The link to the mmdb documentation at ebi no longer works since I think it was in Eugene's personal area. Does anyone know where the documentation can be found now? I didn't see it in the source tarballs I downloaded either.
Thanks, Joel -----Original Message----- From: Mailing list for users of COOT Crystallographic Software [mailto:c...@jiscmail.ac.uk] On Behalf Of Bernhard Lohkamp Sent: Monday, November 15, 2010 7:33 AM To: COOT@JISCMAIL.AC.UK Subject: Re: [COOT] Rigid body fit of trimeric domain You can use the following function in scripting (here pythonic): rigid_body_refine_by_atom_selection(imol, atom_selection_string) where atom_selection_string is the 'standard' mmdb atom selection string, explained in detail in the mmdb manual. Briefly, the string should be formed in this manner: /mdl/chn/seq(res).ic/atm[elm]:aloc e.g. "/1/A/12-130/CA" or e.g. "//*/1-10" for residues 1-10 in all chains (something you may want). Hope this helps, B > Hello, > Having a CRYO-em-map 9A resolution and a trimeric molecule with two > big domains . Each chain comes from the first domain and goes into the > second. After fitting the first domain into the map, I wish to do the > same with the second domain using a rigid body fit (it has to be > shifted and rotated around a triple-helix-connection). Defining the > region to be fitted Coot says always : the residues must be in the same chain. > Is there a possibility to fit the second domain with the intact trimer > into the map? > Thank you, > Juergen > -- *************************************************** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
