On 13/09/14 19:06, Oliver Smart wrote:
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"
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.
I am unconvinced. Helena says that her Coot is recent and therefore the
dictionary against which Helena compared the atoms is recent too. There
haven't been asterisks in Coot for (as you say) about 5 years.
Helena, please try this:
File -> Get Monomer -> NAP
then
Regularize Zone on the imported NAP.
It should just work.
For the refinement to work on your NAP the atom names should match both
the dictionary and the imported NAP.
p.s. you could try a grade dictionary from
http://grade.globalphasing.org/
(thanks Shane) but I shouldn't abuse the coot list :-;
Grade-chat not unwelcome here :-)
Paul.
