Re: [PyMOL] [EXTERNAL] present b factor putty on select
Hi, Blaine,
Thank you, that's helpful. But a problem with creating a new object is that the
conformation of the newly created object for the selection is sightly different
from its counterpart in the original object. If the original object is shown as
cartoon, then both the putty presentation of new object and the cartoon
presentation of its counterpart in the original object at site of the
conformational difference will appear in the image produced in this way, and
that's ugly. Is there a way the avoid this shortcoming?
Best,
--
From:Mooers, Blaine H.M. (HSC)
Sent At:2020 Oct. 27 (Tue.) 18:09
To:孙业平 ; pymol-users
Subject:RE: [PyMOL] [EXTERNAL] present b factor putty on select
I am sorry. I am wrong. I should have tested by suggestion.
Irregardless of the selection that I specify, the entire chain is changed.
I would go with your plan B and create a new object for the selection.
create test, resi 100:150
preset.b_factor_putty("test")
The above worked with pdb file 4dgr.
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: Mooers, Blaine H.M. (HSC) [blaine-moo...@ouhsc.edu]
Sent: Tuesday, October 27, 2020 4:54 AM
To: sunyeping; pymol-users
Subject: Re: [PyMOL] [EXTERNAL] present b factor putty on select
Hi sunyeping,
You are right; there is a way via the command line:
preset.b_factor_putty(selection='all')
Replace "all" with your selection.
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: sunyeping via PyMOL-users [pymol-users@lists.sourceforge.net]
Sent: Tuesday, October 27, 2020 3:09 AM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] present b factor putty on select
Dear all,
I know that if you want to visualize b facotor of a objector in pymol, you can
use A>Present>b factor putty. However, how can show the b factor putty on a
certain selection of the object? Is there any command line to do this or do I
have to create a new object for the selection and still use the A>Present>b
factor putty operation?
Thank you,
Best regards
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Re: [PyMOL] [EXTERNAL] present b factor putty on select
I am sorry. I am wrong. I should have tested by suggestion.
Irregardless of the selection that I specify, the entire chain is changed.
I would go with your plan B and create a new object for the selection.
create test, resi 100:150
preset.b_factor_putty("test")
The above worked with pdb file 4dgr.
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: Mooers, Blaine H.M. (HSC) [blaine-moo...@ouhsc.edu]
Sent: Tuesday, October 27, 2020 4:54 AM
To: sunyeping; pymol-users
Subject: Re: [PyMOL] [EXTERNAL] present b factor putty on select
Hi sunyeping,
You are right; there is a way via the command line:
preset.b_factor_putty(selection='all')
Replace "all" with your selection.
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: sunyeping via PyMOL-users [pymol-users@lists.sourceforge.net]
Sent: Tuesday, October 27, 2020 3:09 AM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] present b factor putty on select
Dear all,
I know that if you want to visualize b facotor of a objector in pymol, you can
use A>Present>b factor putty. However, how can show the b factor putty on a
certain selection of the object? Is there any command line to do this or do I
have to create a new object for the selection and still use the A>Present>b
factor putty operation?
Thank you,
Best regards
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Re: [PyMOL] [EXTERNAL] present b factor putty on select
Hi sunyeping, You are right; there is a way via the command line: preset.b_factor_putty(selection='all') Replace "all" with your selection. 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: sunyeping via PyMOL-users [pymol-users@lists.sourceforge.net] Sent: Tuesday, October 27, 2020 3:09 AM To: pymol-users Subject: [EXTERNAL] [PyMOL] present b factor putty on select Dear all, I know that if you want to visualize b facotor of a objector in pymol, you can use A>Present>b factor putty. However, how can show the b factor putty on a certain selection of the object? Is there any command line to do this or do I have to create a new object for the selection and still use the A>Present>b factor putty operation? Thank you, Best regards ___ 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
