Dear Faisal,
I usually assign in PYMOL the secondary structure generally obeying DSSP
output.
You have to use the alter command. eg:
alter myprotein and resi 103:106, ss='H'
Bytheway, pymol swaps inside and outside color on left handed helices,
wich you might also have.
Hope this helps,
Matthias
-----------------------------------------
Dr. Matthias Zebisch
Division of Structural Biology,
Wellcome Trust Centre for Human Genetics,
University of Oxford,
Roosevelt Drive,
Oxford OX3 7BN, UK
Phone (+44) 1865 287549;
Fax (+44) 1865 287547
Email [log in to unmask]
Website http://www.strubi.ox.ac.uk
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On 9/26/2013 9:02 PM, Faisal Tarique wrote:
>
> Dear all
>
> Sorry for the off topic question.
>
> My protein has few G310 helices. It is clearly visible through STRIDE
> or DSSP, but when i open the structure in PYMOL it didnt show it.
> Other visualization graphics like CHIMERA and VMD are able to pick
> few of them but not all the G310 helices..For manuscript preparation i
> have drawn the topology diagram taking the output from STRIDE and DSSP
> while the overall 3D structure is from PYMOL..Will it be O.K to show
> some helices missing from the output of pymol while they are present
> in the toplogy diagrma ? or the reviewer will raise the issue? hope
> you are able to understand what i mean to say.
>
> Please suggest me
>
> --
> Regards
>
> Faisal
> School of Life Sciences
> JNU
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