Re: [ccp4bb] Scaling question
Check your mosflm input file. If this is an ADSC type detector and you have specified that it is (using DETECTOR TYPE ADSC or SCANNER TYPE ADSC), but have not explicitly specified the overload limit with OVERLOAD CUTOFF, then the default overload cutoff for integration will be 100,000, and this effectively turns off overload detection. Note that there are TWO different overload cutoffs in mosflm, but both are listed in the log next to the string (CUTOFF). I only discovered this myself a few weeks ago, and I have patched the current Elves release: http://bl831.als.lbl.gov/~jamesh/elves/download.html to avoid this problem when they run mosflm, but versions from the last two years may actually miss overloads! -James Holton MAD Scientist Simon Kolstoe wrote: Thanks Tim, Phil and Andrew for your answers. Just one further related question: Why is it that mosflm seems to report higher completeness than XDS on the same data (I've seen this on about 50 datasets)? I always thought it was due to mosflms peak extrapolation but it seems this isn't the answer if SCALA throws those reflections out. Thanks, Simon On 7 Jun 2010, at 15:35, Phil Evans wrote: Mosflm integrates them (profile-fitted overloads) but flags them. Pointless uses them for systematic absence tests. Scala by default ignores them, but you can include them if you want: this is not normally recommended since they are pretty inaccurate (look in the Excluded data tab of ccp4i/Scala) If you are merging strong weak datasets it should do the right thing, I think. Phil On 7 Jun 2010, at 15:09, Simon Kolstoe wrote: Dear CCP4bb, I was wondering if someone could tell me how mosflm and scala deal with overloaded reflections. From my understanding mosflm extrapolates the overloaded peaks but then scala throws them out completely - is this right? If so am I right to not worry about contamination from extrapolated peaks when combining high and low resolution datasets from the same crystal? Thanks Simon
Re: [ccp4bb] Anisotropic Diffraction Examples
The H+-ATPase from A. thaliana had anisotropic diffraction (ca. 3.6/5.5Å). This could be explained by the crystal packing and more specifically the detergent micelles in the packing. See: Pedersen BP, Buch-Pedersen MJ, Morth JP, Palmgren MG, Nissen P. Crystal structure of the plasma membrane proton pump. Nature 450, pp. -4, (2007). Pedersen BP, Morth JP, Nissen P. Structure determination using poorly diffracting membrane protein crystals - Lessons from the H+ and Na+,K+-ATPases. Acta Cryst D, 66, pp. 309-313, (2010). -Bjørn On 2010-06-08 16:38, Matthias Zebisch wrote: Dear everybody! I am currently having an issue with anisotropic diffraction and would like to cite some references. I am sure there are plenty of examples outthere. So, if you are having an own published example at hand, can you please send me the reference and maybe the diffraction limits along good and bad directions as well? Thank you a lot, Matthias
[ccp4bb] Where to find novelty of PDBids?
Hi, for an analysis I need the sequence identity of any PDBid to its closest match in the PDB *at the time it was deposited*. It seems like something somebody would have done before; any thoughts where to find it? Cheers phx
Re: [ccp4bb] Scaling question
Hi I'd be somewhat surprised if this accounted for the difference since it would require the routine collection of many overloads in each dataset before you'd notice that the completion was higher systematically. (The two different cutoffs that James refers to are the absolute cutoff (where reflections aren't integrated) and the profile-fitting cutoff (which is used if you want to profile fit overloads).) Since we've had automatic detector recognition since 2002, and have deprecated the use of the DETECTOR (or SCANNER) keyword unless you have an unusual set-up since then, most people should never come across this as a problem even if they write their own scripts. James does make a good point though - if you use the DETECTOR TYPE keywords, you also need to provide other keywords to make sure the processing proceeds according to expectations! I think you'd need more information on where the extra reflections are, or if they are strong/weak/etc as Phil suggested, before pointing the finger in any particular direction. I replied to Simon yesterday privately with the following - I seem to remember something like this when we started looking at Pilatus images a few years ago, but I didn't do the processing myself so can't be sure about it. In principle, if the rejection and acceptance criteria are the same, then the two programs (and d*Trek and HKL...) should report the same completeness and the same overall stats, once you take into account the different ways the various merging Rs are calculated. I'm always pleased when people give Mosflm a good report, but I don't think there's a huge difference in the data coming out of the different programs. Occasionally, we do find a dataset where one program is better than the others (I put this down to the particular dataset being similar to one that the developer used). However, from memory I think XDS has rather stricter rejection criteria by default - and this gives lower completeness, multiplicity and merging Rs (if you merge fewer bad equivalents you get lower R factors). When we ran tests using Mosflm to reject similarly bad reflections from a high quality dataset, we got similar completeness and merging Rs - but this is entirely artificial. I *think* it comes down to whichever program you're most used to running, and the one you know how to get the best out of. I'm sure that you will get replies from people saying that XDS (or whatever program) always gives higher completeness etc than Mosflm! On 9 Jun 2010, at 07:57, James Holton wrote: Check your mosflm input file. If this is an ADSC type detector and you have specified that it is (using DETECTOR TYPE ADSC or SCANNER TYPE ADSC), but have not explicitly specified the overload limit with OVERLOAD CUTOFF, then the default overload cutoff for integration will be 100,000, and this effectively turns off overload detection. Note that there are TWO different overload cutoffs in mosflm, but both are listed in the log next to the string (CUTOFF). I only discovered this myself a few weeks ago, and I have patched the current Elves release: http://bl831.als.lbl.gov/~jamesh/elves/download.html to avoid this problem when they run mosflm, but versions from the last two years may actually miss overloads! -James Holton MAD Scientist Simon Kolstoe wrote: Thanks Tim, Phil and Andrew for your answers. Just one further related question: Why is it that mosflm seems to report higher completeness than XDS on the same data (I've seen this on about 50 datasets)? I always thought it was due to mosflms peak extrapolation but it seems this isn't the answer if SCALA throws those reflections out. Thanks, Simon On 7 Jun 2010, at 15:35, Phil Evans wrote: Mosflm integrates them (profile-fitted overloads) but flags them. Pointless uses them for systematic absence tests. Scala by default ignores them, but you can include them if you want: this is not normally recommended since they are pretty inaccurate (look in the Excluded data tab of ccp4i/Scala) If you are merging strong weak datasets it should do the right thing, I think. Phil On 7 Jun 2010, at 15:09, Simon Kolstoe wrote: Dear CCP4bb, I was wondering if someone could tell me how mosflm and scala deal with overloaded reflections. From my understanding mosflm extrapolates the overloaded peaks but then scala throws them out completely - is this right? If so am I right to not worry about contamination from extrapolated peaks when combining high and low resolution datasets from the same crystal? Thanks Simon Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] JLigand Coot link
Also, if you happen to use refmac for refinement: it rewrites LINK records as LINKRs in the output pdb file -- and LINKR records are unknown to Coot... JED. -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 15 Stanhope Gate, London W1K 1LN. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Paul Emsley Sent: 08 June 2010 21:30 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] JLigand Coot link Briefly (and top-postingly), Coot does not draw covalent bonds between non-tandem residues. Coot will represent LINK records if they are in the PDB file. Coot will respect the links generated by JLigand if you try to do sphere refinement. The Coot -- JLigand internface will improve in the not too distant future. Paul. From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Tim Gruene [...@shelx.uni-ac.gwdg.de] Sent: 08 June 2010 21:04 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] JLigand Coot link Hi Sean, do the ligand and the Thr belong to the same chain, and did you check that the distance between the bonding atoms is not beyond coot's cut-off? Tim On Tue, Jun 08, 2010 at 11:16:03AM -0700, Sean Gay wrote: I have used JLigand v 0.2.1 to create a link between a Thr residues and a covalent adduct. The adduct refines well and shows up as a covalent bond in PyMOL. However, when I'm in Coot there is no bond present between the Thr OG1 and the ligand. I've loaded the Jligand link.lib file that I created and the cif for the ligand itself into Coot. Any ideas how to fix this? -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
[ccp4bb] sketcher
Hello, Could you please help me with the sketcher? I'm trying to use ccp4 sketcher to generate a new ligand and then complex it with a protein in coot. I've drawn the ligand, numbered each atom and defined each bond type. Then I ran save file, create library description. The pdb file was loaded to coot and worked fine. Then I imported cif file. However, when I tried to refine the ligand, a message popped out, saying 'No restrains'. I double checked the numbering, I think it's Ok. Did I do anything wrong? I'm really struggling on this. If you need more information, please let me know. Thanks very much. Best regards, Yahui
Re: [ccp4bb] JLigand Coot link
This is a REAL PAIN Paul! Eleanor Debreczeni, Judit wrote: Also, if you happen to use refmac for refinement: it rewrites LINK records as LINKRs in the output pdb file -- and LINKR records are unknown to Coot... JED. -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 15 Stanhope Gate, London W1K 1LN. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Paul Emsley Sent: 08 June 2010 21:30 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] JLigand Coot link Briefly (and top-postingly), Coot does not draw covalent bonds between non-tandem residues. Coot will represent LINK records if they are in the PDB file. Coot will respect the links generated by JLigand if you try to do sphere refinement. The Coot -- JLigand internface will improve in the not too distant future. Paul. From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Tim Gruene [...@shelx.uni-ac.gwdg.de] Sent: 08 June 2010 21:04 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] JLigand Coot link Hi Sean, do the ligand and the Thr belong to the same chain, and did you check that the distance between the bonding atoms is not beyond coot's cut-off? Tim On Tue, Jun 08, 2010 at 11:16:03AM -0700, Sean Gay wrote: I have used JLigand v 0.2.1 to create a link between a Thr residues and a covalent adduct. The adduct refines well and shows up as a covalent bond in PyMOL. However, when I'm in Coot there is no bond present between the Thr OG1 and the ligand. I've loaded the Jligand link.lib file that I created and the cif for the ligand itself into Coot. Any ideas how to fix this? -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Re: [ccp4bb] sketcher
Can you send your fragment of the pdb containing the ligand, and the cif file? Eleanor Yahui Yan wrote: Hello, Could you please help me with the sketcher? I'm trying to use ccp4 sketcher to generate a new ligand and then complex it with a protein in coot. I've drawn the ligand, numbered each atom and defined each bond type. Then I ran save file, create library description. The pdb file was loaded to coot and worked fine. Then I imported cif file. However, when I tried to refine the ligand, a message popped out, saying 'No restrains'. I double checked the numbering, I think it's Ok. Did I do anything wrong? I'm really struggling on this. If you need more information, please let me know. Thanks very much. Best regards, Yahui
Re: [ccp4bb] JLigand Coot link
LINKR is not part of the PDB format: http://www.wwpdb.org/documentation/format23/sect6.html It's also not supported by MMDB, for that reason. I think Eugene put in some stuff to store remarks, but I don't know if unrecognized keywords are also stored (Eugene?). So there's a problem here, and the right way to solve it is not immediately obvious. Since coot is used with both refmac and phenix.refine, the obvious question to ask is how are links handled in phenix? Eleanor Dodson wrote: This is a REAL PAIN Paul! Eleanor Debreczeni, Judit wrote: Also, if you happen to use refmac for refinement: it rewrites LINK records as LINKRs in the output pdb file -- and LINKR records are unknown to Coot... JED. -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 15 Stanhope Gate, London W1K 1LN. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Paul Emsley Sent: 08 June 2010 21:30 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] JLigand Coot link Briefly (and top-postingly), Coot does not draw covalent bonds between non-tandem residues. Coot will represent LINK records if they are in the PDB file. Coot will respect the links generated by JLigand if you try to do sphere refinement. The Coot -- JLigand internface will improve in the not too distant future. Paul. From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Tim Gruene [...@shelx.uni-ac.gwdg.de] Sent: 08 June 2010 21:04 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] JLigand Coot link Hi Sean, do the ligand and the Thr belong to the same chain, and did you check that the distance between the bonding atoms is not beyond coot's cut-off? Tim On Tue, Jun 08, 2010 at 11:16:03AM -0700, Sean Gay wrote: I have used JLigand v 0.2.1 to create a link between a Thr residues and a covalent adduct. The adduct refines well and shows up as a covalent bond in PyMOL. However, when I'm in Coot there is no bond present between the Thr OG1 and the ligand. I've loaded the Jligand link.lib file that I created and the cif for the ligand itself into Coot. Any ideas how to fix this? -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -- EMAIL DISCLAIMER http://www.york.ac.uk/docs/disclaimer/email.htm
Re: [ccp4bb] dissolving peptides !
