Re: [ccp4bb] Indexing with XDS
Dear Theresa In response to your first question, one way to do this is to look closely at the image (eg changing the contrast level) with the predicted pattern superimposed after indexing, or alternatively just integrate the image and look at the reported mean I/sigmaI as a function of resolution. Both of these are trivially easy to do with iMosflm. You need to remember that any number of issues (eg zingers, hot pixels, ice diffraction) can give rise to what are apparently significant intensity spots, so to distinguish between real diffraction and artifacts you need to look carefully at the spot size and shape as well as its intensity (and whether it is predicted). The other point to bear in mind is that generally there is no problem integrating the images to a resolution a bit beyond where spots are visible, eg to 3.0-3.2Å when spots are only visible to ~3.4-3.5Å and then using the merging or refinement statistics to decide the true resolution of the data. Best wishes, Andrew Leslie On 8 Oct 2012, at 23:36, Theresa Hsu wrote: Dear all I took some images from test crystal and tried to index them to get cell parameters, not enough for structure solution. I can see spots at 3.5 A with ADXV but when I indexed, XDS reports up to 3.0 A in INCLUDE_RESOLUTION_RANGE in XDS_ASCII.HKL. Questions: 1. How do I know that the spot at 3.0 is not background noise? 2. What is the function of FRAME.cbf file? Thank you. Theresa
Re: [ccp4bb] Indexing with XDS
Dear Theresa, concerning your first sentence which is a bit short to my taste: if you index, you expect to find the cell parameters. These enable you to process the dataset. At the end of processing, a decision has to be made about the spacegroup. Only then structure solution can be tried, using the integrated intensities which are merged in the correct spacegroup. If the structure cannot be solved, one reason may be that the spacegroup decision has to be revised. All of these steps are well supported by software, but in specific cases they may nevertheless be difficult. Concerning your second sentence: INCLUDE_RESOLUTION_RANGE is how the user tells XDS about which reflections to include into scaling. It is _not_ something that XDS tells the user! Concerning your questions: 1) inspect the final table in CORRECT.LP which starts with SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE = -3.0 AS FUNCTION OF RESOLUTION. Look at the CC1/2 column. Those resolution shells which have a * after the numeric value still have statistically significant signal, and it makes sense to scale them. 2) FRAME.cbf is produced by COLSPOT and visualizes spot positions that are used for indexing. It is later overwritten by INTEGRATE and visualizes the last frame of the DATA_RANGE, with expected reflection areas superimposed. You should check the agreement of observed and expected (predicted) spots. Hope this helps, Kay On Mon, 8 Oct 2012 23:36:46 +0100, Theresa Hsu theresah...@live.com wrote: Dear all I took some images from test crystal and tried to index them to get cell parameters, not enough for structure solution. I can see spots at 3.5 A with ADXV but when I indexed, XDS reports up to 3.0 A in INCLUDE_RESOLUTION_RANGE in XDS_ASCII.HKL. Questions: 1. How do I know that the spot at 3.0 is not background noise? 2. What is the function of FRAME.cbf file? Thank you. Theresa
[ccp4bb] Only su (root) can get ccp4i to run
Hi folks, on my SL6.3 box, only su (root) can lauch and run ccp4i. For other users I get this cryptic message, /home/prog/ccp4-6.3.0/bin/ccp4i: line 4: /wish: No such file or directory /home/prog/ccp4-6.3.0/bin/ccp4i: line 4: exec: /wish: cannot execute: No such file or directory Anyone out there knows what to do in order to solve this problem ? Ta. F.V. -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494
Re: [ccp4bb] Only su (root) can get ccp4i to run
