[ccp4bb] AW: [ccp4bb] Dealnig with O-linked mannose
Using your favorite editor, you can copy the LINK record from the pdb file generated by Coot and paste it into the pdb file produced by Phenix. You can also make a script to do this. This is what I did during the time LINK records were not properly handled by coot, refmac and buster. Best regards, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Dmitry Rodionov Gesendet: Donnerstag, 21. November 2013 22:09 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Dealnig with O-linked mannose Thank you all for helpful suggestions. My question was how to properly connect a mannose to a serine and real-space refine the result. My apologies for not being clear enough. Coot can't find MAN-SER or SER-MAN in it's library (Coot 0.7.1, mon_lib 5.41) It does not automatically make the bond between MAN C1 and OG of SER either. Here is the way I finally made the connection followed by refinement it in Coot: 1) Get monomer... MAN 2) real-space refine MAN into reasonable position 3) Delete hydrogens and reducing hydroxyl Bond is not detected 4) Extensions-Modelling ...-make Link (Click 2 atoms) ... Click on C1 of MAN and OG of SER dashed bond appears 5) Sphere refine A whole different issue that was touched in the replies is how this model will be handled by refinement programs. For the sake of a record, I am using Phenix and it seems to not respect the described link without massaging by means of either pdb.edits or apply_link.def. Also, phenix.refine does not produce LINK records in the output PDB, so step 4 might have to be repeated. Best regards, Dmitry
Re: [ccp4bb] Stereo monitor
I'm using a 24 BenQ XL2420TX (emitter builit-in; price 500€) monitor connected to the DisplayPort of a Quadro FX 380 card. Works very well on 64bit ScientificLinux 6.4 with the kmod-nvidia driver from ElRepo. Please also see http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo . HTH, Kay
[ccp4bb] How accurate are refined group-occupancies?
Dear bulletin board members, A referee came back with a question about the accuracy of refined group-occupancies. In the manuscript we describe 3 crystal structures with resolutions between 2.1 and 2.4 Å. In all three cases, the inhibitor has been fitted in two alternative conformations and the group occupancy of each conformation has been refined and the relative occupancies vary depending on the inhibitor. The accuracy will depend on the amount of overlap between the inhibitor densities and the amount of unique density belonging only to one conformation and the amount of additional disorder of the inhibitors, since most of the interactions are non-specific hydrophobic interactions. Also partially occupied solvent molecules could lead to errors in the refined occupancies. My gut feeling is that the error will be somewhere between 20 and 30% or even higher, but I would be very happy if someone could come with a more scientific way, however crude, to get an estimate of this error. Best regards, Herman
Re: [ccp4bb] Sokalan cp 42 as a cryoprotectant
Thank you all for your suggestions. Greetings, On Thu, Nov 21, 2013 at 6:19 PM, Jim Pflugrath jim.pflugr...@rigaku.com wrote: Here's an easy experiment to try: What happens when you flash-cool your reservoir solution in Liquid Nitrogen? Does it remains glass-clear at 100 K or lower? Jim From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of abhimanyu singh [abhisingh@gmail.com] Sent: Thursday, November 21, 2013 10:03 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Sokalan cp 42 as a cryoprotectant Dear all, Recently I got couple of crystallization hits in conditions containing 30-40% sokalan cp 42 provided in MIDAS commercial screen from molecular dimensions. I tried to look up for information regarding its probable cryo protection activity but failed to find anything. Could someone have any clue about this ? Thank you. Greetings, -- Abhimanyu Kumar Singh Ph.D. Student Department of Macromolecular Structures National Center for Biotechnology (CNB-CSIC) C/ Darwin 3, Campus de Cantoblanco, 28049 Madrid, Spain. E-Mail: abhimanyu.si...@cnb.csic.es -- Abhimanyu Kumar Singh Ph.D. Student Department of Macromolecular Structures National Center for Biotechnology (CNB-CSIC) C/ Darwin 3, Campus de Cantoblanco, 28049 Madrid, Spain. E-Mail: abhimanyu.si...@cnb.csic.es
Re: [ccp4bb] How accurate are refined group-occupancies?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Herman, you could apply random shifts to the occupancies, coordinates, and B-values and refine a large number of times, e.g. with 50 variations. Then you can calculate the mean occupancies with standard deviations. That's give you an idea about the precision of the occupancies. I am not sure how to get to the accuracy - you would have to figure out how much all the parameters are interrelated, which I dare say is quite impossible - it is easier for the referee to learn what a crystallographic model represents. Best, Tim On 11/22/2013 10:07 AM, herman.schreu...