Rashmi, To facilitate dissolution of a peptide we found ultrasound (in glass, plastics absorb much of the energy) useful. It might be also helpful to warm the solution mildly. Frank
[ccp4bb] CCP4
Hi Yahui! I am having this problem as well again and agin. Most problematic is it, if you have non-standard atoms in your compound. I don't really know whrere the problem lies, but here is what I do: Do not use sketcher! Simply generate your ligand using coot by placing atoms into the density (you may start from standard compounds if available). Save your ligand in a pdb file and make sure (text editor), that all atoms belong to the same compound indicated by the same 3 letter identfier (e.g. LIG). Merge this PDB file with your protein in Coot and save. Run Refmac. Refmac will abort but before stopping it will put out a library file with recommended bonds and angles and so on. This file you should manually edit putting in your chemical knowlege of the ligand. Use this cif file in a second run for refmac and for all coot real space refinements. Have fun, Matthias PS: sometimes (no non-standard atoms) a simpler way is to leave the field Regularize with Refmac unchecked, when you create your final library file. Am 6/9/2010 12:23 PM, schrieb Yahui Yan: Hello, Could you please help me with the sketcher? I'm trying to use ccp4 sketcher to generate a new ligand and then complex it with a protein in coot. I've drawn the ligand, numbered each atom and defined each bond type. Then I ran save file, create library description. The pdb file was loaded to coot and worked fine. Then I imported cif file. However, when I tried to refine the ligand, a message popped out, saying 'No restrains'. I double checked the numbering, I think it's Ok. Did I do anything wrong? I'm really struggling on this. If you need more information, please let me know. Thanks very much. Best regards, Yahui -- Dr. Matthias Zebisch Universität Leipzig Biotechnologisch-Biomedizinisches Zentrum Strukturanalytik von Biopolymeren Deutscher Platz 5 04103 Leipzig Germany Phone: 0049-341-97-31323 (lab) -31312 (office) Fax : 0049-341-97-31319 email: matthias.zebi...@bbz.uni-leipzig.de
Re: [ccp4bb] sketcher
Hi Yahui! I am having this problem as well again and agin. Most problematic is it, if you have non-standard atoms in your compound. I don't really know whrere the problem lies, but here is what I do: Do not use sketcher! Simply generate your ligand using coot by placing atoms into the density (you may start from standard compounds if available). Save your ligand in a pdb file and make sure (text editor), that all atoms belong to the same compound indicated by the same 3 letter identfier (e.g. LIG). Merge this PDB file with your protein in Coot and save. Run Refmac. Refmac will abort but before stopping it will put out a library file with recommended bonds and angles and so on. This file you should manually edit putting in your chemical knowlege of the ligand. Use this cif file in a second run for refmac and for all coot real space refinements. Have fun, Matthias PS: sometimes (no non-standard atoms) a simpler way is to leave the field Regularize with Refmac unchecked, when you create your final library file. Am 6/9/2010 12:23 PM, schrieb Yahui Yan: Hello, Could you please help me with the sketcher? I'm trying to use ccp4 sketcher to generate a new ligand and then complex it with a protein in coot. I've drawn the ligand, numbered each atom and defined each bond type. Then I ran save file, create library description. The pdb file was loaded to coot and worked fine. Then I imported cif file. However, when I tried to refine the ligand, a message popped out, saying 'No restrains'. I double checked the numbering, I think it's Ok. Did I do anything wrong? I'm really struggling on this. If you need more information, please let me know. Thanks very much. Best regards, Yahui -- Dr. Matthias Zebisch Universität Leipzig Biotechnologisch-Biomedizinisches Zentrum Strukturanalytik von Biopolymeren Deutscher Platz 5 04103 Leipzig Germany Phone: 0049-341-97-31323 (lab) -31312 (office) Fax : 0049-341-97-31319 email: matthias.zebi...@bbz.uni-leipzig.de
Re: [ccp4bb] sketcher
Perhaps you could try to use JLigand. It may do a better job. it is available from: www.ysbl.york.ac.uk/mxstat/ In the jligand session there are two tutorials also. they may help you to run and generate your ligand description. If any problem please let me know. In general refmac is not the best way of generating ligand. In any case you have to check you ligand after it has been generated. One tiny electron or proton can change chemistry completely. regards Garib On 9 Jun 2010, at 12:23, Matthias Zebisch wrote: Hi Yahui! I am having this problem as well again and agin. Most problematic is it, if you have non-standard atoms in your compound. I don't really know whrere the problem lies, but here is what I do: Do not use sketcher! Simply generate your ligand using coot by placing atoms into the density (you may start from standard compounds if available). Save your ligand in a pdb file and make sure (text editor), that all atoms belong to the same compound indicated by the same 3 letter identfier (e.g. LIG). Merge this PDB file with your protein in Coot and save. Run Refmac. Refmac will abort but before stopping it will put out a library file with recommended bonds and angles and so on. This file you should manually edit putting in your chemical knowlege of the ligand. Use this cif file in a second run for refmac and for all coot real space refinements. Have fun, Matthias PS: sometimes (no non-standard atoms) a simpler way is to leave the field Regularize with Refmac unchecked, when you create your final library file. Am 6/9/2010 12:23 PM, schrieb Yahui Yan: Hello, Could you please help me with the sketcher? I'm trying to use ccp4 sketcher to generate a new ligand and then complex it with a protein in coot. I've drawn the ligand, numbered each atom and defined each bond type. Then I ran save file, create library description. The pdb file was loaded to coot and worked fine. Then I imported cif file. However, when I tried to refine the ligand, a message popped out, saying 'No restrains'. I double checked the numbering, I think it's Ok. Did I do anything wrong? I'm really struggling on this. If you need more information, please let me know. Thanks very much. Best regards, Yahui -- Dr. Matthias Zebisch Universität Leipzig Biotechnologisch-Biomedizinisches Zentrum Strukturanalytik von Biopolymeren Deutscher Platz 5 04103 Leipzig Germany Phone: 0049-341-97-31323 (lab) -31312 (office) Fax : 0049-341-97-31319 email: matthias.zebi...@bbz.uni-leipzig.de
Re: [ccp4bb] JLigand Coot link
In the latest, latest version refmac writes LINK instead of LINKR. It is a temporary solution. We need a better solution and hopefully we will have one soon This version of refmac is available from: www.ysbl.york.ac.uk/refmac/data/refmac_experimental/ regards Garib P.S. This version also has some low resolution refinement tools On 9 Jun 2010, at 11:22, Debreczeni, Judit wrote: Also, if you happen to use refmac for refinement: it rewrites LINK records as LINKRs in the output pdb file -- and LINKR records are unknown to Coot... JED. -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 15 Stanhope Gate, London W1K 1LN. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Paul Emsley Sent: 08 June 2010 21:30 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] JLigand Coot link Briefly (and top-postingly), Coot does not draw covalent bonds between non-tandem residues. Coot will represent LINK records if they are in the PDB file. Coot will respect the links generated by JLigand if you try to do sphere refinement. The Coot -- JLigand internface will improve in the not too distant future. Paul. From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Tim Gruene [...@shelx.uni-ac.gwdg.de] Sent: 08 June 2010 21:04 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] JLigand Coot link Hi Sean, do the ligand and the Thr belong to the same chain, and did you check that the distance between the bonding atoms is not beyond coot's cut-off? Tim On Tue, Jun 08, 2010 at 11:16:03AM -0700, Sean Gay wrote: I have used JLigand v 0.2.1 to create a link between a Thr residues and a covalent adduct. The adduct refines well and shows up as a covalent bond in PyMOL. However, when I'm in Coot there is no bond present between the Thr OG1 and the ligand. I've loaded the Jligand link.lib file that I created and the cif for the ligand itself into Coot. Any ideas how to fix this? -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
[ccp4bb] common protein crystallization contaminants
Dear All, I was wondering if anyone has compiled a list of common proteins that can co-purify from E. coli preps (and yeast etc), and crystallize instead of the protein of interest. If list members send me individual examples I will compile a summary for the bulletin board. best wishes James -- Dr. James W. Murray David Phillips Research Fellow Division on Molecular Biosciences Imperial College, LONDON Tel: +44 (0)20 759 48895
[ccp4bb] Anisotropic data and an extremely long c axis
Hi, I also have a question concerning anisotropic data. Collected a data set and the best crystal gave highly anisotropic diffraction patterns ( 3.7 A - 5.8 A). So my first question is how to handle these data. I got only experience with normal data using the ccp4 suite. Are there any program specially for these kind of data? There are? The second question is how anisotropic data occur? The protein I work with has a tetragonal sg with a=b= 86.0 and an extremely long c axis of 651 A. Secondary Structure prediction suggest a lot of beta strands. How can I explain the anisotropy (for my own interest and my thesis)? Thank you very much. Marie
Re: [ccp4bb] common protein crystallization contaminants
On 9 Jun 2010, at 12:54, Murray, James W wrote: I was wondering if anyone has compiled a list of common proteins that can co-purify from E. coli preps (and yeast etc), and crystallize instead of the protein of interest. If list members send me individual examples I will compile a summary for the bulletin board. Biochim Biophys Acta. 2006 Sep;1760(9):1304-13. Structural analysis and classification of native proteins from E. coli commonly co-purified by immobilised metal affinity chromatography. Bolanos-Garcia VM, Davies OR. (the first hit on google for common proteins that can co-purify from E. coli and crystallize) is a good start. There's also: Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Oct 1;64(Pt 10):880-5. There is a baby in the bath water: AcrB contamination is a major problem in membrane-protein crystallization. Veesler D, Blangy S, Cambillau C, Sciara G. Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds
Re: [ccp4bb] JLigand Coot link
But does it follow the PDB format for LINK records; it is a disaster if the LINK read from the PDB have a different definition and information content than LINK records output from REFMAC. At least LINKR is a flagged non-standard record. Eleanor Garib Murshudov wrote: In the latest, latest version refmac writes LINK instead of LINKR. It is a temporary solution. We need a better solution and hopefully we will have one soon This version of refmac is available from: www.ysbl.york.ac.uk/refmac/data/refmac_experimental/ regards Garib P.S. This version also has some low resolution refinement tools On 9 Jun 2010, at 11:22, Debreczeni, Judit wrote: Also, if you happen to use refmac for refinement: it rewrites LINK records as LINKRs in the output pdb file -- and LINKR records are unknown to Coot... JED. -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 15 Stanhope Gate, London W1K 1LN. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Paul Emsley Sent: 08 June 2010 21:30 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] JLigand Coot link Briefly (and top-postingly), Coot does not draw covalent bonds between non-tandem residues. Coot will represent LINK records if they are in the PDB file. Coot will respect the links generated by JLigand if you try to do sphere refinement. The Coot -- JLigand internface will improve in the not too distant future. Paul. From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Tim Gruene [...@shelx.uni-ac.gwdg.de] Sent: 08 June 2010 21:04 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] JLigand Coot link Hi Sean, do the ligand and the Thr belong to the same chain, and did you check that the distance between the bonding atoms is not beyond coot's cut-off? Tim On Tue, Jun 08, 2010 at 11:16:03AM -0700, Sean Gay wrote: I have used JLigand v 0.2.1 to create a link between a Thr residues and a covalent adduct. The adduct refines well and shows up as a covalent bond in PyMOL. However, when I'm in Coot there is no bond present between the Thr OG1 and the ligand. I've loaded the Jligand link.lib file that I created and the cif for the ligand itself into Coot. Any ideas how to fix this? -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Re: [ccp4bb] Anisotropic data and an extremely long c axis
