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 [email protected]
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
