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
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@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
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@cgl.ucsf.edu Date: 2021-07-26 02:00:34 To: "王镐锋" wanghf@tju.edu.cn Cc: chimerax-users@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@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
Dear Haofeng Wang, There is an additional value that needs to be set (ss_id), to tell the program that it is really one long helix and not two helices (some structures have two different helices that are adjacent).
How to do this is described in previous posts, for example,part #2 of this message: https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-February/000902.html
... here are additional messages on the same topic, but they say basically the same thing as the above: https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-August/000629.html https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-March/002006.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 25, 2021, at 9:14 PM, 王镐锋 via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
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
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王镐锋