A first concern with that extreme anisotropy is at the integration and scaling stages. Large swaths of your detector are empty of reflections, but they will still bias the way reference profiles are calculated at integration; while the lots of reflections with intensities around 0 (but with significant sigmas) will bias the statistics for scaling the real reflections (real as in having intensity). You are better off excluding all the parts of the detector that do not contain significant intensities (and taking a hit in completeness) than trying to correct for all the 0 intensities. While the optimum would be to limit integration to an elliptical area of the detector containing the significant intensities, I am not aware of any program that can do this elegantly. In my experience, the strong data almost always end in the horizontal direction of the detector. And in many cases, the significant area while really elliptical, can be approximated to a rectangle, with the long edges horizontal. In that case, a simple trick is to use the excluded areas in the integration programs to limit integration to your rectangle. In Denzo I usually did this by playing with the detector distance, so that the diffraction ends at the edges of the detector, effectively setting the 2 short sides of our rectangle, and set the long edges of the rectangle with the excluded rectangle and excluded circle options (a circle of very large radius centered way out of the detector can be an excellent approximation to a straight line for cutting purposes). I am sure most programs will allow for equivalent ways of limiting integration to a rectangle. Once you have an mtz file with intensities, the UCLA anisotropy correction server can be a great help too. Marie Lacroix lacroix.ma...@rocketmail.com wrote: Hi, I also have a question concerning anisotropic data. Collected a data set and the best crystal gave highly anisotropic diffraction patterns ( 3.7 A - 5.8 A). So my first question is how to handle these data. I got only experience with normal data using the ccp4 suite. Are there any program specially for these kind of data? There are? The second question is how anisotropic data occur? The protein I work with has a tetragonal sg with a=b= 86.0 and an extremely long c axis of 651 A. Secondary Structure prediction suggest a lot of beta strands. How can I explain the anisotropy (for my own interest and my thesis)? Thank you very much. Marie -- *** Jose Antonio Cuesta-Seijo Biophysical Chemistry Group Department of Chemistry University of Copenhagen Tlf: +45-35320261 Universitetsparken 5 DK-2100 Copenhagen, Denmark ***
Re: [ccp4bb] Anisotropic data and an extremely long c axis
Anisotropy in the diffraction pattern could simply be due to the shape of the crystals. The intensity of diffraction is a function of the volume of diffracting matter that is hit by the X-ray beam. Think for example of a thin plate crystal, which you rotate in the X-ray beam. When the plate is perpendicular to the X-ray beam, the volume of matter hit by the X-rays is much smaller than when the plate is parallel to the X-ray beam. When processing data using XDS, at the integration level (INTEGRATE) there is for each frame a single scale factor that is reported (I cannot tell you what the INTEGRATE.LP file says exactly - I am sitting at a conference where I cannot access my data files at home), but you can follow the increase/decrease in intensity of diffraction (and thus the volume of diffracting matter in the X-ray beam) by following the variation of these scale factors. Otherwise, sometimes (once the structure is solved) it is possible, 'a posteriori', to give a plausible explanation to such an anisotropy. For example, by noticing anisotropic crystal contacts (e.g. multiple contacts along two directions, and very few crystal forming contacts with plenty of solvent in the third direction). HTH, Fred. Message du 09/06/10 14:33 De : Marie Lacroix A : CCP4BB@JISCMAIL.AC.UK Copie à : Objet : [ccp4bb] Anisotropic data and an extremely long c axis Hi, I also have a question concerning anisotropic data. Collected a data set and the best crystal gave highly anisotropic diffraction patterns ( 3.7 A - 5.8 A). So my first question is how to handle these data. I got only experience with normal data using the ccp4 suite. Are there any program specially for these kind of data? There are? The second question is how anisotropic data occur? The protein I work with has a tetragonal sg with a=b= 86.0 and an extremely long c axis of 651 A. Secondary Structure prediction suggest a lot of beta strands. How can I explain the anisotropy (for my own interest and my thesis)? Thank you very much. Marie
Re: [ccp4bb] sketcher
Hello Garib, I just tried JLigand. It's amazing. I opened the pdb file which was made by sketcher and save lib file and coordinate file. Then load these files to coot. Everything works fine now. I think I need to double check the ligand as you advised. Thanks a lot to you all. Regards, Yahui On Wed, Jun 9, 2010 at 12:28 PM, Garib Murshudov ga...@ysbl.york.ac.ukwrote: Perhaps you could try to use JLigand. It may do a better job. it is available from: www.ysbl.york.ac.uk/mxstat/ In the jligand session there are two tutorials also. they may help you to run and generate your ligand description. If any problem please let me know. In general refmac is not the best way of generating ligand. In any case you have to check you ligand after it has been generated. One tiny electron or proton can change chemistry completely. regards Garib On 9 Jun 2010, at 12:23, Matthias Zebisch wrote: Hi Yahui! I am having this problem as well again and agin. Most problematic is it, if you have non-standard atoms in your compound. I don't really know whrere the problem lies, but here is what I do: Do not use sketcher! Simply generate your ligand using coot by placing atoms into the density (you may start from standard compounds if available). Save your ligand in a pdb file and make sure (text editor), that all atoms belong to the same compound indicated by the same 3 letter identfier (e.g. LIG). Merge this PDB file with your protein in Coot and save. Run Refmac. Refmac will abort but before stopping it will put out a library file with recommended bonds and angles and so on. This file you should manually edit putting in your chemical knowlege of the ligand. Use this cif file in a second run for refmac and for all coot real space refinements. Have fun, Matthias PS: sometimes (no non-standard atoms) a simpler way is to leave the field Regularize with Refmac unchecked, when you create your final library file. Am 6/9/2010 12:23 PM, schrieb Yahui Yan: Hello, Could you please help me with the sketcher? I'm trying to use ccp4 sketcher to generate a new ligand and then complex it with a protein in coot. I've drawn the ligand, numbered each atom and defined each bond type. Then I ran save file, create library description. The pdb file was loaded to coot and worked fine. Then I imported cif file. However, when I tried to refine the ligand, a message popped out, saying 'No restrains'. I double checked the numbering, I think it's Ok. Did I do anything wrong? I'm really struggling on this. If you need more information, please let me know. Thanks very much. Best regards, Yahui -- Dr. Matthias Zebisch Universität Leipzig Biotechnologisch-Biomedizinisches Zentrum Strukturanalytik von Biopolymeren Deutscher Platz 5 04103 Leipzig Germany Phone: 0049-341-97-31323 (lab) -31312 (office) Fax : 0049-341-97-31319 email: matthias.zebi...@bbz.uni-leipzig.de
[ccp4bb] Univ California boycott of Nature publishing group
Although Bill his as a the return address to his message, it seems to me to be of considerable relevance to the crystallographic community as a whole. My recent experience representing the ACA on the AIP Governing Board and Executive Committee provided considerable introduction into many of the issues facing publishers. Some of these are generic and have to do with the corporatization of increasing portions of human activity. Others are reminiscent of the behavior of BP in the Louisiana Gulf. Still others are spin-offs of the aggressive (and I believe ill-advised) actions of the NIH to enforce Open Access unilaterally, by diluting the responsibility for compliance to the maximum extent (ie., to individual authors) by using the power to fund as a threat in enforcing submission of approved manuscripts to PubMed Central. In short, nobody looks very good from my perspective. The promise of widespread and instant access to publicly-funded information is experiencing serious growing pains, and many kinks have yet to be worked out of the system. I know that publishers are facing serious repercussions from the fact that neither quality peer review nor is cost have factored constructively into the NIH decisions. I am reminded by NPG's actions in California of the recent State School Board actions in Texas regarding the teaching of both evolution and history. It shares with Texas School Board action that it focuses on a large enough market share to aim at a tipping point. If the NPG initiative succeeds in California, it will pave the way to similar increases to all state institutions. This is clearly a tactical device to strengthen the position of NPG among publishers, as budgets will not allow continuation of Nature subscriptions without eliminating subscriptions to other journals, journals which I in fact read more assiduously than I do Nature publications. The consequence will be to the serious detriment of scientific integrity everywhere. I urge all who read Bill's message to consider carefully the long-term consequences of letting Nature win this one. I have no assurance that my action was the right one, but I similarly have no doubt that for me joining the boycott was the only acceptable action for me. Charlie Begin forwarded message: From: Charles W. Carter, Jr car...@med.unc.edu Date: June 9, 2010 9:02:35 AM EDT To: William G. Scott wgsc...@chemistry.ucsc.edu Subject: Re: [ccp4bb] Off-topic: Univ California boycott of Nature publishing group Bill, I was shocked by this news. I am in full agreement with the content of the letter. I have had disagreements with the NPG editorial policies over the years, during which time they have published junk over my objections as a reviewer, so I am already disposed to be hostile to the major publishing interests, including Nature and Science. I have just sent this message to an editor at Nature to whom I had promised a review: Rachel, I have just learned of an effort by Nature Publishing Group to increase subscriptions to Nature Journals four-fold to the University of California library systems. This is unconscionable. The UC library system has suggested that all UC faculty cease to peer review documents for Nature publishing group journals. I have decided to join this boycott, because I strongly believe that the Nature action cannot be left unchallenged. Please take me off your list of reviewers. This refusal to review is also retrospective. I will therefore not be sending you my review of the manuscript by (deleted). I hope that you will relay this action to your superiors. Charlie Carter On Jun 9, 2010, at 12:50 AM, William G. Scott wrote: Hi folks: Sorry about the off-topic nature (so to speak) of this post, especially given that it is not yet Friday, but I am interested what our community thinks of this: http://library.ucsc.edu/sites/default/files/Nature_Faculty_Letter.pdf Something similar happened with UC and Cell Press a few years ago. I worry about the monopolistic tendencies of these journals, but I also worry about the consequences of trying to restrict faculty, students, postdocs, etc from publishing where they see fit. (Admittedly our department already holds it against you if you publish in Nature, so this may be a bit of a moot point.) At the very least, it should be amusing to watch the two beasts do battle. Well? -- Bill
Re: [ccp4bb] Anisotropic data and an extremely long c axis
