Forgot to include the mailing list. doh!
-
Jean-Paul Ebejer
Early Stage Researcher
On 9 July 2012 09:23, JP <jeanpaul.ebe...@inhibox.com> wrote:
>
> On 6 July 2012 21:07, Paul Emsley <paul.ems...@bioch.ox.ac.uk> wrote:
>
>> On 06/07/12 10:27, JP wrote:
>> > The SMILES is in fact, a wget call away - since I am processing PDB
>> > deposited structures.
>> > http://www.rcsb.org/pdb/rest/describeHet?chemicalID=NAG
>>
>> It is not clear to me how the SMILES helps you. You still have to map
>> between rdkit atoms and PDB atom names, do you not? How about using the
>> monomer library?
>>
>
> I was planning to do an rdkit "SubStruct" match between the "PDB rdkit
> ligand" and the smiles-generated rdkit one.
> Then I could use the atom id mappings between the two. Not the most
> performant of solutions...
>
>
>>
>>
>> http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/dictionary.html
>>
>>
> Interesting ... thanks.
>
>
>
>
>> >
>> > For the protein I can somehow "guess" the bonds.
>>
>> What do you mean by "guess" here? Are you worried about histidine
>> protonation?
>>
>>
> I should be, of course. And about the correctness of the ligands in the
> PDB file (as Adrian pointed out earlier), and ...
>
>
> Perhaps this approach is fraught with problems... and needs some serious
> rethinking.
>
>
>
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