Re: [ccp4bb] Easy way to generate symmetry-related protein chains?
You might also be interested in the supercell http://www.pymolwiki.org/index.php/Supercell pymol script, which generates all chains in the unit cell as opposed to within some radius of the asymmetric unit. -Spencer On Fri, May 22, 2015 at 2:45 PM, Roger Rowlett rrowl...@colgate.edu wrote: If you mean generation of pdb coordinates of specific symmetry chains (not just viewing) then you can do this with the symexp command in pymol. Select the desired symmetry partners and save as pdb. You may want to edit duplicate chain id labels in coot or a text editor. Roger Rowlett On May 22, 2015 8:25 AM, Mark J van Raaij mjvanra...@cnb.csic.es wrote: Just wondering if there is an easy way to generate symmetry-related chains, necessary for instance to join protein chains into the biologically relevant multimers. What I do now is look up the correct symmetry and translation operator in COOT or PYMOL and input that in PDBSET, but there may be easier ways. in the CCP4bb archive I found the following tip for COOT: Extensions - Modelling - Symm Shift Reference Chain Here. but that does not appear to be available in COOT, or not anymore. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij
[ccp4bb] Easy way to generate symmetry-related protein chains?
Just wondering if there is an easy way to generate symmetry-related chains, necessary for instance to join protein chains into the biologically relevant multimers. What I do now is look up the correct symmetry and translation operator in COOT or PYMOL and input that in PDBSET, but there may be easier ways. in the CCP4bb archive I found the following tip for COOT: Extensions - Modelling - Symm Shift Reference Chain Here. but that does not appear to be available in COOT, or not anymore. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij
Re: [ccp4bb] Easy way to generate symmetry-related protein chains?
Hi Mark, If the structure has been deposited in the PDB you can download the biological assembly - even works for viruses, cheers, Matt. On 22/05/2015 14:24, Mark J van Raaij wrote: Just wondering if there is an easy way to generate symmetry-related chains, necessary for instance to join protein chains into the biologically relevant multimers. What I do now is look up the correct symmetry and translation operator in COOT or PYMOL and input that in PDBSET, but there may be easier ways. in the CCP4bb archive I found the following tip for COOT: Extensions - Modelling - Symm Shift Reference Chain Here. but that does not appear to be available in COOT, or not anymore. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij -- Matthew Bowler Synchrotron Crystallography Group European Molecular Biology Laboratory 71 avenue des Martyrs CS 90181 F-38042 Grenoble France === Tel: +33 (0) 4.76.20.76.37 Fax: +33 (0) 4.76.20.71.99 http://www.embl.fr/ ===
Re: [ccp4bb] Easy way to generate symmetry-related protein chains?
If you mean generation of pdb coordinates of specific symmetry chains (not just viewing) then you can do this with the symexp command in pymol. Select the desired symmetry partners and save as pdb. You may want to edit duplicate chain id labels in coot or a text editor. Roger Rowlett On May 22, 2015 8:25 AM, Mark J van Raaij mjvanra...@cnb.csic.es wrote: Just wondering if there is an easy way to generate symmetry-related chains, necessary for instance to join protein chains into the biologically relevant multimers. What I do now is look up the correct symmetry and translation operator in COOT or PYMOL and input that in PDBSET, but there may be easier ways. in the CCP4bb archive I found the following tip for COOT: Extensions - Modelling - Symm Shift Reference Chain Here. but that does not appear to be available in COOT, or not anymore. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij
Re: [ccp4bb] Easy way to generate symmetry-related protein chains? (summary)
It seems the easiest way is to Save Symmetry Coordinates in COOT and then assemble the desired chains in a text editor. Extensions - Modelling - Symm Shift Reference Chain Here. is present if you build COOT yourself, but is not in the pre-built releases (for now). Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 22 May 2015, at 14:24, Mark J van Raaij wrote: Just wondering if there is an easy way to generate symmetry-related chains, necessary for instance to join protein chains into the biologically relevant multimers. What I do now is look up the correct symmetry and translation operator in COOT or PYMOL and input that in PDBSET, but there may be easier ways. in the CCP4bb archive I found the following tip for COOT: Extensions - Modelling - Symm Shift Reference Chain Here. but that does not appear to be available in COOT, or not anymore. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij
Re: [ccp4bb] Easy way to generate symmetry-related protein chains?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Mark, you can 'File - Save Symmetry Coordinates' and reload the PDB file. In my Coot 0.8.2-pre, revision 5628, Extensions - Modelling - Symm Shift Reference Chain Here is available works. Cheers, Tim On 05/22/2015 02:24 PM, Mark J van Raaij wrote: Just wondering if there is an easy way to generate symmetry-related chains, necessary for instance to join protein chains into the biologically relevant multimers. What I do now is look up the correct symmetry and translation operator in COOT or PYMOL and input that in PDBSET, but there may be easier ways. in the CCP4bb archive I found the following tip for COOT: Extensions - Modelling - Symm Shift Reference Chain Here. but that does not appear to be available in COOT, or not anymore. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1 iD8DBQFVXyRWUxlJ7aRr7hoRApEHAKCXVn9WxCCVcep8Q8fE94uKP8OQjgCdFQUm S1he0gyS0uevsh4fsnGl+j4= =ulwH -END PGP SIGNATURE-
Re: [ccp4bb] Easy way to generate symmetry-related protein chains? (summary)
Yes, Save Symmetry Coordinates in COOT is a very easy way. To avoid text editing, you can first reload the pdb and use the Copy Fragment ... under Extensions/Modeling to get the desired chains. Then use the Merge Molecules under Calculate to assemble. Yong -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Mark J van Raaij Sent: Friday, May 22, 2015 10:09 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Easy way to generate symmetry-related protein chains? (summary) It seems the easiest way is to Save Symmetry Coordinates in COOT and then assemble the desired chains in a text editor. Extensions - Modelling - Symm Shift Reference Chain Here. is present if you build COOT yourself, but is not in the pre-built releases (for now). Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 22 May 2015, at 14:24, Mark J van Raaij wrote: Just wondering if there is an easy way to generate symmetry-related chains, necessary for instance to join protein chains into the biologically relevant multimers. What I do now is look up the correct symmetry and translation operator in COOT or PYMOL and input that in PDBSET, but there may be easier ways. in the CCP4bb archive I found the following tip for COOT: Extensions - Modelling - Symm Shift Reference Chain Here. but that does not appear to be available in COOT, or not anymore. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij
