Re: [ccp4bb] How to summarize the data statistics (particularly looking for the average Fo_sigma/Fo for each resolution shell)
On Thu, Jul 15, 2010 at 01:02:30AM -0400, Hailiang Zhang wrote: Hi all: Does CCP4 or Phenix provide any utilities which can summarize the data statistics (particularly looking for the average Fo_sigma/Fo for each resolution shell)? Truncate seems to be able to do that but didn't get the desired answer. Any short script will be greatly appreciated! cynical mode If truncate does what you want but does not provide the desired answer it might be your data's fault, not the fault of truncate. /cynical mode Maybe you could explain what exactly you are looking for since you seem to indicate that truncate already does that. If you have access to xprep you can use xprep to get F and F/sigF per resolution shell, even with the shells you want. You can convert the mtz-file to hkl-format with mtz2hkl. Considering that pointless is now the ccp4-equivalent to determine the space group (rather than xprep), pointless might also produce the statistics you are looking for. Cheers, Tim Best Regards, Hailiang -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] How to summarize the data statistics (particularly looking for the average Fo_sigma/Fo for each resolution shell)
Pointless is used before scaling, and this question is asked after scaling, ie it belongs in Scala or [c]truncate in the CCP4 context (at present anyway) Phil On 15 Jul 2010, at 07:29, Tim Gruene wrote: On Thu, Jul 15, 2010 at 01:02:30AM -0400, Hailiang Zhang wrote: Hi all: Does CCP4 or Phenix provide any utilities which can summarize the data statistics (particularly looking for the average Fo_sigma/Fo for each resolution shell)? Truncate seems to be able to do that but didn't get the desired answer. Any short script will be greatly appreciated! cynical mode If truncate does what you want but does not provide the desired answer it might be your data's fault, not the fault of truncate. /cynical mode Maybe you could explain what exactly you are looking for since you seem to indicate that truncate already does that. If you have access to xprep you can use xprep to get F and F/sigF per resolution shell, even with the shells you want. You can convert the mtz-file to hkl-format with mtz2hkl. Considering that pointless is now the ccp4-equivalent to determine the space group (rather than xprep), pointless might also produce the statistics you are looking for. Cheers, Tim Best Regards, Hailiang -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
[ccp4bb] Job posting-Research Fellow
*Research Fellow Position Available* We are currently conducting study on a novel estrogenic compound secreted by a Singapore phytoplankton isolate. Candidates are required to work in the following research activities: 1. Large scale batch culture of chattonella marina 2. Bioassay-guided fractionation and characterization of the novel compound 3. Structural characterization of purified compound E by GCMS, LC-MS/MS, HRMS, 1D 2D NMR 4. Investigate the molecular action of the isolated compound using in vitro and in vivo model. *Qualification:* The prospective candidate should be highly motivated and proactive with a PhD degree or experience in the related field of molecular biology, cellular biology or structural biology. Salary commensurate with experience and qualifications. Interested candidates please send detailed CV by email to: Dr Li Jun / Professor E L Yong Department of Obstetrics Gynaecology Yong Loo Lin School of Medicine National University of Singapore MD Block 11, CRC, #04-16 10 Medical Drive Singapore 119074 Email: ob...@nus.edu.sg Tel: (65) 6516 8175
[ccp4bb] Introducing PDBprints - salient, at-a-glance info about PDB entries
If you were born before the Dutch lost their first World Cup final, you may remember the days when everybody knew that PDB entry 1tim was the structure of chicken triosephosphate isomerase, 1hhb was human haemoglobin, 1lyz was hen egg-white lysozyme, etc. Unfortunately, life for a structural biologist is not that simple any longer. Nevertheless, occasionally it would be very handy to get at-a-glance information about some of the crucial details of a PDB entry or a list of entries. When the Protein Data Bank in Europe (PDBe; pdbe.org) launched its redesigned website recently, we also introduced PDBlogos and PDBprints. PDBlogos are stylised, intuitive icons that convey important information about a PDB entry (e.g., the experimental technique, the source organism of the sample, or the presence of a ligand). PDBprints (short for PDB fingerprints) are collections of PDBlogos displayed in a specific order, where each icon represents a well-defined category of information (and where clicking on any icon will take you to a webpage with more information about that aspect of the PDB entry of interest). PDBprints are used in a number of places already, e.g.: - at the top of PDBe's plain-English summary page for every PDB entry (e.g.: http://pdbe.org/random) - in lists of PDBe database-search results (e.g.: http://pdbe.org/advancedsearch?text=homeobox) - at the top of EDS summary pages (e.g.: http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode=1fcc) A number of other (structural) bioinformatics resources are also considering incorporating PDBprints on their webpages. In fact, they are very easy to include in *any* webpage as evidenced by this page: http://xray.bmc.uu.se/gerard/structures_pdbprints.html For a five-minute illustrated introduction to PDBprints (including instructions on how to include them in your own webpages) point your browser to: http://pdbe.org/pdbprints We hope that you will find PDBprints useful and we value your feedback. --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
Re: [ccp4bb] Introducing PDBprints - salient, at-a-glance info about PDB entries
Gerard DVD Kleywegt wrote: For a five-minute illustrated introduction to PDBprints (including instructions on how to include them in your own webpages) point your browser to: http://pdbe.org/pdbprints Good idea. But the icons for published/unpublished, protein present/protein absent, nucleotide present/nucleotide absent and ligand present/ligand absent look identical to me - I have to read the alt text. Is there some colour thing going on here which is invisible to protanopes? -- EMAIL DISCLAIMER http://www.york.ac.uk/docs/disclaimer/email.htm
Re: [ccp4bb] Introducing PDBprints - salient, at-a-glance info about PDB entries
On Thu, Jul 15, 2010 at 12:20:02PM +0100, Kevin Cowtan wrote: Gerard DVD Kleywegt wrote: For a five-minute illustrated introduction to PDBprints (including instructions on how to include them in your own webpages) point your browser to: http://pdbe.org/pdbprints Good idea. But the icons for published/unpublished, protein present/protein absent, nucleotide present/nucleotide absent and ligand present/ligand absent look identical to me - I have to read the alt text. Is there some colour thing going on here which is invisible to protanopes? Probably: the positive icons are green (#0b6d6d) and the negative ones are grey. Maybe icons which are crossed out might be a better solution for the negative ones. Tim -- EMAIL DISCLAIMER http://www.york.ac.uk/docs/disclaimer/email.htm -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
[ccp4bb] Group leaders IECB 2010 Bordeaux France
