Joel,
Some mmdb information still resides at the EBI (including a tarball -
newer ones may be available here
http://lmb.bioch.ox.ac.uk/coot/software/dependencies/):
http://www.ebi.ac.uk/pdbe/docs/cldoc/
Information about atom selection can be found e.g. here:
http://www.ccp4.ac.uk/html/pdbcur.html#atom_selection
B
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:[email protected]] On Behalf Of Bernhard Lohkamp
Sent: Monday, November 15, 2010 7:33 AM
To: [email protected]
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: [email protected]
--
***************************************************
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: [email protected]
