On Sat, 13 Sep 2014, Shane Caldwell wrote:
Hi Helena,
I'm not sure if this is the same issue, but I've run into a problem where there
is a mismatch between atom names and restraints
files where some programs use 'primes' and others use asterisks (I assume this
is part of ongoing standardization?). The ribose
ring goofs it up. Keeping the restraints and coordinates from the same program
(I have been using GRADE) through all refinement
has kept this from being an issue anymore for me. You just need to load your
own .cif file when you open the coordinates as well.
Cheers,
Shane Caldwell
McGill University
> On Sep 12, 2014 8:36 AM, "Helena Taberman" <[email protected]> wrote:
>>
>> Hi,
>>
>> I am using the coot 0.8-pre (revision 5201) version and having problems with
my ligand cif files. My ligand is just a common
NADP and the atom names at the PDB file match the atom names at the cif file,
but for some reason I am not able to do any real
space refinement ect. at coot for it since the coot fails to match (to the
dictionary) the following model atom names and it
would cause exploding atoms. I have tried to change my NADP to different
molecules downloaded form PDB or just searching with the
three letter code from the dictionary of coot, but having trouble with any
molecule used. There’s also this persistent clash in
the middle of the NADP molecule on both sides of the phosphorous next to the
ribose ring.
>>
>> I’m getting despered. Would you have any ideas?
>>
>> Best regards,
>> Helena
Helena,
Shane is completely correct. You have almost certainly hit
a problem that your PDB file is using old v2 atom names whereas
you recent coot/ccp4 is using the "new" (5 years ago?) atom names.
You can easily see how the atom names differ by visting RCSB ligand expo
for NAP at:
http://ligand-expo.rcsb.org/reports/N/NAP/index.html
Then select the "Atom Nomenclature" tab.
Try to use V3 atom names if at all possible.
To fix: We distribute a utility with BUSTER that converts a pdb file with
V2 name to V3 (or vice versa) called pdb_vconv. But to be honest it would
be easier to use a text editor (emacs, gedit....)
Hope this helps.
Oliver
p.s. you could try a grade dictionary from http://grade.globalphasing.org/
(thanks Shane) but I shouldn't abuse the coot list :-;