Project leader positions at IECB – Bordeaux 2010 Dear Colleagues, Advertisement for opened profiles at IECB, Bordeaux, France. Could you spread this information around and encourage talented young researchers willing to develop innovative projects at the biology-chemistry interface to apply ? Many thanks. Sincerely, Jean-Jacques Toulmé === The European Institute of Chemistry and Biology, “ Institut Européen de Chimie et Biologie ” (IECB) is a research institute sponsored by the University of Bordeaux, CNRS and INSERM. It is located on the University of Bordeaux campus in the Southwest of France. The Institute hosts 17 research groups working at the interface of chemistry and biology in a new building (6000 sq meters) with state of the art equipment and facilities (http://www.iecb.u-bordeaux.fr). The scientific policy of the Institute is under the responsibility of an International Scientific Board in charge of the selection of new group leaders. IECB is recruiting PROJECT LEADERS in - STRUCTURAL BIOLOGY (CRYSTALLOGRAPHY, NMR) We seek biochemists working on structure/function relationship of biological macromolecules or on molecules of biomedical interest in particular in the field of neurobiology. - MOLECULAR MODELLING We seek a molecular modelling chemist with a good practice in proteinligand and protein-protein interactions interested in developing innovative research in biomedically relevant areas including cancer. - BIOINSPIRED NANOTECHNOLOGY We seek a biochemist/biophysicist developing protein/nucleic acid scaffolds, devices of potential interest in the field of technologies for health. - MOLECULAR CELL BIOLOGY We are interested in projects on macromolecules or processes related to cell cycle, gene expression or signal transduction in connection with human pathologies. - BIOLOGICAL CHEMISTRY We seek a chemist to develop a research program aiming at exploring biological processes using the tools of organic synthesis. We are looking for motivated young scientists who will demonstrate a strong potential for the development of an ambitious research programme. The applicants are expected to run independent and creative projects. They should be open to interdisciplinary collaborations with other groups of the Institute. Successful candidates will have access to state of the art facilities in structural biology, chemistry, molecular and cellular biology. The candidates might be asked to apply for startup funding such as ATIP-Avenir Inserm-CNRS programme or ANR support. The applicants should be fluent in English. Knowledge of French would be useful but not mandatory. Applicants are invited to submit -prior to September 20, 2010- a detailed biography together with a research project and a list of potential referees to: Directeur Institut Européen de Chimie et Biologie 2 rue Robert Escarpit 33607 PESSAC Cedex FRANCE email: jean-jacques.tou...@inserm.fr Tel : 33 (0)5 4000 3034 or 2216 Mobile : 33 (0) 6 8038 6230 Fax: 33 (0)5 4000 2215 http://www.iecb.u-bordeaux.fr
Re: [ccp4bb] Introducing PDBprints - salient, at-a-glance info about PDB entries
http://pdbe.org/pdbprints Good idea. But the icons for published/unpublished, protein present/protein absent, nucleotide present/nucleotide absent and ligand present/ligand absent look identical to me - I have to read the alt text. Is there some colour thing going on here which is invisible to protanopes? Thanks. Read The Friendly Manual :-) pdbe.org/pdbprints The default is EMBL green but the icons can also be rendered as transparent images and then whatever colour you set the background to is shown through them. Grey background means absence of feature or information. --Gerard PS: Earlier thoughts of using Brilliant Orange as the default colour were abandoned after the blackest day in Dutch history.
[ccp4bb] Announcement: 2010 Cryo-EM Modelling Challenge and 2011 PSB Workshop
We are pleased to announce the 2010 Cryo-EM Modeling challenge and a PSB 2011 workshop, organized by Steven Ludtke, Wah Chiu, Helen Berman and Gerard Kleywegt. http://ncmi.bcm.edu/challenge * Modeling as a tool for interpretation of cryo-EM reconstructions * Cryo-EM single particle analysis is a method for determining structures of large molecules and macromolecular assemblies at resolutions ranging from 3.5 - 30 A. Interpreting the density maps produced by this technique represents an ongoing challenge, for which molecular modeling techniques offer some unique solutions. Over the last five years, cryo-EM single particle analysis has begun producing structures at resolutions better than 5 A, with subnanometer resolutions becoming common. At resolutions between 5 and 9 A it becomes possible to move beyond simple rigid-body docking and alter atomistic models to reposition helices and sheets, to better fit the cryo-EM based density maps. At 3-5 A resolution de-novo C-alpha traces and in some cases full atomistic models can be constructed directly from the cyro-EM density without invoking x-ray crystallography. We call this a challenge rather than a contest because, unlike CASP, there is no hidden answer to be revealed. In this project, we provide publicly available cryo-EM densities for a selected set of structures at different resolutions, and challenge those in the modeling community to apply their tools to extract as much information as they can from each. At the end, the results will be evaluated by comparing the results of different groups, and validating against any other existing knowledge about each target. We hope this will yield new insights into these published structures, and at the very least, it will establish the capabilities of current modeling methods, and give the cryo-EM community some guidance as to how to proceed with maps in various resolution ranges. For modelers it provides a new area in which to apply/develop their techniques, and demonstrating your tools' capabilities may lead to new opportunities for collaboration. Please see the challenge website for more details.
Re: [ccp4bb] Introducing PDBprints - salient, at-a-glance info about PDB entries
I have trouble distinguishing the green and grey on my MacBook. Herbert, who is colorblind, can just barely distinguish that there are two different colors. Note that 1 of 12 men are colorblind so this is actually quite common. I would suggest using a pale transparent image to suggest absent information. I would have no idea how to change the appearance on my screen and would be afraid to change it in case it affected all my browser use. There is no description of how to change the appearance. And the casual user wouldn't be bothered. - i.e. everyone. The black parts of the logos are hard to see against the dark green background. For published/unpublished why not have two different logos? Perhaps a printed word vs. a handwritten word. Or use the current logo for published and a pen plus sheet of paper, giving the idea of being written or edited, for unpublished. Or you could keep the current logo and include the year of publication in the image, using a ? for unpublished. The general idea is wonderful as there were only a few people who identify all proteins from their entry names back in the days when there were hundreds of entries. By now, I suspect even Jane Richardson doesn't know them all. Frances = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Thu, 15 Jul 2010, Gerard DVD Kleywegt wrote: http://pdbe.org/pdbprints Good idea. But the icons for published/unpublished, protein present/protein absent, nucleotide present/nucleotide absent and ligand present/ligand absent look identical to me - I have to read the alt text. Is there some colour thing going on here which is invisible to protanopes? Thanks. Read The Friendly Manual :-) pdbe.org/pdbprints The default is EMBL green but the icons can also be rendered as transparent images and then whatever colour you set the background to is shown through them. Grey background means absence of feature or information. --Gerard PS: Earlier thoughts of using Brilliant Orange as the default colour were abandoned after the blackest day in Dutch history.