Hi Many years ago I coded up integration using anisotropic resolution limits for Mosflm - it seemed to work well, but the refinement programs available at the time really didn't like huge regions of reciprocal space having no data in them - they preferred to have measurements there with sigmas, even if the measurements were just background. I thought my implementation was rather elegant, since it integrated a rather nicely formed ellipsoidal region of reciprocal space. So although the code is still there, and it still works, I don't make a big deal about it. If the refinement programs are happy to deal with the unmeasured data (in the directions where the crystal doesn't diffract so well), I'm happy to put the effort in to resurrect it. As for how the anisotropy occurs, there are a few good reasons; as Fred said, the illuminated volume of the crystal can contribute. I think another point is that there is no reason why (for a non-cubic crystal) the order in the crystal should be isotropic; for example, if you have molecules that are approximate prolate spheroids (think rugby ball, or football for our American readers), they can obviously pack better with their long axes aligned, but the orientation about that long axis can be rather less well defined. The diffraction is a reflection (ahem) of the internal order... Hi, I also have a question concerning anisotropic data. Collected a data set and the best crystal gave highly anisotropic diffraction patterns ( 3.7 A - 5.8 A). So my first question is how to handle these data. I got only experience with normal data using the ccp4 suite. Are there any program specially for these kind of data? There are? The second question is how anisotropic data occur? The protein I work with has a tetragonal sg with a=b= 86.0 and an extremely long c axis of 651 A. Secondary Structure prediction suggest a lot of beta strands. How can I explain the anisotropy (for my own interest and my thesis)? Thank you very much. Marie Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] Anisotropic data and an extremely long c axis
Dear Marie, I believe that the first of Fred's explanations can mostly be corrected for by scaling (and it could partly be overcome by longer exposure times as long as radiation damage does not kick in). In your case, where one cell axis is about 10x as long as the other two, Fred's second explanation is probably the real cause of anisotropy: the unit cells would have to be in proper order in the c-direction over 10x the range compared to a/b in order to reach the same resolution. Tim On Wed, Jun 09, 2010 at 12:22:59PM +, Marie Lacroix wrote: Hi, I also have a question concerning anisotropic data. Collected a data set and the best crystal gave highly anisotropic diffraction patterns ( 3.7 A - 5.8 A). So my first question is how to handle these data. I got only experience with normal data using the ccp4 suite. Are there any program specially for these kind of data? There are? The second question is how anisotropic data occur? The protein I work with has a tetragonal sg with a=b= 86.0 and an extremely long c axis of 651 A. Secondary Structure prediction suggest a lot of beta strands. How can I explain the anisotropy (for my own interest and my thesis)? Thank you very much. Marie -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] CCP4
I suggest using the PRODRG Server: http://davapc1.bioch.dundee.ac.uk/prodrg/ On Wed, Jun 9, 2010 at 7:22 AM, Matthias Zebisch matthias.zebi...@bbz.uni-leipzig.de wrote: Hi Yahui! I am having this problem as well again and agin. Most problematic is it, if you have non-standard atoms in your compound. I don't really know whrere the problem lies, but here is what I do: Do not use sketcher! Simply generate your ligand using coot by placing atoms into the density (you may start from standard compounds if available). Save your ligand in a pdb file and make sure (text editor), that all atoms belong to the same compound indicated by the same 3 letter identfier (e.g. LIG). Merge this PDB file with your protein in Coot and save. Run Refmac. Refmac will abort but before stopping it will put out a library file with recommended bonds and angles and so on. This file you should manually edit putting in your chemical knowlege of the ligand. Use this cif file in a second run for refmac and for all coot real space refinements. Have fun, Matthias PS: sometimes (no non-standard atoms) a simpler way is to leave the field Regularize with Refmac unchecked, when you create your final library file. Am 6/9/2010 12:23 PM, schrieb Yahui Yan: Hello, Could you please help me with the sketcher? I'm trying to use ccp4 sketcher to generate a new ligand and then complex it with a protein in coot. I've drawn the ligand, numbered each atom and defined each bond type. Then I ran save file, create library description. The pdb file was loaded to coot and worked fine. Then I imported cif file. However, when I tried to refine the ligand, a message popped out, saying 'No restrains'. I double checked the numbering, I think it's Ok. Did I do anything wrong? I'm really struggling on this. If you need more information, please let me know. Thanks very much. Best regards, Yahui -- Dr. Matthias Zebisch Universität Leipzig Biotechnologisch-Biomedizinisches Zentrum Strukturanalytik von Biopolymeren Deutscher Platz 5 04103 Leipzig Germany Phone: 0049-341-97-31323 (lab) -31312 (office) Fax : 0049-341-97-31319 email: matthias.zebi...@bbz.uni-leipzig.de -- Jim Fairman, Ph D. Post-Doctoral Fellow National Institutes of Health - NIDDK Cell: 1-865-748-8672 Lab: 1-301-594-9229 E-mail: fairman@gmail.com james.fair...@nih.gov
Re: [ccp4bb] AW: AW: AW: [ccp4bb] Anisotropic data and an extremely long c axis
I guess then Fred's reply part one explains everything :-) 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/http://web.me.com/bosch_lab/ On Jun 9, 2010, at 10:48 AM, Marie Lacroix wrote: Yes, I just checked this. Von: Bosch, Juergen jubo...@jhsph.edumailto:jubo...@jhsph.edu An: Marie Lacroix lacroix.ma...@rocketmail.commailto:lacroix.ma...@rocketmail.com Gesendet: Mittwoch, den 9. Juni 2010, 16:01:56 Uhr Betreff: Re: AW: AW: [ccp4bb] Anisotropic data and an extremely long c axis Does this coincide with the direction of better diffraction ? 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/http://web.me.com/bosch_lab/ On Jun 9, 2010, at 9:38 AM, Marie Lacroix wrote: The crystal dimensions are 275 x 150 x 100 µm. So in one dimension they are bigger. Von: Bosch, Juergen jubo...@jhsph.edumailto:jubo...@jhsph.edu An: Marie Lacroix lacroix.ma...@rocketmail.commailto:lacroix.ma...@rocketmail.com Gesendet: Mittwoch, den 9. Juni 2010, 15:24:51 Uhr Betreff: Re: AW: [ccp4bb] Anisotropic data and an extremely long c axis but thicker in one dimension ? 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/http://web.me.com/bosch_lab/ On Jun 9, 2010, at 8:41 AM, Marie Lacroix wrote: No, they are really large and beautiful 3D crystals. Von: Jürgen Bosch jubo...@jhsph.edumailto:jubo...@jhsph.edu An: Marie Lacroix lacroix.ma...@rocketmail.commailto:lacroix.ma...@rocketmail.com Gesendet: Mittwoch, den 9. Juni 2010, 14:38:37 Uhr Betreff: Re: [ccp4bb] Anisotropic data and an extremely long c axis Flat crystals ? Is the high resolution diffraction because you are shooting through more crystal volume ? Just a thought 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 Jun 9, 2010, at 8:22, Marie Lacroix lacroix.ma...@rocketmail.commailto:lacroix.ma...@rocketmail.com wrote: Hi, I also have a question concerning anisotropic data. Collected a data set and the best crystal gave highly anisotropic diffraction patterns ( 3.7 A - 5.8 A). So my first question is how to handle these data. I got only experience with normal data using the ccp4 suite. Are there any program specially for these kind of data? There are? The second question is how anisotropic data occur? The protein I work with has a tetragonal sg with a=b= 86.0 and an extremely long c axis of 651 A. Secondary Structure prediction suggest a lot of beta strands. How can I explain the anisotropy (for my own interest and my thesis)? Thank you very much. Marie
[ccp4bb]
NIH funded Postdoctoral Fellowship, structural biology Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke (NINDS) Location: NIH Main Campus Start Date: position available immediately Postdoctoral positions are available in the Cell Biology and Biophysics Unit headed by Dr. Antonina Roll-Mecak at the National Institute of Neurological Disorders and Stroke. The Roll-Mecak lab is interested in understanding the interplay between microtubules and their regulators and how tubulin post-translational modifications tune the behavior of motors and microtubule associated proteins (see for instance Roll-Mecak, A. and Vale, R.D. 2008. Nature, 451(7176):363-7; Roll-Mecak, A. and McNally, F.J. 2010. Curr. Opin. Cell Biol., 22(1):96-103). We use a combination of biochemistry, structural biology, cell biology and single-molecule fluorescence techniques. Thus, a postdoctoral fellow in the lab would have the opportunity to move between these techniques and build upon an already strong background in structural biology. Our lab is located in the Porter Center for Neuroscience on the NIH main campus in Bethesda. The NIH has a long tradition of research excellence in cytoskeletal biology and offers a stimulating environment for postdoctoral fellows interested in interdisciplinary training in biophysics and cell biology. The research facilities at NIH are outstanding and the lab has access to state-of-the-art equipment such as crystallization robots, liquid handling systems, TIRF and confocal microscopes. For more information, please visit: http://intra.ninds.nih.gov/rm_lab/ The position will be fully funded by the NIH. We are looking for candidates who wish to work on structural biology problems related to microtubule cytoskeleton dynamics regulation and have a strong background in X-ray crystallography, protein overexpression and purification. Other details: Candidates should preferably have less than 3 years of postdoctoral experience and a strong publication record. Please send a CV, a one-page research experience summary, and contact information of three references to anton...@mail.nih.gov Please write “Postdoctoral application” in the subject header.
[ccp4bb] postdoctoral position
NIH funded Postdoctoral Fellowship, structural biology Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke (NINDS) Location: NIH Main Campus Start Date: position available immediately Postdoctoral positions are available in the Cell Biology and Biophysics Unit headed by Dr. Antonina Roll-Mecak at the National Institute of Neurological Disorders and Stroke. The Roll-Mecak lab is interested in understanding the interplay between microtubules and their regulators and how tubulin post-translational modifications tune the behavior of motors and microtubule associated proteins (see for instance Roll-Mecak, A. and Vale, R.D. 2008. Nature, 451(7176):363-7; Roll-Mecak, A. and McNally, F.J. 2010. Curr. Opin. Cell Biol., 22(1):96-103). We use a combination of biochemistry, structural biology, cell biology and single-molecule fluorescence techniques. Thus, a postdoctoral fellow in the lab would have the opportunity to move between these techniques and build upon an already strong background in structural biology. Our lab is located in the Porter Center for Neuroscience on the NIH main campus in Bethesda. The NIH has a long tradition of research excellence in cytoskeletal biology and offers a stimulating environment for postdoctoral fellows interested in interdisciplinary training in biophysics and cell biology. The research facilities at NIH are outstanding and the lab has access to state-of-the-art equipment such as crystallization robots, liquid handling systems, TIRF and confocal microscopes. For more information, please visit: http://intra.ninds.nih.gov/rm_lab/ The position will be fully funded by the NIH. We are looking for candidates who wish to work on structural biology problems related to microtubule cytoskeleton dynamics regulation and have a strong background in X-ray crystallography, protein overexpression and purification. Other details: Candidates should preferably have less than 3 years of postdoctoral experience and a strong publication record. Please send a CV, a one-page research experience summary, and contact information of three references to anton...@mail.nih.gov Please write “Postdoctoral application” in the subject header.
