Also, "join_states multitest, (test*)" could not achieve the purpose. The
multiple objects can be combined into one object, but the b-factor in this
object is all the same as the last frame.
------------------ Original ------------------
From:
"ZHANG Cheng"
<272699...@qq.com>;
Date: Mon, Aug 31, 2020 08:58 PM
To: "Mooers, Blaine H.M.
(HSC)"<blaine-moo...@ouhsc.edu>;"pymol-users"<pymol-users@lists.sourceforge.net>;
Subject: Re:RE: Re:RE: [EXTERNAL] [PyMOL] How to color based on b-factor
for all the frames in one object in Pymol?
Dear Blaine,
I tried "split_states protein, prefix=test", it can output multiple objects,
with each object having 1 frame.
However, when each object (test0001, test0002, ...) is saved as PDB, I found
that the b-factor values are all the same as the last frame of the protein.pdb.
Best
Cheng
------------------ Original ------------------
From:
"Mooers, Blaine H.M. (HSC)"
<blaine-moo...@ouhsc.edu>;
Date: Mon, Aug 31, 2020 08:29 PM
To: "ZHANG
Cheng"<272699...@qq.com>;"pymol-users"<pymol-users@lists.sourceforge.net>;
Subject: RE: Re:RE: [EXTERNAL] [PyMOL] How to color based on b-factor for
all the frames in one object in Pymol?
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._______________________________________________
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