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
