Re: [PyMOL] [EXTERNAL] How to color based on b-factor for all the frames in one object in Pymol?

[<272...@qq...>]

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...&gt;;
Date:&nbsp;Mon, Aug 31, 2020 06:13 PM
To:&nbsp;"ZHANG Cheng"<272...@qq...&gt;;"pymol-users"<pym...@li...&gt;;

Subject:&nbsp;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.