Re: [PyMOL] Running PyMol (Linux) on Chromebook

[J.R. W]

> I assume this input on the (base) environment line indicated within the 
> instalpython3.com/chromebook  
> instructions.



This one. This is the command line terminal for instructions to send to the 
computer. Not to be confused with the Python Interpreter REPL (the >>> that 
comes up after typing “python”)

Jordan


> On Jul 5, 2020, at 8:28 PM, Wink, Donald J  wrote:
> 
> Dr. Willis:
> 
> Thank you very much for the suggestion. I will proceed to share it with the 
> students and we will gladly report back what happens.
>  
> As for the instruction line you mention:  Or should we do it on the command 
> line that appears *after* starting python?
>  
> Best wishes
> Donald Wink
>  
> From: Jordan Willis  
> Sent: Sunday, July 5, 2020 8:15 PM
> To: Wink, Donald J 
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] Running PyMol (Linux) on Chromebook
>  
> Might I recommend a conda based solution. 
>  
> https://installpython3.com/chromebook/ 
> 
>  
> Install miniconda on your Chromebook using the attached link. 
>  
> Then you can simply use conda to install pymol
>  
>  
> conda install -c schrodinger pymol
>  
> Jordan Willis, PhD
> 
> 
> On Jul 5, 2020, at 4:36 PM, Wink, Donald J  > wrote:
>  
> I am a university (UIC) faculty member who is directing some entering college 
> students in a structured research programs. Things are going pretty well for 
> those with MacOS or Windows computers. But I have a couple of students with 
> Chromebooks who are attempting to install and run the Linux version.
>  
> We’ve downloaded and extracted the tar files but encountered some library 
> issues that are apparently blocking startup.
>  
> If there are users with experience in managing this environment, I’d love to 
> pose some more detailed questions.
>  
> Thanks
> Donald Wink
>  
>  
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Re: [PyMOL] Copy object distorts cartoon backbone.

[J.R. W]

I’m so sorry to spam. The answer is set cartoon_smooth_loops 1

Jordan

> On Aug 24, 2017, at 2:24 PM, J.R. W <jwillis0...@gmail.com> wrote:
> 
> I have a trimeric structure. It looks great when I show it in a cartoon 
> object. As soon as I copy one of the chains to an object, the backbone 
> immediately distorts. The residues perfectly align with the parent object. 
> Does anyone know what’s happening? Can I copy the representation of the 
> parent object too? Please see the attached pictures from the parent object 
> and the copied object.
> 
> 
> 
> Jordan
> 
> 
> https://drive.google.com/file/d/0BzArdal219l4MFBGQTNqN2dydFE/view?usp=sharing 
> <https://drive.google.com/file/d/0BzArdal219l4MFBGQTNqN2dydFE/view?usp=sharing>
> 

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[PyMOL] Copy object distorts cartoon backbone.

[J.R. W]

I have a trimeric structure. It looks great when I show it in a cartoon object. 
As soon as I copy one of the chains to an object, the backbone immediately 
distorts. The residues perfectly align with the parent object. Does anyone know 
what’s happening? Can I copy the representation of the parent object too? 
Please see the attached pictures from the parent object and the copied object.



Jordan


https://drive.google.com/file/d/0BzArdal219l4MFBGQTNqN2dydFE/view?usp=sharing 


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Re: [PyMOL] which PyMOL to open?

[J.R. W]

I think Tcl-Tk GUI + Console is the most familiar pymol.

Jordan

> On Apr 21, 2017, at 3:06 PM, Jed Goldstone  wrote:
> 
> The 3D stuff (Zalman, etc) is only if you're using 3D glasses. I typically 
> use the Tk + console option that opens two windows (the GUI and a pythonesque 
> console).
> 
> Jed
> 
> On Apr 21, 2017 2:16 PM, "AJ Vincelli"  > wrote:
> Hello all,
> 
> I hate to ask a dumb question, but I need some seriously novice help. I just 
> installed educational-use-only PyMOL (version 1.7.4.5, x64) on a WIndows 10 
> machine, and I'm trying to open the program from the Windows 10 start menu. 
> However, there are many choices! Does anybody know what the difference is 
> between these options (like Tcl-Tk, Console, Quad buffer, Dynamic, etc.)? Or 
> is there a handy webpage that explains the difference? I can't find anything 
> in the Wiki or FAQ websites.
> 
> Screenshot is attached and embedded here:
> 
> 
> 
> Thanks!
> 
> AJ
> 
> 
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[PyMOL] Set fullscreen and grid mode in batch script

[J.R. W]

Hi,

What I’d like to do is set_grid_mode_1, ray trace, and then output a png in 
batch mode (-c)


However if you code this in the .pml:

set_grid_mode, 1
set grid_slot, 2, object2
set grid_slot, 1, object1

viewport 1000,1000 #not sure how to get fullscreen this maybe OS specific

ray 1000,1000
png somepic.png
cmd.save(lookatthis.pse”)

Grid mode does not show up in the picture and the viewport in the session is 
still the default window size. However, grid mode does work in the session. 

So my question(s) are this:

1. Can you use grid mode in batch mode scripts to output an image?
2. Can you encode a full screen GUI in the pymol session so when you open up 
the session, it is full screen?

Using MacPyMOL latest release, can switch to X11 if necessary.

Thanks so much!

Jordan


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