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Re: [PyMOL] [EXTERNAL] How to color based on b-factor for all the frames in one object in Pymol?
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From: Tamas H. <bio...@gm...> - 2020-08-31 12:22:41
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you can also try not to split and set/activate the given frame in the for loop it could happen that spectrum works on the active frame (which was the last one in your case) https://pymolwiki.org/index.php/Frame On 8/31/20 2:16 PM, ZHANG Cheng wrote: > Thank you, this could be a solution. I would still like not splitting > the object if possible. > On 8/31/20 1:54 PM, Tamas Hegedus wrote: > You may write and use a script after splitting the object. > > a pseudo code: > > for i in range(1, 1001): > spectrum b, rainbow, frame_i > enable frame_i > sleep sometime > disable frame_i > > On 8/31/20 12:56 PM, ZHANG Cheng wrote: >> 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)" <Bla...@ou...>; >> *Date:* Mon, Aug 31, 2020 06:13 PM >> *To:* "ZHANG >> Cheng"<272...@qq...>;"pymol-users"<pym...@li...>; >> *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 [272...@qq...] >> 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/pym...@li... >> Unsubscribe:https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > |
