I normally use this command with that purpose: align obj1&(ss h)&name ca, obj2&(ss h)&name ca
That is, obj2 is structurally aligned onto obj1 on the basis the CA trace on the regions where secondary structure matches alfa helix (ss h) Hugo Kerff Frédéric wrote: > Hello, > > Is there a way to perform secondary structure matching with Pymol. I > already tried the align function with different selections without any > success but the 2 proteins obviously share the same fold with low sequence > identity. > I know it can be done in other software like Coot but I'd like to avoid > having to switch from one program to another all the time. > Thank you. > > Fred > > > -- Hugo G. de Teran, PhD. "Parga Pondal" Research fellow Fundación Pública Galega de Medicina Xenómica - SERGAS Santiago de Compostela (SPAIN) Phone +34 981563100 ext 13873 e-mail:hugo.te...@usc.es http://web.usc.es/~hugogdt ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ 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
