Question about viewing chain pdb in ChimeraX
Hello, I am using ChimeraX to save the .pdb file of chains in a protein. Here are my commands: +) open 7oci +) select #1/E + save /.../E.pdb model #1 selectedOnly true Then I opened that E.pdb model in ChimeraX and saw that chain E only contains helices. However, when I checked the .pdb file of chain E in a text editor, I saw that it contains sheets as well. The number of sheets are even larger (Number of helices: 52, sheets: 76). Do you know the reason why I don't see the sheets of chain E in ChimeraX? Am I missing something? I have attached the screenshots and the pdb of chain E. I took this chain from the pdb ID 7oci. Thank you very much. I am looking forward to hearing from you. Best regards, Thu
Hi Thu, ChimeraX is including all the helices/sheets in the structure, despite the fact that you are only writing out a part of the structure. We have a ticket open in our bug-tracking database for fixing this behavior, and I will add you to the recipient list so you will be notified when it gets fixed. In the interim, if you delete the unwanted parts of the structure then the PDB file will only have the relevant helices and sheets, e.g.: open 7oci del ~/E save <path>/E.pdb To save multiple chains you will have to close the partial structure and reopen 7oci, which is a pain but is the best that's available right now. --Eric Eric Pettersen UCSF Computer Graphics Lab
On May 1, 2023, at 10:59 PM, Thu Nguyen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I am using ChimeraX to save the .pdb file of chains in a protein. Here are my commands: +) open 7oci +) select #1/E + save /.../E.pdb model #1 selectedOnly true Then I opened that E.pdb model in ChimeraX and saw that chain E only contains helices. However, when I checked the .pdb file of chain E in a text editor, I saw that it contains sheets as well. The number of sheets are even larger (Number of helices: 52, sheets: 76). Do you know the reason why I don't see the sheets of chain E in ChimeraX? Am I missing something? I have attached the screenshots and the pdb of chain E. I took this chain from the pdb ID 7oci. Thank you very much. I am looking forward to hearing from you.
Best regards, Thu
<Screenshot 2023-05-02 at 1.44.01 AM.png><Screenshot 2023-05-02 at 1.50.03 AM.png><E.pdb>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thank you very much for your explanation and the alternative solution. It really helps. Best regards, Thu On Tue, May 2, 2023 at 1:38 PM Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Thu, ChimeraX is including all the helices/sheets in the structure, despite the fact that you are only writing out a part of the structure. We have a ticket open in our bug-tracking database for fixing this behavior, and I will add you to the recipient list so you will be notified when it gets fixed. In the interim, if you *delete* the unwanted parts of the structure then the PDB file will only have the relevant helices and sheets, *e.g.*:
open 7oci del ~/E save <path>/E.pdb
To save multiple chains you will have to close the partial structure and reopen 7oci, which is a pain but is the best that's available right now.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On May 1, 2023, at 10:59 PM, Thu Nguyen via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello, I am using ChimeraX to save the .pdb file of chains in a protein. Here are my commands: +) open 7oci +) select #1/E + save /.../E.pdb model #1 selectedOnly true Then I opened that E.pdb model in ChimeraX and saw that chain E only contains helices. However, when I checked the .pdb file of chain E in a text editor, I saw that it contains sheets as well. The number of sheets are even larger (Number of helices: 52, sheets: 76). Do you know the reason why I don't see the sheets of chain E in ChimeraX? Am I missing something? I have attached the screenshots and the pdb of chain E. I took this chain from the pdb ID 7oci. Thank you very much. I am looking forward to hearing from you.
Best regards, Thu
<Screenshot 2023-05-02 at 1.44.01 AM.png><Screenshot 2023-05-02 at 1.50.03 AM.png><E.pdb>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (2)
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Eric Pettersen -
Thu Nguyen