-optimal combined dataset after XSCALE. I thought SCALA can take care of that and define cell parameters that fit best all data as scalepack does when it considers all separate frames , from all crystals where-as the input to XSCALE is not separate frames but complete datasets). Peter. On Sun, Apr 25, 2010 at 12:14 PM, Frederic VELLIEUX frederic.velli...@orange.fr wrote: Hi Phil, Indeed it does, both during integration (INTEGRATE, only if you ask for it with the proper keyword) and in the post-refinement step (CORRECT). Normally this should be quite sufficient. I haven't seen a single case where this was not sufficient. Fred. Message du 25/04/10 09:55 De : Phil Evans A : CCP4BB@JISCMAIL.AC.UK Copie à : Objet : Re: [ccp4bb] SUMMARY: scala and xds data Just to point out that Scala does not refine cell parameters: I believe XDS does Phil -- Peter
Re: [ccp4bb] SUMMARY: scala and xds data
Hi, I sense a misunderstanding: Cell parameters are not relevant when scaling together datasets: what matters are intensities and (depending on algorithm) directional cosines and the like. Cell parameters are relevant, along with the other experimental parameters, for knowing where to pick the intensities off the images (integrating). What denzo scalepack do (which I suspect you're referring to) is to split this into separate actions: denzo integrates, and scalepack postrefines, meaning it optimizes the integrated intensities by simultaneously taking into account experimental parameters over whole dataset. Only then does it scale. Xscale and Scala trust the intensities and only scale. Yes, the cell parameters are also an indicator that you may have non-isomorphism, but only that; it's the *intensities* where this is manifested. So you could have different cells yet still perfectly isomorphous intensities; or same cells and terrible non-isomorphism. phx. On 25/04/2010 16:05, Peter Grey wrote: Dear Fred and Phil, However there is no refinement of these parameters in XSCALE so if you need to scale together several crystals (e.g. very small crystals that show severe radiation damage after a few degrees) you end up with a sub-optimal combined dataset after XSCALE. I thought SCALA can take care of that and define cell parameters that fit best all data as scalepack does when it considers all separate frames , from all crystals where-as the input to XSCALE is not separate frames but complete datasets). Peter. On Sun, Apr 25, 2010 at 12:14 PM, Frederic VELLIEUX frederic.velli...@orange.fr mailto:frederic.velli...@orange.fr wrote: Hi Phil, Indeed it does, both during integration (INTEGRATE, only if you ask for it with the proper keyword) and in the post-refinement step (CORRECT). Normally this should be quite sufficient. I haven't seen a single case where this was not sufficient. Fred. Message du 25/04/10 09:55 De : Phil Evans A : CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK Copie à : Objet : Re: [ccp4bb] SUMMARY: scala and xds data Just to point out that Scala does not refine cell parameters: I believe XDS does Phil -- Peter
[ccp4bb] staff scientist position at the EMBL in Hamburg, Germany
STAFF SCIENTIST IN BIOLOGICAL X-RAY CRYSTALLOGRAPHY WITH SYNCHROTRON RADIATION European Molecular Biology Laboratory, Hamburg, Germany A position is available at the Structural Biology Unit of the EMBL in Hamburg. The Unit utilises synchrotron radiation at the German Synchrotron Research Centre (DESY) for research in structural biology. EMBL operates synchrotron beamlines at the DORIS-III storage ring (until the end of 2012), which are used by hundreds of external visitors per year as well as local research groups. EMBL is also building an integrated facility for structural biology at the new PETRA III storage ring at DESY, Hamburg, which will include the operation of world-class synchrotron radiation beamlines, providing an ideal research environment for future challenges in structural biology. We are seeking a scientist who will be involved in support of our crystallographic synchrotron beamline facilities initially at DORIS and subsequently at PETRA III. The post holder will be affiliated to the group of Victor Lamzin (http://www.embl-hamburg.de/research/unit/lamzin/index.html) and will be expected to carry out research projects in, e.g.: • Research and technology development for X-ray crystallography • Automation and integration of user-friendly synchrotron radiation data acquisition facilities • Research in structural biology on, e.g. projects of medical relevance, teaming up with ongoing research projects at the EMBL • Collaborations with external research groups on challenging structural biology and technology development projects Applicants should have a PhD in a relevant field, postdoctoral training, significant research accomplishments and expertise in macromolecular crystallography. Excellent communication and social skills and a good command of English are required. An initial contract of 3 years will be offered to the successful candidate. This can be renewed, depending on circumstances at the time of the review. Closing date for applications is 13 June 2010 For further information please look at http://www.embl-hamburg.de/aboutus/jobs/jobs_embl_hamburg/2010/w_10_039/index.html To apply, please email a cover letter, CV (in English) and contact information of three professional references quoting ref. no. W/10/039 in the subject line, to applicat...@embl.de General enquiries may be sent to j...@embl.de
[ccp4bb] beamline technician position at the EMBL in Hamburg, Germany
