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