Re: [ccp4bb] Anisotropic data and an extremely long c axis
Frederic VELLIEUX wrote: Anisotropy in the diffraction pattern could simply be due to the shape of the crystals. The intensity of diffraction is a function of the volume of diffracting matter that is hit by the X-ray beam. Think for example of a thin plate crystal, which you rotate in the X-ray beam. When the plate is perpendicular to the X-ray beam, the volume of matter hit by the X-rays is much smaller than when the plate is parallel to the X-ray beam. Fred, I think this is a bit misleading. Although diffraction anisotropy is often accompanied by platy or needle-y crystals, the crystal shape is neither necessary nor sufficient to produce an anisotropic B factor. You will get an anisotropic SCALE factor if bits of the crystal are moving in and out of the beam as you describe, but scale factors and B factors are not the same thing! B factors arise from differences between neighboring unit cells (within a few microns of each other), and anisotropic B factors arise when the average displacement of atoms from their ideal lattice points is higher in one direction than another. Admittedly, both scale and B can have an effect on the resolution limit, but the latter kills high-angle spots much more rapidly than the former. Operationally, I recommend treating anisotropic data just like isotropic data. There is nothing wrong with measuring a lot of zeros (think about systematic absences), other than making irrelevant statistics like Rmerge higher. One need only glance at the formula for any R factor to see that it is undefined when the true F is zero. Unfortunately, there are still a lot of reviewers out there who were trained that the Rmerge in the outermost resolution bin must be 20%, and so some very sophisticated ellipsoidal cut-off programs have been written to try and meet this criterion without throwing away good data. I am actually not sure where this idea came from, but I challenge anyone to come up with a sound statistical basis for it. Better to use I/sigma(I) as a guide, as it really does tell you how much information vs noise you have at a given resolution. -James Holton MAD Scientist
Re: [ccp4bb] Anisotropic data and an extremely long c axis
I vaguely recall an email from Kay Diderich about 3 years ago to this board but I couldn't find it, describing a neat method of distorting the diffraction image to meet the ellipsoidal characteristics of the anisotropic diffraction. But I might be confusion myself, anyhow Kay can you comment on this ? I think it involved a feature in Sharp which I never used. 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/http://web.me.com/bosch_lab/ On Jun 9, 2010, at 11:49 AM, James Holton wrote: Frederic VELLIEUX wrote: Anisotropy in the diffraction pattern could simply be due to the shape of the crystals. The intensity of diffraction is a function of the volume of diffracting matter that is hit by the X-ray beam. Think for example of a thin plate crystal, which you rotate in the X-ray beam. When the plate is perpendicular to the X-ray beam, the volume of matter hit by the X-rays is much smaller than when the plate is parallel to the X-ray beam. Fred, I think this is a bit misleading. Although diffraction anisotropy is often accompanied by platy or needle-y crystals, the crystal shape is neither necessary nor sufficient to produce an anisotropic B factor. You will get an anisotropic SCALE factor if bits of the crystal are moving in and out of the beam as you describe, but scale factors and B factors are not the same thing! B factors arise from differences between neighboring unit cells (within a few microns of each other), and anisotropic B factors arise when the average displacement of atoms from their ideal lattice points is higher in one direction than another. Admittedly, both scale and B can have an effect on the resolution limit, but the latter kills high-angle spots much more rapidly than the former. Operationally, I recommend treating anisotropic data just like isotropic data. There is nothing wrong with measuring a lot of zeros (think about systematic absences), other than making irrelevant statistics like Rmerge higher. One need only glance at the formula for any R factor to see that it is undefined when the true F is zero. Unfortunately, there are still a lot of reviewers out there who were trained that the Rmerge in the outermost resolution bin must be 20%, and so some very sophisticated ellipsoidal cut-off programs have been written to try and meet this criterion without throwing away good data. I am actually not sure where this idea came from, but I challenge anyone to come up with a sound statistical basis for it. Better to use I/sigma(I) as a guide, as it really does tell you how much information vs noise you have at a given resolution. -James Holton MAD Scientist
Re: [ccp4bb] Softwares for Protein-Protein docking!
Hi, I suggest you to try HADDOCK if you have some interaction data, such as the binding site, key residues, etc. It can use the interaction data as a restrain and make the dock more accurate. And the web interface of the HADDOCK server is very easy to handle. Best wishes. On Tue, Jun 8, 2010 at 2:59 PM, xaravich ivan xaravich.i...@gmail.comwrote: Dear CCP4 users, Though this is not directly linked to ccp4, i bet many of you have solved crystal structures of the ligand and receptor separately and tried to dock it. is there any program that docks two protein molecules. We have an overall idea where the protein will bind to the receptor. Is there something like AUTODOCK for macromolecules? It will be amzing if I get some suggestions. Thanks in advance, Ivan -- Jiamu Du, Ph.D. Postdoctoral Research Fellow Laboratory of Structural Biology Memorial Sloan-Kettering Cancer Center RRL 269, 430 E 67th Street New York, NY, 10021 E-mail: d...@mskcc.org Tel: (917) - 292 - 4616
Re: [ccp4bb] Anisotropic data and an extremely long c axis
On 09/06/2010 16:49, James Holton wrote: Operationally, I recommend treating anisotropic data just like isotropic data. There is nothing wrong with measuring a lot of zeros (think about systematic absences), other than making irrelevant statistics like Rmerge higher. One need only glance at the formula for any R factor to see that it is undefined when the true F is zero. Unfortunately, there are still a lot of reviewers out there who were trained that the Rmerge in the outermost resolution bin must be 20%, and so some very sophisticated ellipsoidal cut-off programs have been written to try and meet this criterion without throwing away good data. I am actually not sure where this idea came from, but I challenge anyone to come up with a sound statistical basis for it. Better to use I/sigma(I) as a guide, as it really does tell you how much information vs noise you have at a given resolution. So, if my outer shell has 10% reflections I/sigI10, 90% reflections I/sigI=1, will Mean(I/sigI) for that shell tend to 10 or 1? Presumably I'm calculating it wrong in my simulation (very naive: took average of all individual I/sigI), because for me it tends to 1. But if I did get it right, then how does Mean(I/sigI) tell me that 10% of my observations have good signal? phx.
[ccp4bb] Compilation of CNS 1.21 on Mac OSX 10.6.3
Hi all, I've posted this in the hope that somebody in the CCP4 community may have come across this problem and can shed some light. I've posted this question on other lists (cnsbb, ccpnmr and aria - the reason will become clear), but with no success so far. I have recently acquired a Macbook Pro running OSX 10.6.3, (Kernel version 10.3.0) and am unable to compile cns v1.21 from source, using either the gcc 4.2.1/4.4/4.5 compilers (4.4 and 4.5 installed using fink), and the Intel 11.1 (evaluation) compilers. I am aware that there are Mac OSX binaries available, but I am also using CNS for NMR structure calculation with the Aria 2.3 program, and to run that successfully CNS needs to be re-compiled with Aria-specific source code. With the gcc4.5 compilers, CNS compiles and links with no warnings or errors, but fails at the execution stage. When I try to execute cns, either with './cns' or by running one of the test scripts, I get the following: dmemory error code = ** %ALLHP error encountered: fatal coding error (CNS is in mode: SET ABORT=NORMal END) * ABORT mode will terminate program execution. * Program will stop immediately. Maximum dynamic memory allocation: 0 bytes Maximum dynamic memory overhead: 8 bytes Program started at: on Program stopped at: 14:32:05 on 07-Jun-2010 CPU time used: 0.0036 seconds With 4.2.1 (using gfortran), CNS fails at the linking stage with Undefined symbols: errors. With 4.4, CNS compiles successfully, but when executed produces a simple segmentation fault message. With the 11.1 Intel compilers, CNS compiles successfully, but fails on execution: forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PCRoutineLineSource cns00010029C7BE _xtarmoin_ 1813 xdeclare.f cns00010029C68E _xreres_ 764 xdeclare.f cns00010003E04A _MAIN__167 cns.f cns0001184C UnknownUnknown Unknown cns000117E4 UnknownUnknown Unknown I have checked my shell stack limit, and to make sure, I set the shell stacksize using ulimit -s 65532 (which I believe is the upper limit on Mac OSX) and by using the ifort linker option. Both of which made no difference. I then added some compiler options in an attempt to obtain more debugging information, including -check bounds -g and -heap-arrays. The following occurs on execution: forrtl: severe (408): fort: (2): Subscript #1 of the array HEAP has value 155357288 which is greater than the up per bound of 15 Image PCRoutineLineSource cns00010087410C Unknown Unknown Unknown cns000100872C44 Unknown Unknown Unknown cns00010082BCCE Unknown Unknown Unknown cns0001007E36AA Unknown Unknown Unknown cns0001007E3AF7 Unknown Unknown Unknown cns0001002B48A4 _allhp_ 326 heap.f cns0001002B7EC6 _heapvfy_ 93 heapvfy.f cns000100071409 _MAIN__60 cns.f cns00010D5C Unknown Unknown Unknown cns00010CF4 Unknown Unknown Unknown Any help/ideas would be very much appreciated. Best wishes, Pryank attachment: pryank.vcf
Re: [ccp4bb] Anisotropic data and an extremely long c axis
Frank von Delft wrote: On 09/06/2010 16:49, James Holton wrote: Operationally, I recommend treating anisotropic data just like isotropic data. There is nothing wrong with measuring a lot of zeros (think about systematic absences), other than making irrelevant statistics like Rmerge higher. One need only glance at the formula for any R factor to see that it is undefined when the true F is zero. Unfortunately, there are still a lot of reviewers out there who were trained that the Rmerge in the outermost resolution bin must be 20%, and so some very sophisticated ellipsoidal cut-off programs have been written to try and meet this criterion without throwing away good data. I am actually not sure where this idea came from, but I challenge anyone to come up with a sound statistical basis for it. Better to use I/sigma(I) as a guide, as it really does tell you how much information vs noise you have at a given resolution. So, if my outer shell has 10% reflections I/sigI10, 90% reflections I/sigI=1, will Mean(I/sigI) for that shell tend to 10 or 1? Presumably I'm calculating it wrong in my simulation (very naive: took average of all individual I/sigI), because for me it tends to 1. But if I did get it right, then how does Mean(I/sigI) tell me that 10% of my observations have good signal? It doesn't. The mean will not tell you anything about the distribution of I/sigI values, it will just tell you the average. If I may simplify your example case to: one good observation (I/sigI = 10) and 9 weak observations (I/sigI = 1), then Mean(I/sigI) = ~2. This is better than Mean(I/sigI) = 1, but admittedly still not great. I know it is tempting to say: but wait! I've got one really good reflection at that resolution! Doesn't that count for something? Well, it does (a little), but one good reflection does not a clear map make. -James Holton MAD Scientist