Re: [ccp4bb] metal-chelating affinity chromatography and FosCholine detergents
Dear Pascal, be aware that fos-choline detergents are extremely efficient solubilizers of membrane proteins. We found that even partially aggregated membrane proteins could be solubilized with fos-choline 12, while this fraction did sediment using for example dodecylmaltoside (see e.g. fig5 and sfig2 of PNAS,2008;105(15):5722-7; PMID: 18391190). Thus, it might be that your protein is not expressed in a well-folded state, but that it is (partially) aggregated thereby obscuring the His-tag and preventing binding to the column. To determine whether this is the case you could put a fraction of your high-spin supernatant after solubilization on SEC column and detect the protein by immunoblotting the fractions. If most of the protein elutes in the void this is a strong indication that your protein is not expressed in a good state. Good luck, Eric
[ccp4bb] error on installing arp/warp
Hi all, Something wrong has happened when I install arp/warp7.1 in my CentOS machine. What it told me during the installation is as below: [r...@lenovo6 arp_warp_7.1]# ./install.sh ARP/wARP installer is checking your c-shell... c-shell is installed on your machine at /bin/csh Your login shell is: /bin/bash Checking permissions for /dev/null- OK Checking availability of sed command - OK Checking availability of tail command - OK Checking availability of awk command - OK Checking decimal separator- OK Checking ARP/wARP directory path - OK Checking ARP/wARP directory structure - OK Checking java installation- installed version is 1.6.0 Checking java version number - OK Checking python installation - installed version is 2.4.3 Checking python version number- OK Python executables are available in /local/prog/arp_warp_7.1/byte-code/python-2.4 Checking operating system name- Linux Checking processor type - i686 ARP/wARP version 7.1 executables for this platform are available in /local/prog/arp_warp_7.1/bin/bin-i686-Linux Installing script and data files for: bin-athlon-Linux bin-i386-Darwin bin-i686-Linux bin-ia64-Linux bin-powerpc-Darwin bin-x86_64-Linux Checking CCP4 ARP/wARP installation - OK Checking refmac5 installation - installed version is 5.5.0109 Checking refmac5 version number - OK if: Badly formed number. Has anyone have encountered the same problem and what should I do to solve that completely? Any suggestion will be greatly appreciated. Jian -- Jian Wu Ph.D. Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS) Tel: 0086-21-54921217 Email: prote...@gmail.com
Re: [ccp4bb] Introducing PDBprints - salient, at-a-glance info about PDB entries
On Thu, 15 Jul 2010, Tim Gruene wrote: Maybe icons which are crossed out might be a better solution for the negative ones. The problem with this is that X-RAY crossed out suggests no X-rays, i.e. a non X-ray experiment, not an X-ray experiment for which the structure factors are unavailable. A diagonal crossing out would be fine to negate the protein, DNA/RNA, heterogen and published icons though. I agree with the reservations about the use of the background that Frances has expressed, and think that it would be good to use different shapes for positive/negative icons if possible. Maybe for the experimental technique, a thick underlining or an outline font could be used to distinguish between data present or absent. Apart from this PDBprints is excellent IMO. I find it very useful when scanning down a list of search results. Regards, Peter. -- Peter Keller Tel.: +44 (0)1223 353033 Global Phasing Ltd., Fax.: +44 (0)1223 366889 Sheraton House, Castle Park, Cambridge CB3 0AX United Kingdom
Re: [ccp4bb] Introducing PDBprints - salient, at-a-glance info about PDB entries
Better still, I can let you see them though my eyes. Here's what the icons look like to me, and a link to Vizcheck, the tool I used to generate them: http://www.ysbl.york.ac.uk/~cowtan/colour/pdb/pdb.html http://www.vischeck.com/vischeck/vischeckImage.php Running this in various modes you should be able to pick colours which work for everyone, not just for me. Flip Hoedemaeker wrote: Yep, its green-blue vs grey... Bad choice I guess? Perhaps you can provide a set of examples that work for you? Flip On 7/15/2010 13:20, Kevin Cowtan wrote: Gerard DVD Kleywegt wrote: For a five-minute illustrated introduction to PDBprints (including instructions on how to include them in your own webpages) point your browser to: http://pdbe.org/pdbprints Good idea. But the icons for published/unpublished, protein present/protein absent, nucleotide present/nucleotide absent and ligand present/ligand absent look identical to me - I have to read the alt text. Is there some colour thing going on here which is invisible to protanopes? -- EMAIL DISCLAIMER http://www.york.ac.uk/docs/disclaimer/email.htm
Re: [ccp4bb] Introducing PDBprints - salient, at-a-glance info about PDB entries
There are so many ways to address this issue. Perhaps the simplest would be to use a combination of dimming and thick, solid borders vs. dashed borders to distinguish the two states of the icons. Cheers! MM On Jul 15, 2010, at 9:46 AM, Kevin Cowtan wrote: Better still, I can let you see them though my eyes. Here's what the icons look like to me, and a link to Vizcheck, the tool I used to generate them: http://www.ysbl.york.ac.uk/~cowtan/colour/pdb/pdb.html http://www.vischeck.com/vischeck/vischeckImage.php Running this in various modes you should be able to pick colours which work for everyone, not just for me. Flip Hoedemaeker wrote: Yep, its green-blue vs grey... Bad choice I guess? Perhaps you can provide a set of examples that work for you? Flip On 7/15/2010 13:20, Kevin Cowtan wrote: Gerard DVD Kleywegt wrote: For a five-minute illustrated introduction to PDBprints (including instructions on how to include them in your own webpages) point your browser to: http://pdbe.org/pdbprints Good idea. But the icons for published/unpublished, protein present/protein absent, nucleotide present/nucleotide absent and ligand present/ligand absent look identical to me - I have to read the alt text. Is there some colour thing going on here which is invisible to protanopes? -- EMAIL DISCLAIMER http://www.york.ac.uk/docs/disclaimer/email.htm --- Mischa Machius, PhD Director, Center for Structural Biology Assoc. Professor, Dept. of Pharmacology Member, Lineberger Comprehensive Cancer Center University of North Carolina 4079 Genetic Medicine CB#7365 120 Mason Farm Road Chapel Hill, NC 27599-7365, U.S.A. tel: +1-919-843-4485 fax: +1-919-966-5640 email: mach...@med.unc.edu
Re: [ccp4bb] Introducing PDBprints - salient, at-a-glance info about PDB entries
