Dear Cheng, Please note that the original split_states code that I posted has a typo (the dangers of posting a reply before dawn!) The semicolon after pdb should be a comma.
split_states protein, prefix=test; Thank you Tamas for the pseudo code for iterating the application of spectrum!!! After applying the spectrum with Tamas's code, you will want to combine the 1000 objects into one file. join_states multitest, (test*) And then you will want to save the multistate object multisave multitest.pdb,multitest,0 Best regards, Blaine Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 ________________________________________ From: ZHANG Cheng [272699...@qq.com] Sent: Monday, August 31, 2020 5:56 AM To: Mooers, Blaine H.M. (HSC); pymol-users Subject: Re:RE: [EXTERNAL] [PyMOL] How to color based on b-factor for all the frames in one object in Pymol? Hi Blaine, Thank you for your suggestion. "set all_states, on" could not work. For splitting the object, it is an alternatve. But I have 1000 frames in the object, and I want to show a movie by playing the frames. Best Cheng ------------------ Original ------------------ From: "Mooers, Blaine H.M. (HSC)" <blaine-moo...@ouhsc.edu>; Date: Mon, Aug 31, 2020 06:13 PM To: "ZHANG Cheng"<272699...@qq.com>;"pymol-users"<pymol-users@lists.sourceforge.net>; Subject: RE: [EXTERNAL] [PyMOL] How to color based on b-factor for all the frames in one object in Pymol? Hi ZHANG Cheng, Did you try? set all_states, on;spectrum b Another approach would to split the states into separate objects and then apply the spectrum command to each object. split_states protein.pdb; prefix=test;spectrum b,,test* Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 ________________________________________ From: ZHANG Cheng [272699...@qq.com] Sent: Sunday, August 30, 2020 4:40 PM To: pymol-users Subject: [EXTERNAL] [PyMOL] How to color based on b-factor for all the frames in one object in Pymol? I load a protein.pdb file into Pymol. This file has multiple frames (or states), and with different b-factor values at different frames at the PDB file b-factor columns. After running the "spectrum b" command, the colouring is only based on the last state of the object. So can I colour the frames differently using their corresponding b-factor values? In that case, I can see the colour changing throughout the frame playing. _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