@sanofi.com wrote: Dear bulletin board members, A referee came back with a question about the accuracy of refined group-occupancies. In the manuscript we describe 3 crystal structures with resolutions between 2.1 and 2.4 ￅ. In all three cases, the inhibitor has been fitted in two alternative conformations and the group occupancy of each conformation has been refined and the relative occupancies vary depending on the inhibitor. The accuracy will depend on the amount of overlap between the inhibitor densities and the amount of unique density belonging only to one conformation and the amount of additional disorder of the inhibitors, since most of the interactions are non-specific hydrophobic interactions. Also partially occupied solvent molecules could lead to errors in the refined occupancies. My gut feeling is that the error will be somewhere between 20 and 30% or even higher, but I would be very happy if someone could come with a more scientific way, however crude, to get an estimate of this error. Best regards, Herman - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFSjyOsUxlJ7aRr7hoRAhkNAJ45iZLSy+YQnNeu9PMAStScQbu5MgCgwB/G kH9IVkjsDyFpiEItjMJn8MA= =lSi6 -END PGP SIGNATURE-
Re: [ccp4bb] PostDoc - Structural Biology - Cancer
Dear CCP4ers, apologies but the actual deadline for the advertised post is the 29th November 2013 (and not 2014). So only one week left to apply and not one year. Best, Alessandro A post-doctoral position is available immediately in the laboratory of Dr. Alessandro Vannini, within the Division of Structural Biology at The Institute of Cancer Research in Chelsea, London, UK. We are looking for highly motivated individuals with a strong interest in structural characterization of multi-subunit macromolecular complexes. We currently employ single particle electron microscopy analysis and X-ray crystallography, as well as biochemical and biophysical analysis, to elucidate the role of the RNA Polymerase III and associated factors in cancer development. The Division of Structural Biology has managed facilities for protein crystallography (Bruker Microstar and CCD detector and crystallisation robots), cryo-electron microscopy (FEI Tecnai F20 and T12), and protein production with expertise in multi-subunit expression (insect cell, yeast and bacterial expression, including a 60 L fermentor). The Division is also well equipped with equipment for biophysical analysis (e.g. ITC, fluorescence, multi-angle light scattering). Applicants should possess a PhD (or equivalent) in biochemistry or molecular biology and a sound knowledge in production and purification of macromolecular complexes for structural biology analysis. Previous experience with purification of multi-subunit complexes and/or biochemistry of protein-nucleic acid complexes would be beneficial. Previous experience in protein crystallography and/or single particle electron microscopy would be desirable. Appointment will be on Fixed Term Contract for 3 years in the first instance, with a starting salary in the range of £28,425 to £34,944 p.a. inclusive (based on previous post-doctoral experience). CV and covering letter must be submitted online at http://www.icr.ac.uk/jobsearch Job Ref. No. 1378320 Closing Date: 29th November 2013 For informal inquiries you can contact me directly at alessandro.vann...@icr.ac.uk
[ccp4bb] Ph.D studentship in Structural Biology in Oxford
A 4-year Ph.D studentship in Structural Biology starting October 2014 is available in the Research Group led by Dr. Christian Siebold. Our group, based in the Division of Structural Biology (STRUBI) at the Wellcome Trust Centre for Human Genetics, University of Oxford is primarily focused on the structural biology of extracellular recognition and signalling complexes in development and cancer (https://www.strubi.ox.ac.uk/research/christian-siebold). STRUBI harbours a well-developed infrastructure for large-scale soluble and membrane protein production, purification and crystallization with excellent access to the DIAMOND synchrotron and a range of biophysical and cell-based facilities. The doctoral project concerns the structural and functional characterization of the Hedgehog and Bone Morphogenetic Protein signalling pathways. More details can be found under: http://www.ndm.ox.ac.uk/doctoral-projects/project/structural-biology-of-cell-surface-morphogen-signalling The studentship is funded by Cancer Research UK. Applicants should hold or expect to gain a first or upper second class honours degree. Cancer Research UK will pay a competitive stipend (£19.000 p.a.) as well as University and College fees. Ideal candidates have a strong background in biochemistry and molecular or cell biology, but science graduates in general are welcome to apply. It would be an advantage, but is not necessary, for the candidate to have laboratory experience in any of the following: cloning, mutagenesis, protein expression, purification and crystallographic techniques. Candidates whose first language is not English will be asked to submit a certificate of proficiency in the English language (e.g. IELTS 7.5). Applications should be submitted via the Nuffield Department of Medicine (NDM) Prize Studentship application pipeline (http://www.ndm.ox.ac.uk/for-applicants), quoting project number 118 and “Cancer Research UK” as funding source. The closing date for applications is 10 January 2014. Interviews are expected to take place on 29 and 30 January 2014. For further information please contact Christian Siebold (christ...@strubi.ox.ac.uk).