What would be wrong with WORDS? They were such a clever invention. I can tell the difference between colors, but it takes a second step to figure out what they mean anyway. Why not just write no info over the gray ones? And a 1-word caption on all the little icons would help, IMHO. Phoebe Original message Date: Thu, 15 Jul 2010 09:56:58 -0400 From: Mischa Machius mach...@med.unc.edu Subject: Re: [ccp4bb] Introducing PDBprints - salient, at-a-glance info about PDB entries To: CCP4BB@JISCMAIL.AC.UK There are so many ways to address this issue. Perhaps the simplest would be to use a combination of dimming and thick, solid borders vs. dashed borders to distinguish the two states of the icons. Cheers! MM On Jul 15, 2010, at 9:46 AM, Kevin Cowtan wrote: Better still, I can let you see them though my eyes. Here's what the icons look like to me, and a link to Vizcheck, the tool I used to generate them: http://www.ysbl.york.ac.uk/~cowtan/colour/pdb/pdb.html http://www.vischeck.com/vischeck/vischeckImage.php Running this in various modes you should be able to pick colours which work for everyone, not just for me. Flip Hoedemaeker wrote: Yep, its green-blue vs grey... Bad choice I guess? Perhaps you can provide a set of examples that work for you? Flip On 7/15/2010 13:20, Kevin Cowtan wrote: Gerard DVD Kleywegt wrote: For a five-minute illustrated introduction to PDBprints (including instructions on how to include them in your own webpages) point your browser to: http://pdbe.org/pdbprints Good idea. But the icons for published/unpublished, protein present/protein absent, nucleotide present/nucleotide absent and ligand present/ligand absent look identical to me - I have to read the alt text. Is there some colour thing going on here which is invisible to protanopes? -- EMAIL DISCLAIMER http://www.york.ac.uk/docs/disclaimer/email.htm --- Mischa Machius, PhD Director, Center for Structural Biology Assoc. Professor, Dept. of Pharmacology Member, Lineberger Comprehensive Cancer Center University of North Carolina 4079 Genetic Medicine CB#7365 120 Mason Farm Road Chapel Hill, NC 27599-7365, U.S.A. tel: +1-919-843-4485 fax: +1-919-966-5640 email: mach...@med.unc.edu Phoebe A. Rice Assoc. Prof., Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 RNA is really nifty DNA is over fifty We have put them both in one book Please do take a really good look http://www.rsc.org/shop/books/2008/9780854042722.asp
[ccp4bb] Problem with splitting nucleotides into multiple TLS groups in REFMAC
Hi, I am currently refining some reasonably high (1.4-1.6 Å) resolution protein:RNA complex structures and was trying the approach described in Schwartz et al. Nat. Struct. Biol. 8 (2001) 761-765 where they divided each nucleotide into three TLS groups – the ribose, the phosphorus atom plus both nonesterified oxygens and the base. When I define a tlsin file that does this with the ribose, P OP1 and OP2, and base from 3 successive nucleotides everything seems to work fine so the groups are defined correctly. However when I divide a single nucleotide into 3 TLS groups only the first group has its origin calculated and actually has TLS parameters refined: TLS origin for group1 -3.1622999 -6.9280601 -9.6330261 TLS origin for group2 0.000 0.000 0.000 TLS origin for group3 0.000 0.000 0.000 TLS group1: T tensor ( 1) =0.046 0.115 0.103 -0.003 -0.008 0.087 L tensor ( 1) =1.341 1.887 5.684 0.509 -2.040 -0.436 S tensor ( 1) =0.015 0.015 -0.257 -0.220 -0.024 0.071 0.095 0.060 TLS group2: T tensor ( 2) =0.031 0.031 0.031 0.000 0.000 0.000 L tensor ( 2) =0.000 0.000 0.000 0.000 0.000 0.000 S tensor ( 2) =0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 TLS group3: T tensor ( 3) =0.031 0.031 0.031 0.000 0.000 0.000 L tensor ( 3) =0.000 0.000 0.000 0.000 0.000 0.000 S tensor ( 3) =0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 An excerpt from my tlsin is below: TLS RANGE 'B 3.' 'B 3.' P RANGE 'B 3.' 'B 3.' O1P RANGE 'B 3.' 'B 3.' O2P TLS RANGE 'B 3.' 'B 3.' C1* RANGE 'B 3.' 'B 3.' C2* RANGE 'B 3.' 'B 3.' C3* RANGE 'B 3.' 'B 3.' C4* RANGE 'B 3.' 'B 3.' C5* RANGE 'B 3.' 'B 3.' O2* RANGE 'B 3.' 'B 3.' O3* RANGE 'B 3.' 'B 3.' O4* TLS RANGE 'B 3.' 'B 3.' N1 RANGE 'B 3.' 'B 3.' C2 RANGE 'B 3.' 'B 3.' O2 RANGE 'B 3.' 'B 3.' N3 RANGE 'B 3.' 'B 3.' C4 RANGE 'B 3.' 'B 3.' O4 RANGE 'B 3.' 'B 3.' C5 RANGE 'B 3.' 'B 3.' C6 I guess I've got the syntax of the tlsin file wrong? Any suggestions for what's wrong would be much appreciated! Thanks, Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds
[ccp4bb]
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Re: [ccp4bb] Judging a PDB
Hi Pranjal, you can use POLYGON tool for this: Crystallographic model quality at a glance. L. Urzhumtseva, P. V. Afonine, P. D. Adams, A. Urzhumtsev Acta Cryst. D65, 297-300 (2009) Essentially, what it does is it compares your structure with all similar structures in PDB and gives your the result as a colored picture. What is similar - you define, but the default is good in most cases. It is available as part of Comprehensive Validation module of PHENIX. Pavel. On 7/13/10 5:40 AM, Pranjal Mahanta wrote: Dear Sir, I am sorry, I have a very basic quarry regarding the PDB structures. How one can judge the quality of a deposited PDB data set? Suppose,for e.g., two PDB's have same R-values and have determined at same resolutions with same completeness. Thanking you, Pranjal
[ccp4bb] SAXS on a coiled coil protein
Sorry for a non-ccp4 question. We have determined a structure which is mainly a coiled coil motif. The two helices are from the same protein chain linked by a short turn. However, the SAXS data indicates that this protein is probably natively unfolded or may have very flexible domains and linkers as commented by our collaborators who did the SAXS experiments. Could this be due to the shifting of the turn connecting the two helices? Has this kind of flexibility in the turn position in a coiled coil motif been observed in other coiled coil structures? Thank you Rongjin Guan
Re: [ccp4bb] Problem with splitting nucleotides into multiple TLS groups in REFMAC
Hello Huw, what happens when you remove the period '.' in the residue range description, i.e., replace RANGE 'B 3.' 'B 3.' P with RANGE 'B 3' 'B 3' P ? Tim On Thu, Jul 15, 2010 at 03:54:45PM +0100, Huw Jenkins wrote: Hi, I am currently refining some reasonably high (1.4-1.6 Å) resolution protein:RNA complex structures and was trying the approach described in Schwartz et al. Nat. Struct. Biol. 8 (2001) 761-765 where they divided each nucleotide into three TLS groups – the ribose, the phosphorus atom plus both nonesterified oxygens and the base. When I define a tlsin file that does this with the ribose, P OP1 and OP2, and base from 3 successive nucleotides everything seems to work fine so the groups are defined correctly. However when I divide a single nucleotide into 3 TLS groups only the first group has its origin calculated and actually has TLS parameters refined: TLS origin for group1 -3.1622999 -6.9280601 -9.6330261 TLS origin for group2 0.000 0.000 0.000 TLS origin for group3 0.000 0.000 0.000 TLS group1: T tensor ( 1) =0.046 0.115 0.103 -0.003 -0.008 0.087 L tensor ( 1) =1.341 1.887 5.684 0.509 -2.040 -0.436 S tensor ( 1) =0.015 0.015 -0.257 -0.220 -0.024 0.071 0.095 0.060 TLS group2: T tensor ( 2) =0.031 0.031 0.031 0.000 0.000 0.000 L tensor ( 2) =0.000 0.000 0.000 0.000 0.000 0.000 S tensor ( 2) =0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 TLS group3: T tensor ( 3) =0.031 0.031 0.031 0.000 0.000 0.000 L tensor ( 3) =0.000 0.000 0.000 0.000 0.000 0.000 S tensor ( 3) =0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 An excerpt from my tlsin is below: TLS RANGE 'B 3.' 'B 3.' P RANGE 'B 3.' 'B 3.' O1P RANGE 'B 3.' 'B 3.' O2P TLS RANGE 'B 3.' 'B 3.' C1* RANGE 'B 3.' 'B 3.' C2* RANGE 'B 3.' 'B 3.' C3* RANGE 'B 3.' 'B 3.' C4* RANGE 'B 3.' 'B 3.' C5* RANGE 'B 3.' 'B 3.' O2* RANGE 'B 3.' 'B 3.' O3* RANGE 'B 3.' 'B 3.' O4* TLS RANGE 'B 3.' 'B 3.' N1 RANGE 'B 3.' 'B 3.' C2 RANGE 'B 3.' 'B 3.' O2 RANGE 'B 3.' 'B 3.' N3 RANGE 'B 3.' 'B 3.' C4 RANGE 'B 3.' 'B 3.' O4 RANGE 'B 3.' 'B 3.' C5 RANGE 'B 3.' 'B 3.' C6 I guess I've got the syntax of the tlsin file wrong? Any suggestions for what's wrong would be much appreciated! Thanks, Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