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear F.V., you should check read permissions of the setup-files (e.g. $CCP4/include/ccp4-setup.sh). For your user, the variable CCP4 seems to be set, but CCP4I_TCLTK is not (which should be done in the same setup-file). Cheers, Tim On 10/09/2012 09:58 AM, vellieux wrote: Hi folks, on my SL6.3 box, only su (root) can lauch and run ccp4i. For other users I get this cryptic message, /home/prog/ccp4-6.3.0/bin/ccp4i: line 4: /wish: No such file or directory /home/prog/ccp4-6.3.0/bin/ccp4i: line 4: exec: /wish: cannot execute: No such file or directory Anyone out there knows what to do in order to solve this problem ? Ta. F.V. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQc90XUxlJ7aRr7hoRAp55AJwPMbK1+aPnh4VbUWKkNuqQ2JBoMgCg/vmr wufUMHQd6kfaOJXzWSWQPzs= =G4O5 -END PGP SIGNATURE-
Re: [ccp4bb] On maps and doubts
This is interesting. In principle m and D should provide an optimum map, and at high resolution they do a reasonable job. The answer about occupancy is a good point. You don't say what resolution your data is at, but maybe it is rather low? I suspect that below ~ 3A the estimates of both m and D are somewhat unreliable - they are fitted to resolution curves and are influenced severely by scaling problems, all of which are more serious at low resolution. What about consulting Garib! He must be near by.. Eleanor On 4 Oct 2012, at 20:17, Israel Sanchez wrote: Hello everyone, I would like to share my experience with one dataset and request some advice on which is the best way to prove a conformational change seen in a density map. The first issue arose when we were looking for an extra ribosomal factor added to a crystalized ribosome. After careful data collection and refinement (I/sigma last shell 1.2, 3.1A and CC1/2 around 22%) the sigma-A-weighted maps 2mFo-DFc and Fo-Fc does not show any clear difference density that we could interpret as the expected factor. Interestingly, a computed map with coefficients 3mFo-2DFc started to show some features that clearly could be explained as a fragment of the factor. The density improved even more with a B-sharpened map. We have seen this behavior before and I was wondering if someone else is using this kind of maps and may could explain the reason behind this density improvement. Is it a crazy idea to go even higher like 4mFo-3DFc? The second query has to do with which is the best way to prove that a conformational change is present in an specific residue (in this case and RNA base) in your structure. To my knowledge, a classic omit map with simulated annealing would do the job regarding removing the model bias. Actually, I found an interesting alternative in PHENIX called a Kick map, were a series of maps computed from a ramdoinised set of models yields a averaged map ideally free from model bias. Does anyone has a preference for any of those schemes? Are there more alternative to prove a conformational change in a model phased with a molecular replacement solution? Thank you very much in advance. -- Israel Sanchez Fernandez PhD Ramakrishnan-lab MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK
Re: [ccp4bb] Only su (root) can get ccp4i to run
Ta very much Tim, what I did was to edit the ccp4.setup-csh file in order to change the line: setenv CCP4I_TCLTK /usr/local/bin into: setenv CCP4I_TCLTK /home/prog/ccp4-6.3.0/bin Then the ccp4i GUI window popped up fine. Problem solved. I didn't really want to have to su every time I wanted to use ccp4 ! F. On 09/10/12 10:15, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear F.V., you should check read permissions of the setup-files (e.g. $CCP4/include/ccp4-setup.sh). For your user, the variable CCP4 seems to be set, but CCP4I_TCLTK is not (which should be done in the same setup-file). Cheers, Tim On 10/09/2012 09:58 AM, vellieux wrote: Hi folks, on my SL6.3 box, only su (root) can lauch and run ccp4i. For other users I get this cryptic message, /home/prog/ccp4-6.3.0/bin/ccp4i: line 4: /wish: No such file or directory /home/prog/ccp4-6.3.0/bin/ccp4i: line 4: exec: /wish: cannot execute: No such file or directory Anyone out there knows what to do in order to solve this problem ? Ta. F.V. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQc90XUxlJ7aRr7hoRAp55AJwPMbK1+aPnh4VbUWKkNuqQ2JBoMgCg/vmr wufUMHQd6kfaOJXzWSWQPzs= =G4O5 -END PGP SIGNATURE- -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494
