https://pymolwiki.org/index.php/Modeling_and_Editing_Structures
--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431
On Wed, Aug 1, 2018 at 8:29 AM Mohammad Goodarzi <mohammad.goda...@gmail.com>
wrote:
> Hi Kevin,
>
> Yes I am talking about the the C-terminal Ser in the chain A of 2J3S. How
> can I fix that ? I would like to do other work with this chain like
> homology modeling, mutation influence on domian etc using Gromacs. but This
> Ser in C-terminal has a missing so I cannot do anything about it.
> what is your thought?
>
> Thanks
> Mohammad
>
>
>
>
>
> On Wed, Aug 1, 2018 at 10:25 AM Kevin Jude <kj...@stanford.edu> wrote:
>
>> Please be more specific with your questions. Which atoms? Which Ser? How
>> did you remove chain B, etc?
>>
>> For some reason only the N is modeled for the C-terminal Ser in both
>> chains of 2J3S; if that's what you're talking about, then the issue is with
>> the deposited PDB file, and likely the atoms were not visible in electron
>> density. If you're talking about other Ser residues then you'll have to
>> give more information.
>>
>> Best wishes
>> Kevin
>>
>> --
>> Kevin Jude, PhD
>> Structural Biology Research Specialist, Garcia Lab
>> Howard Hughes Medical Institute
>> Stanford University School of Medicine
>> Beckman B177, 279 Campus Drive, Stanford CA 94305
>> Phone: (650) 723-6431
>>
>> On Wed, Aug 1, 2018 at 8:03 AM Mohammad Goodarzi <
>> mohammad.goda...@gmail.com> wrote:
>>
>>> Hello,
>>>
>>> I have a protein that i get from PDB https://www.rcsb.org/structure/2J3S
>>> then I try to remove the chain B, and all water etc except the chain A.
>>> it causes that I miss some atoms on the SER. Can you please advise how
>>> to deal with it?
>>>
>>> Thanks
>>> Mohammad
>>>
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>
>>
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
