Thomas, thanks again!
I want to recall to the ligand assignment via
select motif, (pepseq TYG) and not (name C+N+O)
alter motif, type="HETATM"
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. Also I've checked this new pdb and find alot of
TER strings between each of residues.
I've tried to remove this TER strings and renamed HETATOMS to ATOMS but
this didnt help :(
I suppose that error might be due to the HETATM ussage because when I check
sequence of my structure I'vee found many repeates of the assigned residues
like
THR-THR-THR-THR-TYR-TYR-TYR-TYR-TYR-GLY-GLY-GLY instead of simple
THR-TYR-GLY triplet
What should I do?
2012/1/23 James Starlight <jmsstarli...@gmail.com>
> Thomas, thanks again!
>
>
>
> I want to recall to the ligand assignment via
>
>
> select motif, (pepseq TYG) and not (name C+N+O)
> alter motif, type="HETATM"
>
> 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. Also I've checked this new pdb and find alot of
> TER strings between each of residues.
>
> I've tried to remove this TER strings and renamed HETATOMS to ATOMS but
> this didnt help :(
>
> What should I do?
>
>
> James
>
>
> 2012/1/23 Thomas Holder <spel...@users.sourceforge.net>
>
>> Hi James,
>>
>>
>> How I could select all this visible (relevant) part and save it in the
>>> separate pdb?
>>> I've not found such simple selection by the visible part in the
>>> selection algebra :(
>>>
>>
>> use the "visible" single-word selector :)
>>
>> http://pymolwiki.org/index.**php/Single-word_Selectors<http://pymolwiki.org/index.php/Single-word_Selectors>
>>
>> save onlyvisible.pdb, visible
>>
>>
>> Cheers,
>> Thomas
>>
>> --
>> Thomas Holder
>> MPI for Developmental Biology
>> Spemannstr. 35
>> D-72076 Tübingen
>>
>
>
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