[ccp4bb] Vacancy at PDBe for an enthusiastic junior annotator
Hi all, The Protein Data Bank in Europe (PDBe; pdbe.org) is looking to recruit an expert structural biologist to join the PDBe curation team at the EBI near Cambridge, UK. Applicants should be computer-literate and possess a recent PhD in some area of structural biology or structural chemistry as well as a broad knowledge in molecular biology or biochemistry. An in-depth knowledge of protein structure (including structure determination, analysis and validation) is essential. A few years of post-doctoral research experience in structural biology, as well as hands-on experience in the determination of protein structure is highly desirable. The ideal candidate will be familiar with Linux/Unix operating systems and molecular graphics software. Basic programming skills, e.g. with Perl, Python or Java, would be an advantage. Given the extensive interactions with colleagues in the PDBe team as well as with international collaborators, depositors and users, excellent written and oral communication skills, fluency in English, ability to work in a team and attention to detail are required. More details and a link to the electronic application procedure can be found here: http://ig14.i-grasp.com/fe/tpl_embl01.asp?s=bkMjPUrEcTFkHhTczjobid=49714,9371342323 Feel free to pass this on to suitable candidates! --Gerard PS: Some hints for prospective applicants: it doesn't hurt to add a nice cover letter in which you explain why you would love to be a PDB annotator and why PDBe strikes you as a brilliant place to work. Also, if you should get invited for an interview and we ask you what the main colour of our website is, please don't answer blue... --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
[ccp4bb] Structure example request for large domain movement in crystallo soaking
Dear CCP4 members, Recently, I got a ligand soaking structure to clearly show a large domain (~100 amino acids) movement compared to the no soaking structure. Although there are some reported examples of this enzyme to suggest the flexibility of this large domain which is relevant to substrate binding. *But it is the first time I can see it happen in crystal soaking procedure.* In this case, I am pleased by this result. My question is, do you have any other example like mine, where domain (or loop) movement is observed *in crystal* during ligand *soaking* procedure? It would be very helpful for me to relate my result to other similar examples. Thank you very much. King regards, Wenhe
Re: [ccp4bb] Structure example request for large domain movement in crystallo soaking
Dear Wenhe, One example we have is the protein kinase Nek2. We co-crystallised with ADP and then soaked in the inhibitors. The activation loop was free to move around and adopt a number of different conformations (e.g. to DFG-out conformation). References: Westwood I, Cheary D-M, Baxter JE, Richards MW, van Montfort R, Fry AM, Bayliss R (2009) Insights into the conformational variability and regulation of human Nek2 kinase. J. Mol. Biol. 386(2):476-85 Whelligan DK, Solanki S, Taylor D, Thomson DW, Cheung K-MJ, Boxall K, Mas-Droux C, Barillari C, Burns S, Grummitt CG, Collins I, van Monfort RLM, Aherne W, Bayliss R, Hoelder S (2010) Aminopyrazine inhibitors binding to an unusual inactive conformation of the mitotic kinase Nek2: SAR and structural characterization. J. Med. Chem. 53(21):7682-98. Solanki S, Innocenti P, Mas-Droux C, Boxall K, Barillari C, van Montfort RLM, Aherne GW, Bayliss R, and Hoelder S (2011) Benzimidazole Inhibitors Induce a DFG-Out Conformation of Never in Mitosis Gene A-Related Kinase 2 (Nek2) without Binding to the Back Pocket and Reveal a Nonlinear Structure−Activity Relationship. J. Med. Chem. 54: 1626-1639 