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
