Hi All,
I just installed Pymol on a new computer (Mac OS X 10.15.6 Catalina) using
Homebrew. It appears that the APBS Tools 2.1 is not functioning correctly . I
receive the error below when trying to run the program from the legacy
plug-ins. Has anyone encountered this issue? If so, what was y
It seems that pymol refresh the screen only after the script completed.
I tried cmd.refresh(), cmd.rebuild(obj) in the loop, but they did not
help either. I do not know the solution.
On 8/31/20 8:33 PM, ZHANG Cheng wrote:
Not work.
time.sleep( 5 )
did not outpput any error, but freeze for a f
Not work.
time.sleep( 5 )
did not outpput any error, but freeze for a few seconds. However, nothing come
out on the Pymol interface.
-- Original --
From:
This one?
https://www.tutorialspoint.com/python/time_sleep.htm
On 8/31/20 7:51 PM, ZHANG Cheng wrote:
I use the command below, trying to display the object one by one, with
2 seconds in between. So how to "wait for 2 seconds"?
from pymol import cmd
cmd.enable('protein_1')
# how to hold for 2 s
I use the command below, trying to display the object one by one, with 2
seconds in between. So how to "wait for 2 seconds"?
from pymol import cmd
cmd.enable('protein_1')
# how to hold for 2 seconds?
cmd.disable('protein_1')
cmd.enable('protein_2')
# how to hold for 2 seconds?
cmd.disable('pr
Dear Pymol Team,
I have been playing around with stereo view using NVIDIA 3D vision 2 system
on Windows. I am using a RTX 2070, together with pymol 2.3.3.
Long story short I have managed to get it to work, but exclusively in
Fullscreen mode. When the session is in a windowed mode, it does not eng
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:
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!!!
Afte
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
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
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"
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:
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 Profe
Hi Aswini,
Enter at the PyMOL prompt below the command history window the following
command:
remove not polymer
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.
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 fr
Hello, I am unable to remove non protein moiety. Is it possible?
If so please share the procedure.
Regards
Ashwini s
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