Cheers Richard = Dr Richard Bayliss, Reader in Structural Biology Department of Biochemistry Henry Wellcome Building University of Leicester Lancaster Road, Leicester LE1 9HN Tel: 0116 2297100 Web: http://www2.le.ac.uk/departments/biochemistry/staff/richard-bayliss/research Elite Without Being Elitist Times Higher Awards Winner 2007, 2008, 2009, 2010, 2011 Follow us on Twitter http://twitter.com/uniofleicester On 9 Oct 2012, at 14:33, WENHE ZHONG wrote: Dear CCP4 members, Recently, I got a ligand soaking structure to clearly show a large domain (~100 amino acids) movement compared to the no soaking structure. Although there are some reported examples of this enzyme to suggest the flexibility of this large domain which is relevant to substrate binding. But it is the first time I can see it happen in crystal soaking procedure. In this case, I am pleased by this result. My question is, do you have any other example like mine, where domain (or loop) movement is observed in crystal during ligand soaking procedure? It would be very helpful for me to relate my result to other similar examples. Thank you very much. King regards, Wenhe
Re: [ccp4bb] OFF TOPIC
Hi Rex - You can usually get the three-letter code from the PDB itself. At top of the PDB home page, you can see that one of the options for the search bar is Ligand. If you put in a (mostly) correct name for the ligand, you will get back the three-letter code that the PDB is using. This should match exactly with the Refmac ligand dictionary that Joel mentioned. Another place to look for ligand names is Gerard Kleywegt's HIC-UP site ( http://xray.bmc.uu.se/hicup/ ). I find that their search function isn't so great, so I get the entire 7870-compound list by name here: http://xray.bmc.uu.se/hicup/xname.html and do a text search for something resembling my compound. You can then download coordinates (real and idealized), ligand dictionaries, etc. Furthermore, if the compound you're working with isn't in this list, it's new to the PDB, and you get to give it your own three-letter code! (All the good ones are already taken, unfortunately.) Hope that helps, Matt On 10/7/12 5:43 PM, Joel Tyndall wrote: Hi Rex, In Coot, under the file menu, “Get Fragment” and the type LBT (upper case). This (LBT) is the three letter code for alpha-lactose. Unfortunately it is not that easy to find the codes. However on my windows machine the list is here: C:\CCP4\6.3\lib\data\monomers\list Hope this helps Joel *From:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Rex Palmer *Sent:* Monday, 8 October 2012 9:12 a.m. *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] OFF TOPIC Can anyone please tell me how to extract the pdb for a ligand, eg alpha lactose, from the COOT library, prior to fitting into difference density. Thanks in advance. Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374
Re: [ccp4bb] CCP4 update 6.3.0 006
Dear Ronan et al: I apologize if I have missed it, but is there a simple way to obtain the corresponding changes in the source code for those of us who compile ccp4 ourselves? I looked on the web site and the ftp site but can't seem to find it. Many thanks in advance. Bill On Oct 8, 2012, at 11:20 AM, ronan.kee...@stfc.ac.uk wrote: Dear CCP4 Users, A CCP4 update has just been released, consisting of the following changes: * MrBUMP: model building options added * PISA: new QT interface * AMPLE: bug fixes and expanded interface (Linux and MAC only) * tlsextract: correction of output format which broke parsing of output * DiffractionImage: corrections to reading of pilatus mini-cbf * ccp4i: New AMPLE (Linux and Mac) and MrBUMP interfaces, QT-PISA launcher and bug fixes * crank: bug fix (Windows only) The easiest way to obtain the update is to install the CCP4 update client, if you have not done so already. Note that auto-updates will work correctly only with CCP4 release 6.3.0, therefore upgrade if necessary. Report bugs to c...@stfc.ac.uk. Many thanks for using CCP4, -- Ronan Keegan -- Scanned by iCritical.
