By the way,
C could not find if all those scripts are able to make CAPS on the residues
but if it's not possible Iwant to add some CAP group ( e.g ACE to the N
term) via builder module. So I've chose ACE residue from that module and
obtained message
pick location to attach ace
how now i could specify exactly location of that attachment if i want that
ACE just be the first residue in my pdb ( linked with the actual first
residue on the N term )?
James
2011/11/23 James Starlight <jmsstarli...@gmail.com>
> Thanks Thomas!
>
>
> Those scripts works fine. Could you tell me if there any way to install
> all of those scripts as the pymol plugins ( that I need not to load this
> scripts every time when I sttart pymol de novo )?
>
>
> James
>
> 2011/11/23 James Starlight <jmsstarli...@gmail.com>
>
>> Thanks thomas
>>
>> Those scripts works fine. Could you tell me if there any way to install
>> all of those scripts as the pymol plugins ( that I need not to load this
>> scripts every time when I sttart pymol de novo )?
>>
>>
>> James
>>
>>
>> 2011/11/23 Thomas Holder <spel...@users.sourceforge.net>
>>
>>> Hi James,
>>>
>>> check this PyMOLWiki page:
>>> http://pymolwiki.org/index.**php/Fab<http://pymolwiki.org/index.php/Fab>
>>>
>>> However, the "fab" command does not take user defined phi/psi angles,
>>> only 4 predefined conformations ("ss" argument). User defined phi/psi can
>>> be handled by these scripts:
>>>
>>> http://pymolwiki.org/index.**php/CreateSecondaryStructure<http://pymolwiki.org/index.php/CreateSecondaryStructure>
>>> http://pldserver1.biochem.**queensu.ca/~rlc/work/pymol/#**model<http://pldserver1.biochem.queensu.ca/%7Erlc/work/pymol/#model>
>>>
>>> Cheers,
>>> Thomas
>>>
>>> James Starlight wrote, On 11/23/11 11:43:
>>>
>>> Dear PyMol Users!
>>>>
>>>> I wounder to know about possible ways of creation of the peptide
>>>> structures via PyMol Builder module. In particular I need create a linear
>>>> structure of my protein ( with fixed phi and psi angles) for futher folding
>>>> molecular dynamics simulation of that peptide. But in builder module I
>>>> found only helix and sheet conformations for each aa. residue. How I can
>>>> specify desired values for both torsion angles ?
>>>>
>>>> Also I'd like to know is there any module for pymol wich could be used
>>>> for obtaining linear unfolded structure for the defined sequence or folded
>>>> protein ( in pdb) ?
>>>>
>>>> Thanks,
>>>>
>>>>
>>>> James
>>>>
>>>
>>> --
>>> Thomas Holder
>>> MPI for Developmental Biology
>>> Spemannstr. 35
>>> D-72076 Tübingen
>>>
>>
>>
>
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