[ccp4bb]
Hammer time? On Jul 15, 2010 4:06 PM, Badyal, Sandip K. (Dr.) sk...@leicester.ac.uk wrote: STOP
Re: [ccp4bb] Problem with splitting nucleotides into multiple TLS groups in REFMAC
Hi, Yes, zero origin is a sure sign that it hasn't identified the atoms in the TLS group. There is presumably some problem matching atom names, but am not sure what. If you send me the files, I can have a play. However, you might have problems with the group definitions anyway. I seem to remember that TLS is not stable for 3 atoms. In any case, you have more TLS parameters (20) than anisotropic parameters (3*6). It does sound like that's what they did in the Nat. Struct. Biol. but they seem to have deposited the pre-TLS coordinates from CNS, so hard to tell. Cheers Martyn On Thu, 2010-07-15 at 15:54 +0100, Huw Jenkins wrote: Hi, I am currently refining some reasonably high (1.4-1.6 Å) resolution protein:RNA complex structures and was trying the approach described in Schwartz et al. Nat. Struct. Biol. 8 (2001) 761-765 where they divided each nucleotide into three TLS groups – the ribose, the phosphorus atom plus both nonesterified oxygens and the base. When I define a tlsin file that does this with the ribose, P OP1 and OP2, and base from 3 successive nucleotides everything seems to work fine so the groups are defined correctly. However when I divide a single nucleotide into 3 TLS groups only the first group has its origin calculated and actually has TLS parameters refined: TLS origin for group1 -3.1622999 -6.9280601 -9.6330261 TLS origin for group2 0.000 0.000 0.000 TLS origin for group3 0.000 0.000 0.000 TLS group1: T tensor ( 1) =0.046 0.115 0.103 -0.003 -0.008 0.087 L tensor ( 1) =1.341 1.887 5.684 0.509 -2.040 -0.436 S tensor ( 1) =0.015 0.015 -0.257 -0.220 -0.024 0.071 0.095 0.060 TLS group2: T tensor ( 2) =0.031 0.031 0.031 0.000 0.000 0.000 L tensor ( 2) =0.000 0.000 0.000 0.000 0.000 0.000 S tensor ( 2) =0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 TLS group3: T tensor ( 3) =0.031 0.031 0.031 0.000 0.000 0.000 L tensor ( 3) =0.000 0.000 0.000 0.000 0.000 0.000 S tensor ( 3) =0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 An excerpt from my tlsin is below: TLS RANGE 'B 3.' 'B 3.' P RANGE 'B 3.' 'B 3.' O1P RANGE 'B 3.' 'B 3.' O2P TLS RANGE 'B 3.' 'B 3.' C1* RANGE 'B 3.' 'B 3.' C2* RANGE 'B 3.' 'B 3.' C3* RANGE 'B 3.' 'B 3.' C4* RANGE 'B 3.' 'B 3.' C5* RANGE 'B 3.' 'B 3.' O2* RANGE 'B 3.' 'B 3.' O3* RANGE 'B 3.' 'B 3.' O4* TLS RANGE 'B 3.' 'B 3.' N1 RANGE 'B 3.' 'B 3.' C2 RANGE 'B 3.' 'B 3.' O2 RANGE 'B 3.' 'B 3.' N3 RANGE 'B 3.' 'B 3.' C4 RANGE 'B 3.' 'B 3.' O4 RANGE 'B 3.' 'B 3.' C5 RANGE 'B 3.' 'B 3.' C6 I guess I've got the syntax of the tlsin file wrong? Any suggestions for what's wrong would be much appreciated! Thanks, Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk* * Fax: +44 1925 603634Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***
Re: [ccp4bb] Problem with splitting nucleotides into multiple TLS groups in REFMAC
On 15 Jul 2010, at 16:24, Tim Gruene wrote: what happens when you remove the period '.' in the residue range description, i.e., replace RANGE 'B 3.' 'B 3.' P with RANGE 'B 3' 'B 3' P No difference unfortunately. Thanks, Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds
Re: [ccp4bb] SAXS on a coiled coil protein
Rongjin, With regards to the SAXS part of post: I'm guessing your collaborators are making this determination from the SAXS data based on a Kratky plot analysis? Given the inherently low resolution of this technique, it may be difficult to assign the profile observed to a specific secondary structure element without more analysis or other data. Is the profile concentration dependent? How well does the profile correlate with the theoretical scattering from your crystal structure? It could be simply that your two helices are not crossing in solution in the conditions tested. Using bead model approach like GASBOR or the EOM approach with your two atomic models of the helical portions linked by beads and modeled against the SAXS data might be very informative (ie: generating an ensemble of shapes and seeing what type of shapes best agree with the data). There's a very active community of small-angle scattering geeks on the forum at www.saxier.org - might be worth posting this question there as well. Cheers, Kushol Kushol Gupta, Ph.D. Research Associate Van Duyne Laboratory - HHMI/Univ. of Pennsylvania School of Medicine BLOCKED::mailto:kgu...@stwing.upenn.edu kgu...@mail.med.upenn.edu 215-573-7260 / 267-259-0082 From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Rongjin Guan Sent: Thursday, July 15, 2010 11:24 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] SAXS on a coiled coil protein Sorry for a non-ccp4 question. We have determined a structure which is mainly a coiled coil motif. The two helices are from the same protein chain linked by a short turn. However, the SAXS data indicates that this protein is probably natively unfolded or may have very flexible domains and linkers as commented by our collaborators who did the SAXS experiments. Could this be due to the shifting of the turn connecting the two helices? Has this kind of flexibility in the turn position in a coiled coil motif been observed in other coiled coil structures? Thank you Rongjin Guan
Re: [ccp4bb] Problem with splitting nucleotides into multiple TLS groups in REFMAC
On 15 Jul 2010, at 16:28, Martyn Winn wrote: Yes, zero origin is a sure sign that it hasn't identified the atoms in the TLS group. There is presumably some problem matching atom names, but am not sure what. If you send me the files, I can have a play. I thought that too but if I change the tlsin to: TLS RANGE 'B 3.' 'B 3.' P RANGE 'B 3.' 'B 3.' O1P RANGE 'B 3.' 'B 3.' O2P TLS RANGE 'B 4.' 'B 4.' C1* RANGE 'B 4.' 'B 4.' C2* RANGE 'B 4.' 'B 4.' C3* RANGE 'B 4.' 'B 4.' C4* RANGE 'B 4.' 'B 4.' C5* RANGE 'B 4.' 'B 4.' O2* RANGE 'B 4.' 'B 4.' O3* RANGE 'B 4.' 'B 4.' O4* TLS RANGE 'B 5.' 'B 5.' N1 RANGE 'B 5.' 'B 5.' C2 RANGE 'B 5.' 'B 5.' O2 RANGE 'B 5.' 'B 5.' N3 RANGE 'B 5.' 'B 5.' C4 RANGE 'B 5.' 'B 5.' O4 RANGE 'B 5.' 'B 5.' C5 RANGE 'B 5.' 'B 5.' C6 It seems to work: TLS origin for group1 -2.2276921 -6.9033170 -8.5974026 TLS origin for group2 -7.7841640 -4.9628205 -12.587447 TLS origin for group3 -13.281846 1.4794188 -10.456101 So it's only when I have 3 groups for the same nucleotide. I'll send the files in a minute. It does sound like that's what they did in the Nat. Struct. Biol. but they seem to have deposited the pre-TLS coordinates from CNS, so hard to tell. I noticed that too - I'm not sure if that's not that the PDB removed/didn't accept the TLS info though - the header for the Howlin et al. RNase A TLS groups for rigid sidechains structure (3RN3) also has no TLS information in. Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds
Re: [ccp4bb] Problem with splitting nucleotides into multiple TLS groups in REFMAC