Re: [ccp4bb] CCP4 update 6.3.0 006
On 09/10/12 15:09, William G. Scott wrote: Dear Ronan et al: I apologize if I have missed it, but is there a simple way to obtain the corresponding changes in the source code for those of us who compile ccp4 ourselves? I looked on the web site and the ftp site but can't seem to find it. Can I second that as well. Thanks Andrew Many thanks in advance. Bill On Oct 8, 2012, at 11:20 AM, ronan.kee...@stfc.ac.uk wrote: Dear CCP4 Users, A CCP4 update has just been released, consisting of the following changes: * MrBUMP: model building options added * PISA: new QT interface * AMPLE: bug fixes and expanded interface (Linux and MAC only) * tlsextract: correction of output format which broke parsing of output * DiffractionImage: corrections to reading of pilatus mini-cbf * ccp4i: New AMPLE (Linux and Mac) and MrBUMP interfaces, QT-PISA launcher and bug fixes * crank: bug fix (Windows only) The easiest way to obtain the update is to install the CCP4 update client, if you have not done so already. Note that auto-updates will work correctly only with CCP4 release 6.3.0, therefore upgrade if necessary. Report bugs to c...@stfc.ac.uk. Many thanks for using CCP4, -- Ronan Keegan -- Scanned by iCritical. -- -- *Dr. Andrew J. Sharff D.Phil** *Research Scientist / Software Developer Global Phasing Ltd Sheraton House Castle Park Cambridge CB3 0AX UK Tel: +(0)1223 353033 Fax: +(0)1223 366889
Re: [ccp4bb] Structure example request for large domain movement in crystallo soaking
Dear Wenhe, We too have had similar experiences with a couple of other other kinases - CDK2 (PMID: 21291269) and Aurora A (PMID: 22248356), where both soaking and co-crystallization has resulted in large conformational rearrangement. Best wishes, Mat. From: WENHE ZHONG wenhezhong.xmu@gmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, 9 October 2012, 9:33 Subject: [ccp4bb] Structure example request for large domain movement in crystallo soaking Dear CCP4 members, Recently, I got a ligand soaking structure to clearly show a large domain (~100 amino acids) movement compared to the no soaking structure. Although there are some reported examples of this enzyme to suggest the flexibility of this large domain which is relevant to substrate binding. But it is the first time I can see it happen in crystal soaking procedure. In this case, I am pleased by this result. My question is, do you have any other example like mine, where domain (or loop) movement is observed in crystal during ligand soaking procedure? It would be very helpful for me to relate my result to other similar examples. Thank you very much. King regards, Wenhe
Re: [ccp4bb] OFF TOPIC
On 10/7/12 5:43 PM, Joel Tyndall wrote: Hi Rex, In Coot, under the file menu, “Get Fragment” and the type LBT (upper case). Get Monomer..., IIUC. This (LBT) is the three letter code for alpha-lactose. Unfortunately it is not that easy to find the codes. I use Search monomer Library - it does for me. However on my windows machine the list is here: C:\CCP4\6.3\lib\data\monomers\list Hope this helps Joel *From:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Rex Palmer *Sent:* Monday, 8 October 2012 9:12 a.m. *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] OFF TOPIC Can anyone please tell me how to extract the pdb for a ligand, eg alpha lactose, from the COOT library, prior to fitting into difference density. Thanks in advance.
[ccp4bb] Postdoctoral fellow position available
--- Job Available: --- Postdoctoral Fellowship Position in Biochemistry/Structural Biology The research group of Yunsun Nam, Ph.D. at UT Southwestern Medical Center is seeking a postdoctoral fellow with expertise in protein biochemistry. The laboratory is housed in a newly renovated space at the heart of the Cecil H. and Ida Green Center. The overarching goal of our group is to elucidate the mechanistic details of RNA-regulated gene expression. We are particularly interested in the gene regulation pathways relevant to mammalian development and cancer. Postdoctoral fellows will have many opportunities to learn the newest methods in biochemistry and biophysics, in addition to working in an exciting, fast evolving area in the field of biological and biomedical sciences. We use various approaches, including X-ray crystallography, NMR spectroscopy, molecular biology, nucleic acid and protein biochemistry, high throughput sequencing, and eukaryotic cell-based studies. For more information, please refer to the lab website: www.ynamlab.org Candidates must have a Ph.D. degree and a strong background in molecular biology and protein or nucleic acid biochemistry. Experience in structural biology is preferred. Interested individuals must submit a CV including contact information for 3 references, as a single pdf file to: Yunsun.Nam AT UTSouthwestern.edu. *UT Southwestern is an Equal Opportunity/Affirmative Action Employer.