Re: [ccp4bb] Compilation of CNS 1.21 on Mac OSX 10.6.3
I have often wondered how it is that one can actually run and play games like Pac-Man(R) on a modern PC using the actual bit-for-bit contents of the EPROM cartridges that I used to put into my Atari 2600 (circa 1982), but for some reason programs written just a few years ago will neither compile nor run on the latest and greatest linux/gcc systems. Am I missing something? (Other than an enormous amount of mutually incompatible library files that will trash my system if I install them incorrectly?). -James Holton MAD Scientist Pryank Patel wrote: Hi all, I've posted this in the hope that somebody in the CCP4 community may have come across this problem and can shed some light. I've posted this question on other lists (cnsbb, ccpnmr and aria - the reason will become clear), but with no success so far. I have recently acquired a Macbook Pro running OSX 10.6.3, (Kernel version 10.3.0) and am unable to compile cns v1.21 from source, using either the gcc 4.2.1/4.4/4.5 compilers (4.4 and 4.5 installed using fink), and the Intel 11.1 (evaluation) compilers. I am aware that there are Mac OSX binaries available, but I am also using CNS for NMR structure calculation with the Aria 2.3 program, and to run that successfully CNS needs to be re-compiled with Aria-specific source code. With the gcc4.5 compilers, CNS compiles and links with no warnings or errors, but fails at the execution stage. When I try to execute cns, either with './cns' or by running one of the test scripts, I get the following: dmemory error code = ** %ALLHP error encountered: fatal coding error (CNS is in mode: SET ABORT=NORMal END) * ABORT mode will terminate program execution. * Program will stop immediately. Maximum dynamic memory allocation: 0 bytes Maximum dynamic memory overhead: 8 bytes Program started at: on Program stopped at: 14:32:05 on 07-Jun-2010 CPU time used: 0.0036 seconds With 4.2.1 (using gfortran), CNS fails at the linking stage with Undefined symbols: errors. With 4.4, CNS compiles successfully, but when executed produces a simple segmentation fault message. With the 11.1 Intel compilers, CNS compiles successfully, but fails on execution: forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PCRoutineLine Source cns00010029C7BE _xtarmoin_ 1813 xdeclare.f cns00010029C68E _xreres_ 764 xdeclare.f cns00010003E04A _MAIN__167 cns.f cns0001184C UnknownUnknown Unknown cns000117E4 UnknownUnknown Unknown I have checked my shell stack limit, and to make sure, I set the shell stacksize using ulimit -s 65532 (which I believe is the upper limit on Mac OSX) and by using the ifort linker option. Both of which made no difference. I then added some compiler options in an attempt to obtain more debugging information, including -check bounds -g and -heap-arrays. The following occurs on execution: forrtl: severe (408): fort: (2): Subscript #1 of the array HEAP has value 155357288 which is greater than the up per bound of 15 Image PCRoutineLineSource cns00010087410C Unknown Unknown Unknown cns000100872C44 Unknown Unknown Unknown cns00010082BCCE Unknown Unknown Unknown cns0001007E36AA Unknown Unknown Unknown cns0001007E3AF7 Unknown Unknown Unknown cns0001002B48A4 _allhp_ 326 heap.f cns0001002B7EC6 _heapvfy_ 93 heapvfy.f cns000100071409 _MAIN__60 cns.f cns00010D5C Unknown Unknown Unknown cns00010CF4 Unknown Unknown Unknown Any help/ideas would be very much appreciated. Best wishes, Pryank
Re: [ccp4bb] Anisotropic data and an extremely long c axis
But at some point, getting a clear map might not be the goal. If you're in refinement mode, the weak reflections also provide information that your model needs to fit. I find I/sig(I) (or I/sig(I)) to be about as useful as Rmerge (or its relatives). Ron On Wed, 9 Jun 2010, James Holton wrote: Frank von Delft wrote: On 09/06/2010 16:49, James Holton wrote: Operationally, I recommend treating anisotropic data just like isotropic data. There is nothing wrong with measuring a lot of zeros (think about systematic absences), other than making irrelevant statistics like Rmerge higher. One need only glance at the formula for any R factor to see that it is undefined when the true F is zero. Unfortunately, there are still a lot of reviewers out there who were trained that the Rmerge in the outermost resolution bin must be 20%, and so some very sophisticated ellipsoidal cut-off programs have been written to try and meet this criterion without throwing away good data. I am actually not sure where this idea came from, but I challenge anyone to come up with a sound statistical basis for it. Better to use I/sigma(I) as a guide, as it really does tell you how much information vs noise you have at a given resolution. So, if my outer shell has 10% reflections I/sigI10, 90% reflections I/sigI=1, will Mean(I/sigI) for that shell tend to 10 or 1? Presumably I'm calculating it wrong in my simulation (very naive: took average of all individual I/sigI), because for me it tends to 1. But if I did get it right, then how does Mean(I/sigI) tell me that 10% of my observations have good signal? It doesn't. The mean will not tell you anything about the distribution of I/sigI values, it will just tell you the average. If I may simplify your example case to: one good observation (I/sigI = 10) and 9 weak observations (I/sigI = 1), then Mean(I/sigI) = ~2. This is better than Mean(I/sigI) = 1, but admittedly still not great. I know it is tempting to say: but wait! I've got one really good reflection at that resolution! Doesn't that count for something? Well, it does (a little), but one good reflection does not a clear map make. -James Holton MAD Scientist
Re: [ccp4bb] Compilation of CNS 1.21 on Mac OSX 10.6.3
My sincere apologies for not being clear. When I said gcc, I meant I installed the full compiler package which includes gfortran. I did use gfortran for the compilation. I have also tried the commercial Intel compilers (albeit the evaluation version), which produced the errors I described below. Best wishes, Pryank On 9 Jun 2010, at 18:27, Axel Brunger wrote: Please use gfortran instead or obtain the commercial Intel compilers. Gcc is not reliable for CNS compilation. On Jun 9, 2010, at 10:10 AM, Pryank Patel wrote: Hi all, I've posted this in the hope that somebody in the CCP4 community may have come across this problem and can shed some light. I've posted this question on other lists (cnsbb, ccpnmr and aria - the reason will become clear), but with no success so far. I have recently acquired a Macbook Pro running OSX 10.6.3, (Kernel version 10.3.0) and am unable to compile cns v1.21 from source, using either the gcc 4.2.1/4.4/4.5 compilers (4.4 and 4.5 installed using fink), and the Intel 11.1 (evaluation) compilers. I am aware that there are Mac OSX binaries available, but I am also using CNS for NMR structure calculation with the Aria 2.3 program, and to run that successfully CNS needs to be re-compiled with Aria-specific source code. With the gcc4.5 compilers, CNS compiles and links with no warnings or errors, but fails at the execution stage. When I try to execute cns, either with './cns' or by running one of the test scripts, I get the following: dmemory error code = ** %ALLHP error encountered: fatal coding error (CNS is in mode: SET ABORT=NORMal END) * ABORT mode will terminate program execution. * Program will stop immediately. Maximum dynamic memory allocation: 0 bytes Maximum dynamic memory overhead: 8 bytes Program started at: on Program stopped at: 14:32:05 on 07-Jun-2010 CPU time used: 0.0036 seconds With 4.2.1 (using gfortran), CNS fails at the linking stage with Undefined symbols: errors. With 4.4, CNS compiles successfully, but when executed produces a simple segmentation fault message. With the 11.1 Intel compilers, CNS compiles successfully, but fails on execution: forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PCRoutineLineSource cns00010029C7BE _xtarmoin_ 1813xdeclare.f cns00010029C68E _xreres_ 764 xdeclare.f cns00010003E04A _MAIN__167 cns.f cns0001184C UnknownUnknown Unknown cns000117E4 UnknownUnknown Unknown I have checked my shell stack limit, and to make sure, I set the shell stacksize using ulimit -s 65532 (which I believe is the upper limit on Mac OSX) and by using the ifort linker option. Both of which made no difference. I then added some compiler options in an attempt to obtain more debugging information, including -check bounds -g and -heap-arrays. The following occurs on execution: forrtl: severe (408): fort: (2): Subscript #1 of the array HEAP has value 155357288 which is greater than the up per bound of 15 Image PCRoutineLineSource cns00010087410C Unknown Unknown Unknown cns000100872C44 Unknown Unknown Unknown cns00010082BCCE Unknown Unknown Unknown cns0001007E36AA Unknown Unknown Unknown cns0001007E3AF7 Unknown Unknown Unknown cns0001002B48A4 _allhp_ 326 heap.f cns0001002B7EC6 _heapvfy_ 93 heapvfy.f cns000100071409 _MAIN__60 cns.f cns00010D5C Unknown Unknown Unknown cns00010CF4 Unknown Unknown Unknown Any help/ideas would be very much appreciated. Best wishes, Pryank pryank.vcf Axel T. Brunger Investigator, Howard Hughes Medical Institute Professor of Molecular and Cellular Physiology Stanford University Web:http://atbweb.stanford.eduhttp://atbweb.stanford.edu/ Email: brun...@stanford.edumailto:brun...@stanford.edu Phone: +1 650-736-1031 Fax:+1 650-745-1463
Re: [ccp4bb] Compilation of CNS 1.21 on Mac OSX 10.6.3