Re: [ccp4bb] Orientation of molecules
If you suspect your MR solution is crystallographically correct but it does not represent the biological entity - eg - you will generate a dimer if you move molecule B by a symmetry operator such -x,y-1/2,1-z then the easy way is to submit the coordinates to PISA - either in the CCP4 GUI or send them to PDBe to search for quaternary structure, and let PISA sort out the best orientations of possible crystal symmetry Eleanor But Phils suggestion should do the same thing.. On 21 November 2013 18:24, Phil Jeffrey pjeff...@princeton.edu wrote: * Open molecular replacement solution in Coot * Display crystal packing (DrawCell Symmetry), perhaps as Calphas only * Find the symmetry-related instance of copyB that is in the correct position relative to copyA according to your preferences * Use FileSave Symmetry Coordinates to write the structure transposed by that operator (note: select the menu option, then click on the copyB instance) * Since Coot will write the entire structure transposed by that symop, assemble the desired solution from copyA from the mol.rep. solution and copyB from the transposed solution. I'm a Luddite so I use emacs and/or grep for this. Phil Jeffrey Princeton 11/21/13 1:11 PM, Appu kumar wrote: Dear All, I think i have not explained my problem precisely. This may be weird one but let me elaborate more. I have have a protein moleculeA, having N-term, and C-term end. Structurally, it is dimer with anti-parallel arrangement i.e N-terminal of one copyA of molecule form dimer in such a way that it copyB would be arranged in antiparallel fashioned (N-term of copyA is besides C-term of CopyB). So when i am searching for two copy of molecule in phaser it is giving me two copy of molecule in parallel arrangement. So my question is, how to tell phaser that after fixing the orientation of first copy, to change the orientation of 2nd copy with respect to first one so that their n-teminal and c-terminal lies beside each other. I am looking for your valuable suggestion. Thank you
Re: [ccp4bb] AW: [ccp4bb] Dealnig with O-linked mannose
Thanks, Herman. Zhijie, what is the difference between LINK and LINKR? Maybe this will help somebody (though phenix-related): phenix.link_edits parses the pdb for LINK records and outputs the pdb.edits file. Alternatively, phenix.ligand_linking can guess what should be bonded in the absence of LINK records and produce apply_link.def Best rgards, Dmitry On 2013-11-22, at 3:18 AM, herman.schreu...@sanofi.com wrote: Using your favorite editor, you can copy the LINK record from the pdb file generated by Coot and paste it into the pdb file produced by Phenix. You can also make a script to do this. This is what I did during the time LINK records were not properly handled by coot, refmac and buster. Best regards, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Dmitry Rodionov Gesendet: Donnerstag, 21. November 2013 22:09 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Dealnig with O-linked mannose Thank you all for helpful suggestions. My question was how to properly connect a mannose to a serine and real-space refine the result. My apologies for not being clear enough. Coot can't find MAN-SER or SER-MAN in it's library (Coot 0.7.1, mon_lib 5.41) It does not automatically make the bond between MAN C1 and OG of SER either. Here is the way I finally made the connection followed by refinement it in Coot: 1) Get monomer... MAN 2) real-space refine MAN into reasonable position 3) Delete hydrogens and reducing hydroxyl Bond is not detected 4) Extensions-Modelling ...-make Link (Click 2 atoms) ... Click on C1 of MAN and OG of SER dashed bond appears 5) Sphere refine A whole different issue that was touched in the replies is how this model will be handled by refinement programs. For the sake of a record, I am using Phenix and it seems to not respect the described link without massaging by means of either pdb.edits or apply_link.def. Also, phenix.refine does not produce LINK records in the output PDB, so step 4 might have to be repeated. Best regards, Dmitry smime.p7s Description: S/MIME cryptographic signature
Re: [ccp4bb] Orientation of molecules
Hi, If you get the 0.8-pre prerelease version of coot, there's a fantastic new feature that makes this much easier. Instead of File-Save Symmetry Coordinates, you just center on the symmetry copy that you want to use as the master copy and select Extensions-Modelling-Symm Shift Reference Chain Here, and then it just moves the original copy of that chain to the new symmetry position. Once you've adjusted all the chains to what you want, you just save the model. No more need for emacs or grep or even vi! Regards, Randy Read On 21 Nov 2013, at 18:24, Phil Jeffrey pjeff...@princeton.edu wrote: * Open molecular replacement solution in Coot * Display crystal packing (DrawCell Symmetry), perhaps as Calphas only * Find the symmetry-related instance of copyB that is in the correct position relative to copyA according to your preferences * Use FileSave Symmetry Coordinates to write the structure transposed by that operator (note: select the menu option, then click on the copyB instance) * Since Coot will write the entire structure transposed by that symop, assemble the desired solution from copyA from the mol.rep. solution and copyB from the transposed solution. I'm a Luddite so I use emacs and/or grep for this. Phil Jeffrey Princeton 11/21/13 1:11 PM, Appu kumar wrote: Dear All, I think i have not explained my problem precisely. This may be weird one but let me elaborate more. I have have a protein moleculeA, having N-term, and C-term end. Structurally, it is dimer with anti-parallel arrangement i.e N-terminal of one copyA of molecule form dimer in such a way that it copyB would be arranged in antiparallel fashioned (N-term of copyA is besides C-term of CopyB). So when i am searching for two copy of molecule in phaser it is giving me two copy of molecule in parallel arrangement. So my question is, how to tell phaser that after fixing the orientation of first copy, to change the orientation of 2nd copy with respect to first one so that their n-teminal and c-terminal lies beside each other. I am looking for your valuable suggestion. Thank you -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Re: [ccp4bb] AW: [ccp4bb] Dealnig with O-linked mannose
Hi Dimetry, The difference between LINK and LINKR can't be explained better: http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg11865.html Older versions of COOT used to not display the LINKR record, but now the newer versions display both LINK and LINKR records as dotted bonds. I assume that means COOT will now treat LINKR as LINK, otherwise there is no point displaying a bond but not taking its meanings. However outside the refmac-COOT universe, LINKR is not a legitimate record. Zhijie -Original Message- From: Dmitry Rodionov Sent: Friday, November 22, 2013 11:11 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] AW: [ccp4bb] Dealnig with O-linked mannose Thanks, Herman. Zhijie, what is the difference between LINK and LINKR? Maybe this will help somebody (though phenix-related): phenix.link_edits parses the pdb for LINK records and outputs the pdb.edits file. Alternatively, phenix.ligand_linking can guess what should be bonded in the absence of LINK records and produce apply_link.def Best rgards, Dmitry On 2013-11-22, at 3:18 AM, herman.schreu...@sanofi.com wrote: Using your favorite editor, you can copy the LINK record from the pdb file generated by Coot and paste it into the pdb file produced by Phenix. You can also make a script to do this. This is what I did during the time LINK records were not properly handled by coot, refmac and buster. Best regards, Herman -Urspr�ngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Dmitry Rodionov Gesendet: Donnerstag, 21. November 2013 22:09 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Dealnig with O-linked mannose Thank you all for helpful suggestions. My question was how to properly connect a mannose to a serine and real-space refine the result. My apologies for not being clear enough. Coot can't find MAN-SER or SER-MAN in it's library (Coot 0.7.1, mon_lib 5.41) It does not automatically make the bond between MAN C1 and OG of SER either. Here is the way I finally made the connection followed by refinement it in Coot: 1) Get monomer... MAN 2) real-space refine MAN into reasonable position 3) Delete hydrogens and reducing hydroxyl Bond is not detected 4) Extensions-Modelling ...-make Link (Click 2 atoms) ... Click on C1 of MAN and OG of SER dashed bond appears 5) Sphere refine A whole different issue that was touched in the replies is how this model will be handled by refinement programs. For the sake of a record, I am using Phenix and it seems to not respect the described link without massaging by means of either pdb.edits or apply_link.def. Also, phenix.refine does not produce LINK records in the output PDB, so step 4 might have to be repeated. Best regards, Dmitry
[ccp4bb] hello.
http://portal.limon.gen.tr/gm/itfhmazeeuauqaqvqmzusuu.html Rex Palmer 11/23/2013 2:52:00 AM
[ccp4bb] 3D stereo notebook
Dear all, I am looking into ordering a stereo notebook to view 3D protein structure. Which notebook can you recommended? I require that the 3D notebook will be used with Linux and Windows, so support of the correspoding graphics card with both systems is required. In addition, I found that Dell XPS17XPS17D-428 can be used in windows. However I do not know whether 3D view is OK or not in Linux? Moreover, the displayer is 17 inch, I think that it is a little larger. Any comments or experience are welcome. Thanks and best wishes, zhongzhou chen china agricultural university
