Hi Scott,
this is getting messy. Sorry about this. A few points to clarify and
maybe a solution:
In 0.6.1 mutate_by_overlap (and hence 'Replace Residue..') would always
use libcheck to get the replacement monomer. In the development releases
this got changed so that you can use monomers which are not in the
standard dictionary but for which you have a pdb and library (cif file)
loaded. You will require the up-to-date coot_utils.py file for this.
However replacing the old coot_utils.py with this new file will break
other things (which is possibly what you observe now)(x). To fix this
and make it backwards compatible may require quite a bit of extra work.
As a remedy for now please update your WinCoot to the latest pre-release
(if this is not revision 3211 or later, then replace extensions.py and
coot_utils.py with the ones found in the directory
http://code.google.com/p/coot/source/browse/#svn/branches/release-0.6.2/python
). This works for me (*).
Hope this helps at least a bit,
B
(x) and some required functions are actually not available in 0.6.1
(*) the discussed functions work in 0.6.1 as well - besides that you
cannot use your 'own' pdb/cif files as described above. Not sure how
this problem occurred in the first place?!
Yes, I tried this as well, with both the old extensions.py as well as
the new version I downloaded today, but received an error saying that
the monomer I'm looking for wasn't found, despite the fact that I had
previously loaded the .cif dictionary and was able to edit restraints.
Scott
On Sun, Oct 10, 2010 at 8:05 PM, Paul Emsley <[email protected]
<mailto:[email protected]>> wrote:
Scott Horowitz wrote:
I just tried using the new coot_utils.py, but now most of the
extensions menu actually won't show up at all, including the
replace residue menu item.
If this is going to be difficult to figure out, is there a
version I could go back to that might have this function intact?
You could do what it says in the manual, instead of trying to use
the gui, i.e. (in the python scripting window):
mutate_by_overlap(imol, chain_id, res_no, new_three_letter_code)
Paul
--
***************************************************
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]
