In addition I'd like to know more about possible flexibility in the
representation of the protein-ligand contacts by means of the present->
ligand site option.
For instance sometimes I have ligand group situated in the some distance
from the interiour group. So this space forms empty cavity around ligand.
So if I use present- ligand sites by default pymol didnt see the interiour
residues due to its remoteness from ligand. But could I vary some cutoff
distance to represent POSSIBLE polar and packing contacts like as this
interiour would be in the contact with the ligand? I'd like to use this for
better prediction of the mutations wich will change the shape and geometry
of the ligand binding pockets in the above cases. \
Thanks again,
James
2012/1/23 James Starlight <jmsstarli...@gmail.com>
> Thanks Thomas
>
> The reversible convertion indeed solved problem.
>
> James
>
>
> 2012/1/23 Thomas Holder <spel...@users.sourceforge.net>
>
>> Hi James,
>>
>>
>> I have no problems with the representation of the assigned ligand with
>>> its environment but when I save this as new pdb via
>>>
>>> save test.pdb, visible
>>>
>>> my output pdb contains some errors like missing bonds between HETATM
>>> residues ( ligand ) etc.
>>>
>>
>> maybe this trick was too dirty... change the type back to ATOM before
>> saving:
>>
>>
>> select motif, (pepseq TYG) and not (name C+N+O)
>> alter motif, type="HETATM"
>> preset.ligand_cartoon("all")
>> alter motif, type="ATOM"
>>
>>
>> Also I've checked this new pdb and find alot of
>>> TER strings between each of residues.
>>>
>>
>> This is because you only selected the local environment which has only
>> short pieces of the polymer. PyMOL sees chain breaks there. You can
>> suppress TER records by:
>>
>> unset pdb_use_ter_records
>>
>>
>> Cheers,
>> Thomas
>>
>> --
>> Thomas Holder
>> MPI for Developmental Biology
>> Spemannstr. 35
>> D-72076 Tübingen
>>
>
>
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