On Wednesday 09 June 2010 10:45:07 am James Holton wrote: I have often wondered how it is that one can actually run and play games like Pac-Man(R) on a modern PC using the actual bit-for-bit contents of the EPROM cartridges that I used to put into my Atari 2600 (circa 1982), but for some reason programs written just a few years ago will neither compile nor run on the latest and greatest linux/gcc systems. I seriously doubt that your Atari PacMan program was written in Fortran! But more to the point, to run it now you run an emulator for the original Atari chipset. PacMac runs around thinking he really is on an Atari console, blissfully unaware that the console is only an emulated simulation of the original long-gone world. Welcome to the matrix. Am I missing something? I think you are missing the mark twice in mentioning linux/gcc. The complaint under discussion is with OSX, not a linux system. With rare exceptions, old linux programs run just fine on an up-to-date linux system, so long as you also install equally old versions of the support libraries. Do you have a counter-example in mind? In the specific case of old Fortran programs, the reality is that in the era of commercial Fortran compilers there was great divergence in the details of the implementation, particular with regard to I/O commands. gcc/f77/g77 was never a good Fortran compiler, and was particularly bad at compiling code idioms used by real-world Fortran code written for compilers supported by IBM, DEC, CDC, etc. gfortran is somewhat better, but still far from perfect. As to Pryank's problem: Pryank Patel wrote: Hi all, I've posted this in the hope that somebody in the CCP4 community may have come across this problem and can shed some light. I've posted this question on other lists (cnsbb, ccpnmr and aria - the reason will become clear), but with no success so far. I have recently acquired a Macbook Pro running OSX 10.6.3, (Kernel version 10.3.0) and am unable to compile cns v1.21 from source, using either the gcc 4.2.1/4.4/4.5 compilers (4.4 and 4.5 installed using fink), and the Intel 11.1 (evaluation) compilers. I may be mis-remembering, but I have it in mind that the cns source code requires selecting or porting a set of compiler-specific routines in one of the source modules. These are work-arounds for the variability in Fortran implementations mentioned above. Did you tweak this file appropriately for each of the compilers you tried? As a practical matter, you might want to look into running a VMWare layer on your machine so that you can compile and run linux executables rather than fighting the native OSX environment. You too can join PacMac in the happy world recreated in the matrix :-) Ethan I am aware that there are Mac OSX binaries available, but I am also using CNS for NMR structure calculation with the Aria 2.3 program, and to run that successfully CNS needs to be re-compiled with Aria-specific source code. With the gcc4.5 compilers, CNS compiles and links with no warnings or errors, but fails at the execution stage. When I try to execute cns, either with './cns' or by running one of the test scripts, I get the following: dmemory error code = ** %ALLHP error encountered: fatal coding error (CNS is in mode: SET ABORT=NORMal END) * ABORT mode will terminate program execution. * Program will stop immediately. Maximum dynamic memory allocation: 0 bytes Maximum dynamic memory overhead: 8 bytes Program started at: on Program stopped at: 14:32:05 on 07-Jun-2010 CPU time used: 0.0036 seconds With 4.2.1 (using gfortran), CNS fails at the linking stage with Undefined symbols: errors. With 4.4, CNS compiles successfully, but when executed produces a simple segmentation fault message. With the 11.1 Intel compilers, CNS compiles successfully, but fails on execution: forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PCRoutineLine Source cns00010029C7BE _xtarmoin_ 1813 xdeclare.f cns00010029C68E _xreres_ 764 xdeclare.f cns00010003E04A _MAIN__167 cns.f cns0001184C UnknownUnknown Unknown cns000117E4 UnknownUnknown Unknown I have checked my shell stack limit, and to make sure, I set the shell stacksize using ulimit -s 65532 (which I
Re: [ccp4bb] Compilation of CNS 1.21 on Mac OSX 10.6.3
Hello Ethan, I may be mis-remembering, but I have it in mind that the cns source code requires selecting or porting a set of compiler-specific routines in one of the source modules. These are work-arounds for the variability in Fortran implementations mentioned above. The CNS build system does this automatically these days. I'm not sure what Pryank is doing wrong, but I don't think this has anything to do with either CNS or the Aria routines. Intel does release glitchy versions of their compilers, so that's possibly the issue: (sbgrid-dev-turbo:cns/aria-test/cns_solve_1.21) sw_vers ProductName: Mac OS X ProductVersion: 10.6.3 BuildVersion: 10D573 (sbgrid-dev-turbo:cns/aria-test/cns_solve_1.21) ifort --version ifort (IFORT) 11.1 20091130 Copyright (C) 1985-2009 Intel Corporation. All rights reserved. (sbgrid-dev-turbo:cns/aria-test/cns_solve_1.21) ./mac-intel-darwin/source/cns_solve-1006091423.exe | | |Crystallography NMR System (CNS)| | CNSsolve | | | Version: 1.2 at patch level 1 Status: General release with ARIA enhancements Written by: A.T.Brunger, P.D.Adams, G.M.Clore, W.L.DeLano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warren. Copyright (c) 1997-2007 Yale University Running on machine: sbgrid-dev-turbo.in.hwlab (Mac/Intel,32-bit) Program started by: sbgrid Program started at: 14:44:03 on 09-Jun-2010 It was 5 minutes of work for someone with the right background. Some days I hate computers. :-/ -ben -- | Ben Eisenbraun | Software Sysadmin | | Structural Biology Grid | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |
Re: [ccp4bb] Compilation of CNS 1.21 on Mac OSX 10.6.3
Please note that the latest version of Xcode in Mac OS X 10.6.3 breaks the Intel Fortran and C compilers. It is possible that Xcode also breaks gfortran, but I haven't tested it. I've reverted to the Xcode version that came with the original Snow Leopard release. Intel is aware of the problem, but so far there have been no updates of the Intel compilers to fix the problem with Xcode. Axel Brunger On Jun 9, 2010, at 11:35 AM, Ethan Merritt wrote: On Wednesday 09 June 2010 10:45:07 am James Holton wrote: I have often wondered how it is that one can actually run and play games like Pac-Man(R) on a modern PC using the actual bit-for-bit contents of the EPROM cartridges that I used to put into my Atari 2600 (circa 1982), but for some reason programs written just a few years ago will neither compile nor run on the latest and greatest linux/gcc systems. I seriously doubt that your Atari PacMan program was written in Fortran! But more to the point, to run it now you run an emulator for the original Atari chipset. PacMac runs around thinking he really is on an Atari console, blissfully unaware that the console is only an emulated simulation of the original long-gone world. Welcome to the matrix. Am I missing something? I think you are missing the mark twice in mentioning linux/gcc. The complaint under discussion is with OSX, not a linux system. With rare exceptions, old linux programs run just fine on an up-to-date linux system, so long as you also install equally old versions of the support libraries. Do you have a counter-example in mind? In the specific case of old Fortran programs, the reality is that in the era of commercial Fortran compilers there was great divergence in the details of the implementation, particular with regard to I/O commands. gcc/f77/g77 was never a good Fortran compiler, and was particularly bad at compiling code idioms used by real-world Fortran code written for compilers supported by IBM, DEC, CDC, etc. gfortran is somewhat better, but still far from perfect. As to Pryank's problem: Pryank Patel wrote: Hi all, I've posted this in the hope that somebody in the CCP4 community may have come across this problem and can shed some light. I've posted this question on other lists (cnsbb, ccpnmr and aria - the reason will become clear), but with no success so far. I have recently acquired a Macbook Pro running OSX 10.6.3, (Kernel version 10.3.0) and am unable to compile cns v1.21 from source, using either the gcc 4.2.1/4.4/4.5 compilers (4.4 and 4.5 installed using fink), and the Intel 11.1 (evaluation) compilers. I may be mis-remembering, but I have it in mind that the cns source code requires selecting or porting a set of compiler-specific routines in one of the source modules. These are work-arounds for the variability in Fortran implementations mentioned above. Did you tweak this file appropriately for each of the compilers you tried? As a practical matter, you might want to look into running a VMWare layer on your machine so that you can compile and run linux executables rather than fighting the native OSX environment. You too can join PacMac in the happy world recreated in the matrix :-) Ethan I am aware that there are Mac OSX binaries available, but I am also using CNS for NMR structure calculation with the Aria 2.3 program, and to run that successfully CNS needs to be re-compiled with Aria-specific source code. With the gcc4.5 compilers, CNS compiles and links with no warnings or errors, but fails at the execution stage. When I try to execute cns, either with './cns' or by running one of the test scripts, I get the following: dmemory error code = ** %ALLHP error encountered: fatal coding error (CNS is in mode: SET ABORT=NORMal END) * ABORT mode will terminate program execution. * Program will stop immediately. Maximum dynamic memory allocation: 0 bytes Maximum dynamic memory overhead: 8 bytes Program started at: on Program stopped at: 14:32:05 on 07-Jun-2010 CPU time used: 0.0036 seconds With 4.2.1 (using gfortran), CNS fails at the linking stage with Undefined symbols: errors. With 4.4, CNS compiles successfully, but when executed produces a simple segmentation fault message. With the 11.1 Intel compilers, CNS compiles successfully, but fails on execution: forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PCRoutineLine Source cns00010029C7BE _xtarmoin_ 1813 xdeclare.f cns
[ccp4bb] SGI O2 again
Hi All, As I've said, I'm trying to put some version of Linux on an old SGI O2. I have found a couple of versions of Linux that I'd like to try but I think the problem now might be that the O2 isn't configured to read from CD ROM on start up. Does anyone know how to go about changing this setting? Thanks, ~Brennan~
Re: [ccp4bb] Softwares for Protein-Protein docking!
Hello, I have tried HADDOCK recently and have got some parsing related error! (indicative of some errors in the input PDB files.). I have checked my pdb files and did not figure out anything wrong. May I please get some suggestions about it from any of the experienced ones in this area? regards, Anil --- On Wed, 9/6/10, Jiamu Du jiam...@gmail.com wrote: From: Jiamu Du jiam...@gmail.com Subject: Re: [ccp4bb] Softwares for Protein-Protein docking! To: CCP4BB@JISCMAIL.AC.UK Date: Wednesday, 9 June, 2010, 10:25 PM Hi, I suggest you to try HADDOCK if you have some interaction data, such as the binding site, key residues, etc. It can use the interaction data as a restrain and make the dock more accurate. And the web interface of the HADDOCK server is very easy to handle. Best wishes. On Tue, Jun 8, 2010 at 2:59 PM, xaravich ivan xaravich.i...@gmail.com wrote: Dear CCP4 users, Though this is not directly linked to ccp4, i bet many of you have solved crystal structures of the ligand and receptor separately and tried to dock it. is there any program that docks two protein molecules. We have an overall idea where the protein will bind to the receptor. Is there something like AUTODOCK for macromolecules? It will be amzing if I get some suggestions. Thanks in advance, Ivan -- Jiamu Du, Ph.D. Postdoctoral Research Fellow Laboratory of Structural Biology Memorial Sloan-Kettering Cancer Center RRL 269, 430 E 67th Street New York, NY, 10021 E-mail: d...@mskcc.org Tel: (917) - 292 - 4616
Re: [ccp4bb] Softwares for Protein-Protein docking!