BEAMLINE TECHNICIAN European Molecular Biology Laboratory, Hamburg, Germany A position is available at the Structural Biology Unit of the EMBL in Hamburg. The Unit utilises synchrotron radiation at the German Synchrotron Research Centre (DESY) for research in structural biology. EMBL operates synchrotron beamlines, which are used by hundreds of external visitors per year as well as local research groups. EMBL is also building an integrated facility for structural biology at the new PETRA III storage ring at DESY, Hamburg, which will include the operation from 2011 of world-class synchrotron radiation beamlines in biological macromolecular crystallography and small angle X-ray scattering, providing an ideal research environment for future challenges in structural biology. The Beamline Technician will be involved in the support of the external visitors at our beamlines in macromolecular crystallography at DORIS and beamlines at PETRA. This includes maintenance and servicing of beamline end-station infrastructure, log-book keeping and direct responsibility for beamline cryogenic equipment. (S)he is expected to actively interact with a broad variety of international visitors and improve the efficiency of the experimental support. The post holder will be expected to take responsibility for the administration of (pre-frozen) crystals shipped to EMBL Hamburg for data collection. The ideal candidate should have a technician or engineering degree in electronics or electro-mechanics, physics technical assistant or a related discipline. Experience in cryogenics, vacuum technology and control electronics is desirable. Skills in Macintosh/PC desktop software are essential; familiarity with control software like LabVIEW, TwinCAD or SPS programming would be an advantage. Knowledge about macromolecular crystallography is a plus. Excellent communication and social skills and a good command of English are required. An initial contract of 3 years will be offered to the successful candidate. This can be renewed, depending on circumstances at the time of the review. Closing date for applications is 13 June 2010 For further information please look at http://www.embl-hamburg.de/aboutus/jobs/jobs_embl_hamburg/2010/w_10_038/index.html To apply, please email a cover letter, CV (in English) and contact information of three professional references quoting ref. no. W/10/038 in the subject line, to applicat...@embl.de General enquiries may be sent to j...@embl.de
Re: [ccp4bb] SUMMARY: scala and xds data
Thank you for enlightening me and sorry for my ignorance, Peter. On Sun, Apr 25, 2010 at 5:33 PM, Frank von Delft frank.vonde...@sgc.ox.ac.uk wrote: Hi, I sense a misunderstanding: Cell parameters are not relevant when scaling together datasets: what matters are intensities and (depending on algorithm) directional cosines and the like. Cell parameters are relevant, along with the other experimental parameters, for knowing where to pick the intensities off the images (integrating). What denzo scalepack do (which I suspect you're referring to) is to split this into separate actions: denzo integrates, and scalepack postrefines, meaning it optimizes the integrated intensities by simultaneously taking into account experimental parameters over whole dataset. Only then does it scale. Xscale and Scala trust the intensities and only scale. Yes, the cell parameters are also an indicator that you may have non-isomorphism, but only that; it's the *intensities* where this is manifested. So you could have different cells yet still perfectly isomorphous intensities; or same cells and terrible non-isomorphism. phx. On 25/04/2010 16:05, Peter Grey wrote: Dear Fred and Phil, However there is no refinement of these parameters in XSCALE so if you need to scale together several crystals (e.g. very small crystals that show severe radiation damage after a few degrees) you end up with a sub-optimal combined dataset after XSCALE. I thought SCALA can take care of that and define cell parameters that fit best all data as scalepack does when it considers all separate frames , from all crystals where-as the input to XSCALE is not separate frames but complete datasets). Peter. On Sun, Apr 25, 2010 at 12:14 PM, Frederic VELLIEUX frederic.velli...@orange.fr wrote: Hi Phil, Indeed it does, both during integration (INTEGRATE, only if you ask for it with the proper keyword) and in the post-refinement step (CORRECT). Normally this should be quite sufficient. I haven't seen a single case where this was not sufficient. Fred. Message du 25/04/10 09:55 De : Phil Evans A : CCP4BB@JISCMAIL.AC.UK Copie à : Objet : Re: [ccp4bb] SUMMARY: scala and xds data Just to point out that Scala does not refine cell parameters: I believe XDS does Phil -- Peter -- Peter
Re: [ccp4bb] programmatic symmetry mate generation
cctbx is cool in principle, but I would be very happy to know how to use it with a pre-existing python like most other packages are capable of. I'm starting to lose patience reverse-engineering the install scripts to figure out how to do it. I can't seem to find instructions on the web page. What am I missing? Is it that I must migrate my entire python environment to cctbx.python? Isn't it better to add cctbx to a current environment rather than the other way around? If every package required the user's migrating his python environment to the package's environment, then we wouldn't be able to use more than one package with a given python install. It seems ridiculous. It doesn't make sense, so I must be missing something fundamental. I think this is the reason I have never used cctbx before. I last tried about 4 years and I thought that it was because the package was immature. James On Apr 24, 2010, at 7:16 PM, Peter Zwart wrote: cctbx? 2010/4/24 James Stroud xtald...@gmail.com: Hello All, I want to programmatically generate the symmetry mates for a molecule and write out the files containing the symmetry related molecules. I'm resisting the urge to reinvent the wheel. What is the best way to do this? I'd prefer to do it within a python program using an open source library, but I'd settle for scripting an external program if that is the only option. James -- - P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -
[ccp4bb] how to model an average of two different amino acids at the same position in a crystal structure
