[PyMOL] To remove non protein moiety

Hello, I am unable to remove non protein moiety. Is it possible? If so please share the procedure. Regards Ashwini s ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourcefor

[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 fr

Re: [PyMOL] [EXTERNAL] To remove non protein moiety

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.

Re: [PyMOL] [EXTERNAL] 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 Profe

Re: [PyMOL] [EXTERNAL] 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:

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

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"

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

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

Re: [PyMOL] [EXTERNAL] 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

Re: [PyMOL] [EXTERNAL] 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!!! Afte

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

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:

[PyMOL] Quad-Buffered Stereo 3D in Windows and Windowed Mode?

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

[PyMOL] How to hold/wait for some time?

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

Re: [PyMOL] How to hold/wait for some time?

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

Re: [PyMOL] How to hold/wait for some time?

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:

Re: [PyMOL] How to hold/wait for some time?

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

[PyMOL] APBSTools

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