I am not sure what is the problem you have. Usually, I use O formated PDB files. It works well. I think you can report your bug to the Dr. A.M.J.J. Bonvin who is maintaining the server. On Wed, Jun 9, 2010 at 6:08 PM, anil kumar anilkumar...@yahoo.co.in wrote: Hello, I have tried HADDOCK recently and have got some parsing related error! (indicative of some errors in the input PDB files.). I have checked my pdb files and did not figure out anything wrong. May I please get some suggestions about it from any of the experienced ones in this area? regards, Anil --- On *Wed, 9/6/10, Jiamu Du jiam...@gmail.com* wrote: From: Jiamu Du jiam...@gmail.com Subject: Re: [ccp4bb] Softwares for Protein-Protein docking! To: CCP4BB@JISCMAIL.AC.UK Date: Wednesday, 9 June, 2010, 10:25 PM Hi, I suggest you to try HADDOCK if you have some interaction data, such as the binding site, key residues, etc. It can use the interaction data as a restrain and make the dock more accurate. And the web interface of the HADDOCK server is very easy to handle. Best wishes. On Tue, Jun 8, 2010 at 2:59 PM, xaravich ivan xaravich.i...@gmail.comhttp://mc/compose?to=xaravich.i...@gmail.com wrote: Dear CCP4 users, Though this is not directly linked to ccp4, i bet many of you have solved crystal structures of the ligand and receptor separately and tried to dock it. is there any program that docks two protein molecules. We have an overall idea where the protein will bind to the receptor. Is there something like AUTODOCK for macromolecules? It will be amzing if I get some suggestions. Thanks in advance, Ivan -- Jiamu Du, Ph.D. Postdoctoral Research Fellow Laboratory of Structural Biology Memorial Sloan-Kettering Cancer Center RRL 269, 430 E 67th Street New York, NY, 10021 E-mail: d...@mskcc.org http://mc/compose?to=...@mskcc.org Tel: (917) - 292 - 4616 -- Jiamu Du, Ph.D. Postdoctoral Research Fellow Laboratory of Structural Biology Memorial Sloan-Kettering Cancer Center RRL 269, 430 E 67th Street New York, NY, 10021 E-mail: d...@mskcc.org Tel: (917) - 292 - 4616
Re: [ccp4bb] Compilation of CNS 1.21 on Mac OSX 10.6.3 - Solved
Hi all, Thanks to everybody who has contributed over the past couple of days on the various bulletin boards I have posted to. As is always the case, the solution was quite simple but completely passed me by. I'm going to use Mac inexperience as an excuse here... :-) So the original problem was not being able to compile a working executable of CNS v1.21 from source on Mac OSX 10.6.3. The reason for compiling from source is because in order to run CNS from Aria 2.3, a program used in NMR automated peak assignment and structure calculation, CNS needs to be recompiled with Aria-specific source code. With fink-installed gfortran/gcc 4.5 compilers, CNS compiles and links with no warnings or errors, but fails at the execution stage. With fink-installed 4.4, CNS compiles successfully but when executed produces a simple segmentation fault message. The problem here is the fink-installed compilers. Harry Powell and Daniel O'Donovan have guided me to the light - the High Performance Computing for Mac OS X webpage (http://hpc.sourceforge.net) has binaries for the gcc 4.5 compiler package, which installs in /usr/local/. Compilation with this compiler set produces a working CNS executable. The only other modification is to copy the Makefile.header.2.gfortran file from cns_solve_1.21/instlib/machine/supported/intel-x86_64bit-linux to cns_solve_1.21/instlib/machine/supported/intel-x86_64bit-linux. Compile with 'make install compiler=gfortran', making sure that /usr/local/path is in $PATH. With the Intel 11.1 compilers (and I used the evaluation version here), CNS compiles successfully, but fails on execution. Thanks to Axel Brunger and Benjamin Bardiaux, for sharing that the Intel fortran compiler is not compatible with Xcode 3.2.2, although it does not seem to break gfortran in this case. A little more information can be found here: http://software.intel.com/en-us/articles/intel-fortran-for-mac-os-x-incompatible-with-xcode-322/ Thanks goes to Benjamin Bardiaux for the link. The webpage suggests two fixes. One is to add the '-use-asm' option to both the compilation and linker lines. This seems to work, and produces a working CNS executable. Not until now did I consider Xcode to be the problem, and at no point over the past few days did I come across or register the intel webpage linked above during my hours of google-trawling. The other option is to reinstall Xcode 3.2.1, which I assume is the version Axel Brunger said he reinstalled. This can be downloaded from the Mac Development Centre. Then reinstall the Intel fortran compiler. I have not tried this option, since the first option seems to have worked quite well. Thanks once again, Pryank On 9 Jun 2010, at 19:54, Axel Brunger wrote: Please note that the latest version of Xcode in Mac OS X 10.6.3 breaks the Intel Fortran and C compilers. It is possible that Xcode also breaks gfortran, but I haven't tested it. I've reverted to the Xcode version that came with the original Snow Leopard release. Intel is aware of the problem, but so far there have been no updates of the Intel compilers to fix the problem with Xcode. Axel Brunger On Jun 9, 2010, at 11:35 AM, Ethan Merritt wrote: On Wednesday 09 June 2010 10:45:07 am James Holton wrote: I have often wondered how it is that one can actually run and play games like Pac-Man(R) on a modern PC using the actual bit-for-bit contents of the EPROM cartridges that I used to put into my Atari 2600 (circa 1982), but for some reason programs written just a few years ago will neither compile nor run on the latest and greatest linux/gcc systems. I seriously doubt that your Atari PacMan program was written in Fortran! But more to the point, to run it now you run an emulator for the original Atari chipset. PacMac runs around thinking he really is on an Atari console, blissfully unaware that the console is only an emulated simulation of the original long-gone world. Welcome to the matrix. Am I missing something? I think you are missing the mark twice in mentioning linux/gcc. The complaint under discussion is with OSX, not a linux system. With rare exceptions, old linux programs run just fine on an up-to-date linux system, so long as you also install equally old versions of the support libraries. Do you have a counter-example in mind? In the specific case of old Fortran programs, the reality is that in the era of commercial Fortran compilers there was great divergence in the details of the implementation, particular with regard to I/O commands. gcc/f77/g77 was never a good Fortran compiler, and was particularly bad at compiling code idioms used by real-world Fortran code written for compilers supported by IBM, DEC, CDC, etc. gfortran is somewhat better, but still far from perfect. As to Pryank's problem: Pryank Patel wrote: Hi all, I've posted this in the hope that somebody in the CCP4 community may have come across this problem and can shed some light. I've posted this question on
Re: [ccp4bb] Compilation of CNS 1.21 on Mac OSX 10.6.3 - Solved
A PS on the Intel compiler / Xcode issue: the first work-around (-use-asm) does not work in conjunction with OpenMP enabled. Thus, I recommend to revert to Xcode 3.2.1 (and then reinstall the compilers) until the issue has been fixed by Intel. Axel On Jun 9, 2010, at 5:19 PM, Patel, Pryank wrote: Hi all, Thanks to everybody who has contributed over the past couple of days on the various bulletin boards I have posted to. As is always the case, the solution was quite simple but completely passed me by. I'm going to use Mac inexperience as an excuse here... :-) So the original problem was not being able to compile a working executable of CNS v1.21 from source on Mac OSX 10.6.3. The reason for compiling from source is because in order to run CNS from Aria 2.3, a program used in NMR automated peak assignment and structure calculation, CNS needs to be recompiled with Aria-specific source code. With fink-installed gfortran/gcc 4.5 compilers, CNS compiles and links with no warnings or errors, but fails at the execution stage. With fink-installed 4.4, CNS compiles successfully but when executed produces a simple segmentation fault message. The problem here is the fink-installed compilers. Harry Powell and Daniel O'Donovan have guided me to the light - the High Performance Computing for Mac OS X webpage (http://hpc.sourceforge.net) has binaries for the gcc 4.5 compiler package, which installs in /usr/local/. Compilation with this compiler set produces a working CNS executable. The only other modification is to copy the Makefile.header.2.gfortran file from cns_solve_1.21/instlib/machine/supported/intel-x86_64bit-linux to cns_solve_1.21/instlib/machine/supported/intel-x86_64bit-linux. Compile with 'make install compiler=gfortran', making sure that /usr/local/path is in $PATH. With the Intel 11.1 compilers (and I used the evaluation version here), CNS compiles successfully, but fails on execution. Thanks to Axel Brunger and Benjamin Bardiaux, for sharing that the Intel fortran compiler is not compatible with Xcode 3.2.2, although it does not seem to break gfortran in this case. A little more information can be found here: http://software.intel.com/en-us/articles/intel-fortran-for-mac-os-x-incompatible-with-xcode-322/ Thanks goes to Benjamin Bardiaux for the link. The webpage suggests two fixes. One is to add the '-use-asm' option to both the compilation and linker lines. This seems to work, and produces a working CNS executable. Not until now did I consider Xcode to be the problem, and at no point over the past few days did I come across or register the intel webpage linked above during my hours of google-trawling. The other option is to reinstall Xcode 3.2.1, which I assume is the version Axel Brunger said he reinstalled. This can be downloaded from the Mac Development Centre. Then reinstall the Intel fortran compiler. I have not tried this option, since the first option seems to have worked quite well. Thanks once again, Pryank On 9 Jun 2010, at 19:54, Axel Brunger wrote: Please note that the latest version of Xcode in Mac OS X 10.6.3 breaks the Intel Fortran and C compilers. It is possible that Xcode also breaks gfortran, but I haven't tested it. I've reverted to the Xcode version that came with the original Snow Leopard release. Intel is aware of the problem, but so far there have been no updates of the Intel compilers to fix the problem with Xcode. Axel Brunger On Jun 9, 2010, at 11:35 AM, Ethan Merritt wrote: On Wednesday 09 June 2010 10:45:07 am James Holton wrote: I have often wondered how it is that one can actually run and play games like Pac-Man(R) on a modern PC using the actual bit-for-bit contents of the EPROM cartridges that I used to put into my Atari 2600 (circa 1982), but for some reason programs written just a few years ago will neither compile nor run on the latest and greatest linux/gcc systems. I seriously doubt that your Atari PacMan program was written in Fortran! But more to the point, to run it now you run an emulator for the original Atari chipset. PacMac runs around thinking he really is on an Atari console, blissfully unaware that the console is only an emulated simulation of the original long-gone world. Welcome to the matrix. Am I missing something? I think you are missing the mark twice in mentioning linux/gcc. The complaint under discussion is with OSX, not a linux system. With rare exceptions, old linux programs run just fine on an up-to-date linux system, so long as you also install equally old versions of the support libraries. Do you have a counter-example in mind? In the specific case of old Fortran programs, the reality is that in the era of commercial Fortran compilers there was great divergence in the details of the implementation, particular with regard to I/O commands. gcc/f77/g77 was never a good Fortran compiler,
Re: [ccp4bb] Off-topic: Univ California boycott of Nature publishing group
On Tue, 8 Jun 2010 21:50:10 -0700 William G. Scott wgsc...@chemistry.ucsc.edu wrote: Sorry about the off-topic nature (so to speak) of this post, especially given that it is not yet Friday, but I am interested what our community thinks of this: http://library.ucsc.edu/sites/default/files/Nature_Faculty_Letter.pdf There has been a rather extensive discussion on slashdot: http://science.slashdot.org/story/10/06/09/213256/Univ-of-California-Faculty-May-Boycott-Nature-Publisher Also take a gander at Donald Knuth's section crisis in scientific publishing on his webapge: http://www-cs-faculty.stanford.edu/~uno/news03.html with a link to an excellent letter he sent to Journal of Algorithms a few years ago: http://www-cs-faculty.stanford.edu/~uno/joalet.pdf -Tim -- - Tim Fenn f...@stanford.edu Stanford University, School of Medicine James H. Clark Center 318 Campus Drive, Room E300 Stanford, CA 94305-5432 Phone: (650) 736-1714 FAX: (650) 736-1961 -
Re: [ccp4bb] Softwares for Protein-Protein docking!
Thank you Rotem and everyone else who replied to mypost. I am replying to Rotem's mail as his link has everything inclusive of what others had suggested. I love ccp4 bb You always get more than what you ask for. Thanks guys. Ivan On Tue, Jun 8, 2010 at 10:41 PM, Rotem Sertchook rotem.sertch...@weizmann.ac.il wrote: See the list in the following link http://bip.weizmann.ac.il/toolbox/structure/binding.htm#pp Good Luck Rotem Sertchook On 8 Jun, 2010, at 21:59, xaravich ivan wrote: Dear CCP4 users, Though this is not directly linked to ccp4, i bet many of you have solved crystal structures of the ligand and receptor separately and tried to dock it. is there any program that docks two protein molecules. We have an overall idea where the protein will bind to the receptor. Is there something like AUTODOCK for macromolecules? It will be amzing if I get some suggestions. Thanks in advance, Ivan