Hi All, I have a structure where electron density shows that the complex crystallized is not in a unique conformation in the crystal lattice. It seems the electron density is an average of two possible orientations of the same complex. Since, the protein is bound to its substrate as a dimer, where the sequence of the two monomers (forming the dimer) is different at only a couple of positions, two different amino acids can be built in the same electron density. For example, serine vs alanine. From our previous experience in crystallizing the same complex, we know that its an averaged density. I am wondering what is the most accurate and acceptable way to represent it in the actual pdb file without complicating the analysis. I am hoping to resolve this issue by getting some inputs from this expert community. Thanks in advance, Best, Seema Mittal Graduate Research Assistant, Department of Biochemistry Molecular Pharmacology, 970L Lazare Research Building, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605
[ccp4bb] Please remove me from this list
Thank you. Best regards, Randy Byrne Malvern Instruments Inc. 117 Flanders Road Westborough, MA 01581-1042 Tel: 508-768-6415 Fax: 508-768-6403 Help Desk: support...@malvern.com http://www.malvern.com Malvern’s web site http://www.malvern.com/malvernmovie An exciting 4 minute overview of Malvern http://www.malvernevents.com Malvern’s Interactive Learning Center __ This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the originator of the message. Any views expressed in this message are those of the individual sender, except where the sender specifies and with authority, states them to be the views of Malvern Instruments. http://www.malvern.com __
Re: [ccp4bb] programmatic symmetry mate generation
Hi James, On Sun, 25 Apr 2010 15:41:32 -0700, James Stroud xtald...@gmail.com wrote: cctbx is cool in principle, but I would be very happy to know how to use it with a pre-existing python like most other packages are capable of. I'm starting to lose patience reverse-engineering the install scripts to figure out how to do it. I can't seem to find instructions on the web page. What am I missing? Is it that I must migrate my entire python environment to cctbx.python? Isn't it better to add cctbx to a current environment rather than the other way around? If every package required the user's migrating his python environment to the package's environment, then we wouldn't be able to use more than one package with a given python install. It seems ridiculous. I don't have a problem doing this (at least with Linux). I simply download the Self-extracting cctbx sources for Unix and put it somewhere appropriate and run the installation command perl cctbx_bundle.selfx. After it finishes installing I modify my login shell script according to the installers instructions. Actually I modify a large setup script that allows me and all the users to set up any particular program. This will add the cctbx/cctbx_build/bin directory to the beginning of the PATH variable. In order for cctbx to work with any python script then I simply add a link in the cctbx/cctbx_build/bin directory so that python points at cctbx.python: i.e. cd cctbx_build/bin ln -s cctbx.python python Any other python scripts that call cctbx then start with #! /usr/bin/env python rather than #! /usr/bin/python In order to have cctbx play nice with PyMOL, then I also install PyMOL from the SVN sources (also not too difficult). Then I make sure that my PyMOL start up script uses python and not /usr/bin/python and then I can use both PyMOL and cctbx with the system's python. Perhaps this still sounds ridiculous to you, but I don't have a problem with it. Once the initial set up is done there isn't much to it. Of course I have left myself little instruction files in my installation directories to remind myself what I need to do. It doesn't make sense, so I must be missing something fundamental. I think this is the reason I have never used cctbx before. I last tried about 4 years and I thought that it was because the package was immature. There is also a new PyMOL script in the PyMOL wiki called supercell http://pymolwiki.org/index.php/Supercell that will build a unit cell, or a block of multiple unit cells. I think this should work in a script to PyMOL, hence not needing the graphics nor any interactive work. I haven't tried it that way, though. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc
Re: [ccp4bb] how to model an average of two different amino acids at the same position in a crystal structure
Hi, I you need to use altLocs to model alternative locations. A good example is this PDB file (of course there are many more in PDB): http://www.rcsb.org/pdb/files/1EJG.pdb see residues #22, 25 etc. Once you have prepared a similar PDB file, phenix.refine will take of the rest automatically. Pavel. On 4/25/10 3:48 PM, Seema Mittal wrote: Hi All, I have a structure where electron density shows that the complex crystallized is not in a unique conformation in the crystal lattice. It seems the electron density is an average of two possible orientations of the same complex. Since, the protein is bound to its substrate as a dimer, where the sequence of the two monomers (forming the dimer) is different at only a couple of positions, two different amino acids can be built in the same electron density. For example, serine vs alanine. From our previous experience in crystallizing the same complex, we know that its an averaged density. I am wondering what is the most accurate and acceptable way to represent it in the actual pdb file without complicating the analysis. I am hoping to resolve this issue by getting some inputs from this expert community. Thanks in advance, Best, Seema Mittal Graduate Research Assistant, Department of Biochemistry Molecular Pharmacology, 970L Lazare Research Building, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605
[ccp4bb] Please remove me from this list
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