Mea culpa,
I reworked using_active_atom and forgot to update some calls to it.
FIX:
replace extensions.py (in YourWincootDirectory\share\coot\python\) with
the following
http://code.google.com/p/coot/source/browse/branches/release-0.6.2/python/extensions.py
or wait for a build revision 3211 or newer.
B
Thanks for the quick reply- I tried the replace residue box as well, but
it didn't work for me either. After checking that the restraint did
read L-peptide under group, the standard, unmutated amino acid remained
on-screen after hitting the mutate button. Here's what it says at the
bottom of the coot dos box at when I try to do this:
File "C:\WinCoot\share\coot\python\coot_utils.py, line 103, in
using_active_atom
for <func, aa_args, extra_args> in funcs:
TypeError: an integer is required.
Any ideas on how to fix this would be greatly appreciated.
Thanks,
Scott
On Sun, Oct 10, 2010 at 11:58 AM, Paul Emsley
<[email protected] <mailto:[email protected]>> wrote:
________________________________________
From: Mailing list for users of COOT Crystallographic Software
[[email protected] <mailto:[email protected]>] On Behalf Of
Scott Horowitz [[email protected] <mailto:[email protected]>]
Sent: 10 October 2010 15:59
To: [email protected] <mailto:[email protected]>
Subject: mutate to unnatural amino acid
I'm trying to solve a structure with an unnatural amino acid not in
the coot or ccp4 libraries, and I'd like to be able to mutate a
preliminary structure to have this amino acid for further
refinement. I successfully created a .cif file using libcheck and
sketcher in CCP4 (specified when created to be an L-peptide), and by
converting this to a SMILES file, was able to load it into coot and
see it on the screen. I am also able to directly import the residue
by clicking "import cif dictionary", and importing the files created
using libcheck and sketcher. The following things are true either
way I import the residue: In coot, when i go to edit restraints, it
recognizes the residue, and I can make changes; however, when I open
the simple mutate window, the unnatural amino acid I have imported
does not show up. Is there another way to do this?
-----
Yes , if you have a non-standard residue/monomer, you need to use
Extensions -> Modelling -> Replace Residue...
Section 5.17.3 in the Manual.
Paul
(from wretched Microsoft web mail)
--
***************************************************
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]
