Re: [PyMOL] export sequence alignment
Hi Joel, you can save alignment objects to clustalw format with the save command. Creating alignment objects with cealign is supported since version 1.5.0.5. The latest 1.6alpha also fixed swapped mobile/target arguments for creating alignment objects (only matters if aligning more than 2 structures). PyMOL fetch 1oky 1pkg 1t45, async=0 PyMOL remove not chain A PyMOL cealign 1oky, 1pkg, object=aln PyMOL cealign 1oky, 1t45, object=aln PyMOL save alignment.aln, aln Also keep in mind that this is a all-to-one alignment, not a real multiple (all-to-all) alignment. Cheers, Thomas Joel Tyndall wrote, On 04/08/13 01:05: Sorry forgot to add, I want to use multiple structures Hi folks, Sorry if this has already been asked but can I export the sequence alignment from PyMOL? I am looking to use cealign to do this (on windows) and I need the structural alignment based sequence alignment. Other tools maybe? I have mustang already Cheers Joel -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Minimize network downtime and maximize team effectiveness. Reduce network management and security costs.Learn how to hire the most talented Cisco Certified professionals. Visit the Employer Resources Portal http://www.cisco.com/web/learning/employer_resources/index.html ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] export sequence alignment
Sorry forgot to add, I want to use multiple structures Hi folks, Sorry if this has already been asked but can I export the sequence alignment from PyMOL? I am looking to use cealign to do this (on windows) and I need the structural alignment based sequence alignment. Other tools maybe? I have mustang already Cheers Joel _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall Ph: +64 3 479 7293 -- Minimize network downtime and maximize team effectiveness. Reduce network management and security costs.Learn how to hire the most talented Cisco Certified professionals. Visit the Employer Resources Portal http://www.cisco.com/web/learning/employer_resources/index.html___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] export sequence alignment
Hi folks, Sorry if this has already been asked but can I export the sequence alignment from PyMOL? I am looking to use cealign to do this (on windows) and I need the structural alignment based sequence alignment. Other tools maybe? I have mustang already Cheers Joel _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall Ph: +64 3 479 7293 -- Minimize network downtime and maximize team effectiveness. Reduce network management and security costs.Learn how to hire the most talented Cisco Certified professionals. Visit the Employer Resources Portal http://www.cisco.com/web/learning/employer_resources/index.html___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
