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] 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] Orientation of molecules
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 On 21/11/2013, Matthias Zebisch matth...@strubi.ox.ac.uk wrote: i think you need to explain the problem in greater detail to the community eg. how do you come to know that the orientation of mol2 is 180° flipped - perhaps it is correct as phaser puts it? No one will be able to help you with so little information Best wishes, Matthias - Dr. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Phone (+44) 1865 287549; Fax (+44) 1865 287547 Email matth...@strubi.ox.ac.uk Website http://www.strubi.ox.ac.uk - On 11/21/2013 5:38 PM, Appu kumar wrote: Dear All, I seek your valuable suggestion on a MR problem. I am asking phaser to search for two molecules in ASU, first molecules phaser searched right but when placing the second molecule, it orientation has got flipped by 180 deegree. Is there any way to tell phaser to fix the orientation of second copy of molecules. ? Looking forward for your valuable suggestion Thank you very much in advance Appu -- - Dr. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Phone (+44) 1865 287549; Fax (+44) 1865 287547 Email matth...@strubi.ox.ac.uk Website http://www.strubi.ox.ac.uk -
[ccp4bb] Orientation of molecules
Dear All, I seek your valuable suggestion on a MR problem. I am asking phaser to search for two molecules in ASU, first molecules phaser searched right but when placing the second molecule, it orientation has got flipped by 180 deegree. Is there any way to tell phaser to fix the orientation of second copy of molecules. ? Looking forward for your valuable suggestion Thank you very much in advance Appu
Re: [ccp4bb] Orientation of molecules
* 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