[ccp4bb] Crystallization position available at Bristol-Myers Squibb in Princeton-NJ
(The only way to apply for this position is through BMS HR website http://bms.com/careers/Pages/home.aspx) RESEARCH SCIENTIST Description: As a key member of the Protein Science and Structures team, the successful candidate will be responsible for purification, characterization, and crystallization of recombinant proteins utilizing knowledge of conventional and affinity chromatography methods, gel electrophoresis, crystallization, and general laboratory procedures. As a member of a team involved in the early stages of discovery, the position requires close collaboration with molecular biologists and structural biologists as well as scientists working in the various disease biology and translational areas within preclinical research. The candidate must be self-motivated, possess good communication skills, and work both independently as well as in teams. Personal attributes of integrity and scientific creativity are required. Requirements: * The candidate is required to have experience in protein crystallization and crystal harvesting. * The candidate is also required to have experience in protein purification / characterization as well as a thorough understanding of protein chromatography principles. * Capable of independently designing experiments, generating data and interpreting results * Demonstrated ability to work in a team environment. * Strong, concise, and consistent written and oral communication, including good listening skills, required. * The following skills, while not required, would be a plus o Experience in the use of drop setting robotics and imaging. o Ability to independently troubleshoot purification systems and protocols. o Experience in E. coli fermentation and protein expression. o Experience with data collection, indexing, and processing data. o Familiarity with structure determination methods. BS, MS in Biochemistry, Structural Biology, or related field. 3-10 years of experience. To apply for this position, go online to http://bms.com/careers/Pages/home.aspx and register to view current career openings and apply to Job Number #1202830. Please be aware that you must apply online via our web site to be officially considered an applicant to any Bristol-Myers Squibb job posting. Bristol-Myers Squibb Company is an Equal Opportunity Employer M/F/D/V This message (including any attachments) may contain confidential, proprietary, privileged and/or private information. The information is intended to be for the use of the individual or entity designated above. If you are not the intended recipient of this message, please notify the sender immediately, and delete the message and any attachments. Any disclosure, reproduction, distribution or other use of this message or any attachments by an individual or entity other than the intended recipient is prohibited.
Re: [ccp4bb] Structure example request for large domain movement in crystallo soaking
Depends on what you mean by large, but we saw very obvious domain movement when we soaked a protein (transcription factor TFIIS) into crystals of RNA Polymerase II (PMIDs 12914699/21346759/22726432). We recently animated this conformational change, and you can watch it at: http://www.youtube.com/watch?v=WlMV_l88Lus ...fast forward to about 5 mins 20 second to watch TFIIS binding. And, er, sorry for the shameless plug ;) Alan On 09/10/2012 15:33, WENHE ZHONG wrote: Dear CCP4 members, Recently, I got a ligand soaking structure to clearly show a large domain (~100 amino acids) movement compared to the no soaking structure. Although there are some reported examples of this enzyme to suggest the flexibility of this large domain which is relevant to substrate binding. _But it is the first time I can see it happen in crystal soaking procedure._ In this case, I am pleased by this result. My question is, do you have any other example like mine, where domain (or loop) movement is observed _*in crystal*_ during ligand _*soaking*_ procedure? It would be very helpful for me to relate my result to other similar examples. Thank you very much. King regards, Wenhe -- Alan Cheung Gene Center Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax: +49-89-2180-76999 E-mail: che...@lmb.uni-muenchen.de
Re: [ccp4bb] Only su (root) can get ccp4i to run
On Tue, Oct 09, 2012 at 11:18:29AM +0200, vellieux wrote: Ta very much Tim, what I did was to edit the ccp4.setup-csh file in order to change the line: setenv CCP4I_TCLTK /usr/local/bin into: setenv CCP4I_TCLTK /home/prog/ccp4-6.3.0/bin You may source bin/ccp4.setup-csh instead. In ccp4 6.3.0 setup files are in bin/, these in include/ don't work (unless you edit them). Sorry for confusion. Marcin -- Scanned by iCritical.