On Thursday 15 July 2010, Huw Jenkins wrote: Hi, I am currently refining some reasonably high (1.4-1.6 Å) resolution protein:RNA complex structures and was trying the approach described in Schwartz et al. Nat. Struct. Biol. 8 (2001) 761-765 where they divided each nucleotide into three TLS groups – the ribose, the phosphorus atom plus both nonesterified oxygens and the base. Aside from issues of describing the groups at all, I would not recommend this as a refinement protocol. The number of atoms in each group is too small for TLS refinement to be well-behaved in the absence of additional restraints that the current generation of programs (refmac, phenix.refine) does not implement. It is in principle an attractive idea to treat at least the planar bases as individual TLS groups, but I have not had the time or opportunity to explore this in practice. Ideally, one might like to try constraining the group so that the glycosyl bond defined the libration axis (see for instance the section on ADP representations in the Newsletter that Pavel Afonine posted recently). Unfortunately again this is not implemented in current refinement programs. My gut feeling is that the best TLS description would be each base (or base pair) in its own group, the use TLSMD to analyse and assign groups for the backbone atoms. But again I have no actual experience with this, so it's only a suggestion. Ethan Just as an aside: The B factors in the PDB file 1j75, which I think corresponds to the paper you cite, are very far from reasonable. I would not use this structure as an example of success in choosing a refinement protocol for ADPs. Although I also note that it is possible the B factors archived in the PDB file have become mangled during deposition of the output from a non-standard protocol. When I define a tlsin file that does this with the ribose, P OP1 and OP2, and base from 3 successive nucleotides everything seems to work fine so the groups are defined correctly. However when I divide a single nucleotide into 3 TLS groups only the first group has its origin calculated and actually has TLS parameters refined: TLS origin for group1 -3.1622999 -6.9280601 -9.6330261 TLS origin for group2 0.000 0.000 0.000 TLS origin for group3 0.000 0.000 0.000 TLS group1: T tensor ( 1) =0.046 0.115 0.103 -0.003 -0.008 0.087 L tensor ( 1) =1.341 1.887 5.684 0.509 -2.040 -0.436 S tensor ( 1) =0.015 0.015 -0.257 -0.220 -0.024 0.071 0.095 0.060 TLS group2: T tensor ( 2) =0.031 0.031 0.031 0.000 0.000 0.000 L tensor ( 2) =0.000 0.000 0.000 0.000 0.000 0.000 S tensor ( 2) =0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 TLS group3: T tensor ( 3) =0.031 0.031 0.031 0.000 0.000 0.000 L tensor ( 3) =0.000 0.000 0.000 0.000 0.000 0.000 S tensor ( 3) =0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 An excerpt from my tlsin is below: TLS RANGE 'B 3.' 'B 3.' P RANGE 'B 3.' 'B 3.' O1P RANGE 'B 3.' 'B 3.' O2P TLS RANGE 'B 3.' 'B 3.' C1* RANGE 'B 3.' 'B 3.' C2* RANGE 'B 3.' 'B 3.' C3* RANGE 'B 3.' 'B 3.' C4* RANGE 'B 3.' 'B 3.' C5* RANGE 'B 3.' 'B 3.' O2* RANGE 'B 3.' 'B 3.' O3* RANGE 'B 3.' 'B 3.' O4* TLS RANGE 'B 3.' 'B 3.' N1 RANGE 'B 3.' 'B 3.' C2 RANGE 'B 3.' 'B 3.' O2 RANGE 'B 3.' 'B 3.' N3 RANGE 'B 3.' 'B 3.' C4 RANGE 'B 3.' 'B 3.' O4 RANGE 'B 3.' 'B 3.' C5 RANGE 'B 3.' 'B 3.' C6 I guess I've got the syntax of the tlsin file wrong? Any suggestions for what's wrong would be much appreciated! Thanks, Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds
Re: [ccp4bb] Problem with splitting nucleotides into multiple TLS groups in REFMAC
On 15 Jul 2010, at 17:06, Ethan Merritt wrote: My gut feeling is that the best TLS description would be each base (or base pair) in its own group, the use TLSMD to analyse and assign groups for the backbone atoms. But again I have no actual experience with this, so it's only a suggestion. Yes that's exactly what I was using before I found that paper! I think I'll stick with it. Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds
Re: [ccp4bb] Problem with splitting nucleotides into multiple TLS groups in REFMAC
Dear Huw, at 1.4-1.6A resolution I would actually try anisotropic refinement and tighten the restraints a little in case the resolution is not quite high enough. You can do this with refmac5, phenix.refine, and shelxl and you would not have to worry about TLS groups anymore. Cheers, Tim On Thu, Jul 15, 2010 at 05:18:33PM +0100, Huw Jenkins wrote: On 15 Jul 2010, at 17:06, Ethan Merritt wrote: My gut feeling is that the best TLS description would be each base (or base pair) in its own group, the use TLSMD to analyse and assign groups for the backbone atoms. But again I have no actual experience with this, so it's only a suggestion. Yes that's exactly what I was using before I found that paper! I think I'll stick with it. Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] Problem with splitting nucleotides into multiple TLS groups in REFMAC
Refinement with rigid-base TLS parameterization has been previously explored: Holbrook, Dickerson, Kim (1985) Acta Cryst B41, 255-262. (the photocopy is located in the pile of dust that I maintain adjacent to my desk) Ethan Merritt wrote: On Thursday 15 July 2010, Huw Jenkins wrote: Hi, I am currently refining some reasonably high (1.4-1.6 Å) resolution protein:RNA complex structures and was trying the approach described in Schwartz et al. Nat. Struct. Biol. 8 (2001) 761-765 where they divided each nucleotide into three TLS groups – the ribose, the phosphorus atom plus both nonesterified oxygens and the base. Aside from issues of describing the groups at all, I would not recommend this as a refinement protocol. The number of atoms in each group is too small for TLS refinement to be well-behaved in the absence of additional restraints that the current generation of programs (refmac, phenix.refine) does not implement. It is in principle an attractive idea to treat at least the planar bases as individual TLS groups, but I have not had the time or opportunity to explore this in practice. Ideally, one might like to try constraining the group so that the glycosyl bond defined the libration axis (see for instance the section on ADP representations in the Newsletter that Pavel Afonine posted recently). Unfortunately again this is not implemented in current refinement programs. My gut feeling is that the best TLS description would be each base (or base pair) in its own group, the use TLSMD to analyse and assign groups for the backbone atoms. But again I have no actual experience with this, so it's only a suggestion. Ethan Just as an aside: The B factors in the PDB file 1j75, which I think corresponds to the paper you cite, are very far from reasonable. I would not use this structure as an example of success in choosing a refinement protocol for ADPs. Although I also note that it is possible the B factors archived in the PDB file have become mangled during deposition of the output from a non-standard protocol. When I define a tlsin file that does this with the ribose, P OP1 and OP2, and base from 3 successive nucleotides everything seems to work fine so the groups are defined correctly. However when I divide a single nucleotide into 3 TLS groups only the first group has its origin calculated and actually has TLS parameters refined: TLS origin for group1 -3.1622999 -6.9280601 -9.6330261 TLS origin for group2 0.000 0.000 0.000 TLS origin for group3 0.000 0.000 0.000 TLS group1: T tensor ( 1) =0.046 0.115 0.103 -0.003 -0.008 0.087 L tensor ( 1) =1.341 1.887 5.684 0.509 -2.040 -0.436 S tensor ( 1) =0.015 0.015 -0.257 -0.220 -0.024 0.071 0.095 0.060 TLS group2: T tensor ( 2) =0.031 0.031 0.031 0.000 0.000 0.000 L tensor ( 2) =0.000 0.000 0.000 0.000 0.000 0.000 S tensor ( 2) =0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 TLS group3: T tensor ( 3) =0.031 0.031 0.031 0.000 0.000 0.000 L tensor ( 3) =0.000 0.000 0.000 0.000 0.000 0.000 S tensor ( 3) =0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 An excerpt from my tlsin is below: TLS RANGE 'B 3.' 'B 3.' P RANGE 'B 3.' 'B 3.' O1P RANGE 'B 3.' 'B 3.' O2P TLS RANGE 'B 3.' 'B 3.' C1* RANGE 'B 3.' 'B 3.' C2* RANGE 'B 3.' 'B 3.' C3* RANGE 'B 3.' 'B 3.' C4* RANGE 'B 3.' 'B 3.' C5* RANGE 'B 3.' 'B 3.' O2* RANGE 'B 3.' 'B 3.' O3* RANGE 'B 3.' 'B 3.' O4* TLS RANGE 'B 3.' 'B 3.' N1 RANGE 'B 3.' 'B 3.' C2 RANGE 'B 3.' 'B 3.' O2 RANGE 'B 3.' 'B 3.' N3 RANGE 'B 3.' 'B 3.' C4 RANGE 'B 3.' 'B 3.' O4 RANGE 'B 3.' 'B 3.' C5 RANGE 'B 3.' 'B 3.' C6 I guess I've got the syntax of the tlsin file wrong? Any suggestions for what's wrong would be much appreciated! Thanks, Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds
