[chimerax-users] dssp works on whole chain

[王镐锋]

Dear Elaine C. Meng,      Thanks for your advice. It helps me a lot with redefining secondary structure of  amino acid residues. But one problem described by my picture, the red helix showed in the picture in chimeraX break into two helixes. But from the corresponding sequence, it show a constant helix in the sequence viewer. Also, when I use PyMOL or chimera to open this pdb file, this part is presented as a constant helix. It confused me a lot and I don't how to solve this, although I have tried the setattr command on this zone, but the cartoon doesn't change. Could you please help me combine this two seperate helixes to form constant one? Thanks so much.Best,
Haofeng Wang
Ph.D student 
Tianjin University, China




                     




From: Elaine Meng <meng at cgl.ucsf.edu>
Date: 2021-07-26 02:00:34
To:  "王镐锋" <wanghf at tju.edu.cn>
Cc:  chimerax-users at cgl.ucsf.edu
Subject: dssp works on whole chain>Dear Haofeng Wang,
>The "dssp" secondary structure calculation works by identifing hydrogen-bonding patterns throughout the whole protein, so even if you specify few atoms, it will still apply to the whole chain:
>
>From the help page, <https://rbvi.ucsf.edu/chimerax/docs/user/commands/dssp.html>:
>
>"The calculation applies to all protein/peptide chains in models containing the specified atoms."
>
>If you want to manually change the secondary structure of any amino acid residues, you could use the "setattr" command instead.  See for example this previous post:
><https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-February/000362.html>
>
>I hope this helps,
>Elaine
>-----
>Elaine C. Meng, Ph.D.                       
>UCSF Chimera(X) team
>Department of Pharmaceutical Chemistry
>University of California, San Francisco
>
>> On Jul 24, 2021, at 9:48 PM, 王镐锋 via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>> 
>> Dear guys, 
>>     Sorry to disturb you guys. When I use the UCSF ChimeraX, I try to define the second structure for part of model. I type the command like "dssp (#1 & sel) energy cutoff 0.5 minheliexlen 3", it works for the whole model instead of what I choose specially. Could you please help me? Thanks so much!
>> Best,
>> Haofeng Wang
>> Ph.D student 
>> Tianjin University, China
>




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