Re: [ccp4bb] CCP4 update 6.3.0 006
Dear Bill, You have not missed anything, we do not have a mechanism for delivering source code *updates* in automatic fashion as yet. Our statistics shows that source code distributions make only 2-3% of binary downloads, therefore, I hope that you would understand that we have to prioritise our efforts. CCP4 is currently in transitional state regarding its repository system and build mechanism, so that not everything is in due shape, and I apologise for any inconvenience this is causing to you. Current source codes are available from FusionForge at http://fg.oisin.rc-harwell.ac.uk just choose Project-Project List-Project Name (e.g. sfcheck) - SCM and a checkout command will be on the screen. These are our new repositories, but we have not finished migration to them yet. Codes that you do not see on FusionForge, are still available from CVS: http://www.ccp4.ac.uk/cvs We do realise that checking out sources and building them on client's side may be a non-trivial task to do. In order to help that, we are developing a completely new build system, which allows one to automatically check out CCP4 components and build them individually or all at once with a single command. This is meant to be our build system for next release (hopefully), and, in fact, Windows part of 6.3.0 was actually built with it. I would like to encourage you to have a look at http://devtools.fg.oisin.rc-harwell.ac.uk which is a not-so-long instruction on how to use the new system. It can be used right away to build current source codes, so that you do not have to browse the repositories. We would be highly appreciative if you give it a try and communicate your feedback to us. As I mentioned, things are currently being shaped, and we are prepared to have any suggestions. Please do not put it away if it does not work for you for any reason, and speak to us instead. Responsible people, who are to be contacted for feedback/clarification/help: New build system: Marcin Wojdyr at marcin.woj...@stfc.ac.uk New repositories: Charles Ballard at charles.ball...@stfc.ac.uk and/or Ville Uski at ville.u...@stfc.ac.uk I hope that this clarifies the issue, but let me know if it does not. Best regards, Eugene On 9 Oct 2012, at 15:09, William G. Scott wrote: Dear Ronan et al: I apologize if I have missed it, but is there a simple way to obtain the corresponding changes in the source code for those of us who compile ccp4 ourselves? I looked on the web site and the ftp site but can't seem to find it. Many thanks in advance. Bill On Oct 8, 2012, at 11:20 AM, ronan.kee...@stfc.ac.uk wrote: Dear CCP4 Users, A CCP4 update has just been released, consisting of the following changes: *MrBUMP: model building options added *PISA: new QT interface *AMPLE: bug fixes and expanded interface (Linux and MAC only) *tlsextract: correction of output format which broke parsing of output *DiffractionImage: corrections to reading of pilatus mini-cbf *ccp4i: New AMPLE (Linux and Mac) and MrBUMP interfaces, QT-PISA launcher and bug fixes *crank: bug fix (Windows only) The easiest way to obtain the update is to install the CCP4 update client, if you have not done so already. Note that auto-updates will work correctly only with CCP4 release 6.3.0, therefore upgrade if necessary. Report bugs to c...@stfc.ac.uk. Many thanks for using CCP4, -- Ronan Keegan -- Scanned by iCritical. -- Scanned by iCritical.
Re: [ccp4bb] Structure example request for large domain movement in crystallo soaking
I saw also a great domain (around 150aa) movement on one of the subunits when crystals of the protein (yeast acetylglutamate kinase) were soaked with its inhibitor (arginine): http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0034734 2012/10/9 Alan Cheung che...@lmb.uni-muenchen.de Depends on what you mean by large, but we saw very obvious domain movement when we soaked a protein (transcription factor TFIIS) into crystals of RNA Polymerase II (PMIDs 12914699/21346759/22726432). We recently animated this conformational change, and you can watch it at: http://www.youtube.com/watch?**v=WlMV_l88Lushttp://www.youtube.com/watch?v=WlMV_l88Lus ...fast forward to about 5 mins 20 second to watch TFIIS binding. And, er, sorry for the shameless plug ;) Alan On 09/10/2012 15:33, WENHE ZHONG wrote: Dear CCP4 members, Recently, I got a ligand soaking structure to clearly show a large domain (~100 amino acids) movement compared to the no soaking structure. Although there are some reported examples of this enzyme to suggest the flexibility of this large domain which is relevant to substrate binding. _But it is the first time I can see it happen in crystal soaking procedure._ In this case, I am pleased by this result. My question is, do you have any other example like mine, where domain (or loop) movement is observed _*in crystal*_ during ligand _*soaking*_ procedure? It would be very helpful for me to relate my result to other similar examples. Thank you very much. King regards, Wenhe -- Alan Cheung Gene Center Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax: +49-89-2180-76999 E-mail: che...@lmb.uni-muenchen.de