[ccp4bb] anisotropic/isotropic
Dear CCP4bb, Can I refine anisotropic ADPs for macromolecule only, while isotropic ADPs for water, simultaneously in ccp4? I have a 1.1.5 Angs data and when I refine anisotropically the rfactor/rfree difference is 6. Is it true that if I could refine the macromolecule anisotropically and the waters isotropically it would result in better R values? Ivan
Re: [ccp4bb] Problem with splitting nucleotides into multiple TLS groups in REFMAC
On Thursday 15 July 2010 09:18:33 am Huw Jenkins wrote: On 15 Jul 2010, at 17:06, Ethan Merritt wrote: My gut feeling is that the best TLS description would be each base (or base pair) in its own group, then use TLSMD to analyse and assign groups for the backbone atoms. But again I have no actual experience with this, so it's only a suggestion. Yes that's exactly what I was using before I found that paper! I think I'll stick with it. Huw To be clear, if one splits the model into very small TLS groups like this then the idea is to do so _instead_ of refining individual atomic B's. That is, set all the individual Biso terms to a constant and then refine only the TLS descriptions. I call this a pure TLS model. Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] anisotropic/isotropic
But of course. This is what mixed refinement is for - the easiest was to get it to work is probably somehow generating anisou records for all the atoms and then doing something like egrep -v 'ANISOU|HOH' on the pdb file. Mixed refinement will then refine only the atoms with pre-existing anisou records (e.g. non-waters) anisotropically. On Thu, 2010-07-15 at 10:06 -0700, xaravich ivan wrote: Dear CCP4bb, Can I refine anisotropic ADPs for macromolecule only, while isotropic ADPs for water, simultaneously in ccp4? I have a 1.1.5 Angs data and when I refine anisotropically the rfactor/rfree difference is 6. Is it true that if I could refine the macromolecule anisotropically and the waters isotropically it would result in better R values? Ivan -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] anisotropic/isotropic
Thank you guys. I will try and let you know if there is a problem. I realy appreciate your suggestions. Ivan On Thu, Jul 15, 2010 at 10:16 AM, Ed Pozharski epozh...@umaryland.eduwrote: But of course. This is what mixed refinement is for - the easiest was to get it to work is probably somehow generating anisou records for all the atoms and then doing something like egrep -v 'ANISOU|HOH' on the pdb file. Mixed refinement will then refine only the atoms with pre-existing anisou records (e.g. non-waters) anisotropically. On Thu, 2010-07-15 at 10:06 -0700, xaravich ivan wrote: Dear CCP4bb, Can I refine anisotropic ADPs for macromolecule only, while isotropic ADPs for water, simultaneously in ccp4? I have a 1.1.5 Angs data and when I refine anisotropically the rfactor/rfree difference is 6. Is it true that if I could refine the macromolecule anisotropically and the waters isotropically it would result in better R values? Ivan -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] Introducing PDBprints - salient, at-a-glance info about PDB entries
I like the species icon for 2cbr, human crabp in your list http://xray.bmc.uu.se/gerard/structures_pdbprints.html. Is it something from Greek mythology? From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Gerard DVD Kleywegt [ger...@xray.bmc.uu.se] Sent: Thursday, July 15, 2010 4:02 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Introducing PDBprints - salient, at-a-glance info about PDB entries If you were born before the Dutch lost their first World Cup final, you may remember the days when everybody knew that PDB entry 1tim was the structure of chicken triosephosphate isomerase, 1hhb was human haemoglobin, 1lyz was hen egg-white lysozyme, etc. Unfortunately, life for a structural biologist is not that simple any longer. Nevertheless, occasionally it would be very handy to get at-a-glance information about some of the crucial details of a PDB entry or a list of entries. When the Protein Data Bank in Europe (PDBe; pdbe.org) launched its redesigned website recently, we also introduced PDBlogos and PDBprints. PDBlogos are stylised, intuitive icons that convey important information about a PDB entry (e.g., the experimental technique, the source organism of the sample, or the presence of a ligand). PDBprints (short for PDB fingerprints) are collections of PDBlogos displayed in a specific order, where each icon represents a well-defined category of information (and where clicking on any icon will take you to a webpage with more information about that aspect of the PDB entry of interest). PDBprints are used in a number of places already, e.g.: - at the top of PDBe's plain-English summary page for every PDB entry (e.g.: http://pdbe.org/random) - in lists of PDBe database-search results (e.g.: http://pdbe.org/advancedsearch?text=homeobox) - at the top of EDS summary pages (e.g.: http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode=1fcc) A number of other (structural) bioinformatics resources are also considering incorporating PDBprints on their webpages. In fact, they are very easy to include in *any* webpage as evidenced by this page: http://xray.bmc.uu.se/gerard/structures_pdbprints.html For a five-minute illustrated introduction to PDBprints (including instructions on how to include them in your own webpages) point your browser to: http://pdbe.org/pdbprints We hope that you will find PDBprints useful and we value your feedback. --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
Re: [ccp4bb] Introducing PDBprints - salient, at-a-glance info about PDB entries
On Thursday 15 July 2010 11:33:30 am Dunten, Pete W. wrote: I like the species icon for 2cbr, human crabp in your list http://xray.bmc.uu.se/gerard/structures_pdbprints.html. Is it something from Greek mythology? Ah yes, the minotaur genome project. I like the species icons to some extent, but I find it disconcerting to have a mushroom icon represent S. cerevisiae. I find 3328 hits for fungi under taxonomy 2150 for yeast 1875 for saccharomyces and only 202 for basidiomycetes(the heirarchy that includes mushrooms) 50 for mushroom Couldn't we have a beer mug instead? -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
[ccp4bb] waaay off-topic: P-1 pumps
Does anyone know how to disassemble a P-1 peristaltic pump from Pharmacia/Amersham/GE? We have a couple that need simple repairs to either a switch or a rheostat on the control panel, but I'm stumped as to how to actually get the damn thing open. If you've succeeded in doing this, I'd be grateful for any pointers. Pat --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.l...@drexelmed.edu
Re: [ccp4bb] Introducing PDBprints - salient, at-a-glance info about PDB entries
Also road signs can be cleverly replaced inline: attachment.jpeginline: attachment.jpeg On 15/07/2010, at 16.40, Phoebe Rice wrote: What would be wrong with WORDS? They were such a clever invention. I can tell the difference between colors, but it takes a second step to figure out what they mean anyway. Why not just write no info over the gray ones? And a 1-word caption on all the little icons would help, IMHO. Phoebe Original message Date: Thu, 15 Jul 2010 09:56:58 -0400 From: Mischa Machius mach...@med.unc.edu Subject: Re: [ccp4bb] Introducing PDBprints - salient, at-a-glance info about PDB entries To: CCP4BB@JISCMAIL.AC.UK There are so many ways to address this issue. Perhaps the simplest would be to use a combination of dimming and thick, solid borders vs. dashed borders to distinguish the two states of the icons. Cheers! MM On Jul 15, 2010, at 9:46 AM, Kevin Cowtan wrote: Better still, I can let you see them though my eyes. Here's what the icons look like to me, and a link to Vizcheck, the tool I used to generate them: http://www.ysbl.york.ac.uk/~cowtan/colour/pdb/pdb.html http://www.vischeck.com/vischeck/vischeckImage.php Running this in various modes you should be able to pick colours which work for everyone, not just for me. Flip Hoedemaeker wrote: Yep, its green-blue vs grey... Bad choice I guess? Perhaps you can provide a set of examples that work for you? Flip On 7/15/2010 13:20, Kevin Cowtan wrote: Gerard DVD Kleywegt wrote: For a five-minute illustrated introduction to PDBprints (including instructions on how to include them in your own webpages) point your browser to: http://pdbe.org/pdbprints Good idea. But the icons for published/unpublished, protein present/protein absent, nucleotide present/nucleotide absent and ligand present/ligand absent look identical to me - I have to read the alt text. Is there some colour thing going on here which is invisible to protanopes? -- EMAIL DISCLAIMER http://www.york.ac.uk/docs/disclaimer/email.htm --- Mischa Machius, PhD Director, Center for Structural Biology Assoc. Professor, Dept. of Pharmacology Member, Lineberger Comprehensive Cancer Center University of North Carolina 4079 Genetic Medicine CB#7365 120 Mason Farm Road Chapel Hill, NC 27599-7365, U.S.A. tel: +1-919-843-4485 fax: +1-919-966-5640 email: mach...@med.unc.edu Phoebe A. Rice Assoc. Prof., Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 RNA is really nifty DNA is over fifty We have put them both in one book Please do take a really good look http://www.rsc.org/shop/books/2008/9780854042722.asp
[ccp4bb] postdoctoral position at Yale University
Fully funded postdoctoral positions at Yale University School of Medicine are available immediately from highly motivated, enthusiastic individuals with a strong interest in the structure, function, and pharmacology of signaling proteins implicated in neurological and neuropsychiatric diseases. We are presently focusing our efforts on central nervous system transporters using a combination of steady-state kinetics, radioligand binding, and X-ray crystallography. The laboratory is located in newly-renovated space in the Department of Cellular and Molecular Physiology in a highly collaborative environment. We have regular access to a Mosquito crystallization robot, in-house X-ray generator w/ R-axis IV++ detectors, LINUX workstations, and synchrotron beamlines. The lab's proximity to the renowned W.M. Keck facility will additionally enable the successful candidate to conduct detailed experiments in static and dynamic light scattering, isothermal titration calorimetry, steady-state and stopped-flow fluorometry, and surface plasmon resonance. Candidates must hold (or soon expect to hold) a Ph.D. in biochemistry, biophysics, or a related field. A strong background in recombinant DNA methods, protein expression and purification, and X-ray crystallography is required. Prior work with membrane proteins, tissue culture, and functional assays is preferred but not necessary. The ideal candidate will also possess excellent oral and written English communication skills and work well in a collaborative environment. For more information, please contact satinder.k.si...@yale.edu You may also be interested in reading the following review article: Singh, S.K. (2008) LeuT: a prokaryotic stepping stone on the way to a eukaryotic neurotransmitter transporter structure. Channels 2, 380-389 Applicants should send a CV along with a one-page summary of previous research experience and interests and arrange to have 3 reference letters sent to satinder.k.si...@yale.edu - Satinder K. Singh, Ph.D. Assistant Professor Dept. Cellular Molecular Physiology Yale University School of Medicine 333 Cedar Street, SHM B147 Lab room #: SHM BE11/BE17 P.O. Box 208026 New Haven, CT 06520-8026 Office: 203-737-6477 Lab: 203-737-4861 Fax: 203-785-4951 Cell: 612-961-4948 E-mail: satinder.k.si...@yale.edu -
Re: [ccp4bb] Zalman ZM-M215W and ZM-M240W with coot and pymol
On 7/13/10 11:05 AM, Daniel Lietha wrote: Does anyone know if the ZM-M215W and ZM-M240W Zalman monitors work in 3D with Coot and Pymol (would use them on Mac OS10.6)? If so, does the increased resolution improve things compared to the ZM-M220W? Thanks, Daniel Let me bring back to life the thread Daniel started two days ago. Do any of the Zalman monitors related to ZM-M220W work with coot and pymol in stereo mode (for linux)? We are looking for as large a monitor we can buy, and at least one lab member finds it an offense to even consider buying a 22-inch monitor. In the age of huge flat display TVs, it appears that one cannot force others to look at small screens (somehow smartphones are an exception to this). We can definitely use extra space on the monitor when we have all those pymol, coot, ccp4i and phenix GUIs on, but we also want the stereo option possible for that rare event. Thanks, Engin -- Engin Özkan Post-doctoral Scholar Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
Re: [ccp4bb] Zalman ZM-M215W and ZM-M240W with coot and pymol
I find the 22 sufficient if run at highest resolution 1680x1050. If you really need more space get a second one and run the machine in dual mode. I'm waiting for Apple to announce finally the new MacPro's to get one of them. It will be connected to a 24 Cinema Display and a 22 Zalman. Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Jul 15, 2010, at 7:52 PM, Engin Ozkan wrote: On 7/13/10 11:05 AM, Daniel Lietha wrote: Does anyone know if the ZM-M215W and ZM-M240W Zalman monitors work in 3D with Coot and Pymol (would use them on Mac OS10.6)? If so, does the increased resolution improve things compared to the ZM-M220W? Thanks, Daniel Let me bring back to life the thread Daniel started two days ago. Do any of the Zalman monitors related to ZM-M220W work with coot and pymol in stereo mode (for linux)? We are looking for as large a monitor we can buy, and at least one lab member finds it an offense to even consider buying a 22-inch monitor. In the age of huge flat display TVs, it appears that one cannot force others to look at small screens (somehow smartphones are an exception to this). We can definitely use extra space on the monitor when we have all those pymol, coot, ccp4i and phenix GUIs on, but we also want the stereo option possible for that rare event. Thanks, Engin -- Engin Özkan Post-doctoral Scholar Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
