[PyMOL] Pymol spheres/circles

[Smith, Laura]

Hi,

I'm pretty new to Pymol and not that great with all the syntax etc.

I am wanting to easily show where a mutation is located in  cartoon model. I've 
tried to label the residues with spheres but it generates more than one dot and 
that's not what I want. I just want one single sphere/circle/dot localised to 
an atom on the structure for me to label myself.

Basically like figure 2A in this paper >> 
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1326319/

Thanks,
Laura


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Re: [PyMOL] Pymol spheres/circles

[Osvaldo Martin]

Hi Laura,

Read here

how to select a single atom using the GUI. Or using the command line and
the selection albegra 
do something like:

select mutant, resi 2 and name ca

This will create a selection named mutant consisting on the alpha carbon of
residue 2.

Once the atom is selected you can choose the most convenient representation
for you, like an sphere.

Cheers,
Osvaldo.

On Tue, Aug 30, 2016 at 2:18 PM, Smith, Laura 
wrote:

Hi,
>
>
>
> I’m pretty new to Pymol and not that great with all the syntax etc.
>
>
>
> I am wanting to easily show where a mutation is located in  cartoon model.
> I’ve tried to label the residues with spheres but it generates more than
> one dot and that’s not what I want. I just want one single
> sphere/circle/dot localised to an atom on the structure for me to label
> myself.
>
>
>
> Basically like figure 2A in this paper >> http://www.ncbi.nlm.nih.gov/
> pmc/articles/PMC1326319/
>
>
>
> Thanks,
>
> Laura
>
>
>
>
>
> 
> --
>
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
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>
​
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Re: [PyMOL] Pymol spheres/circles

[Sampson, Jared M.]

Hi Laura -

You can also choose single atom selection mode through the menu: click Mouse > 
Selection mode > Atoms and then click your alpha carbon atom.  However, it can 
be tricky to hit the right atom if you're only looking at a cartoon 
representation, so I usually prefer to use the PyMOL command line as Osvaldo 
mentioned with something like:

```
select mutant, myprotein and resi 2
show spheres, mutant and name CA
```

Hope that helps.

Cheers,
Jared



On Aug 30, 2016, at 8:18 AM, Smith, Laura 
mailto:laura.j.sm...@ucl.ac.uk>> wrote:

Hi,

I’m pretty new to Pymol and not that great with all the syntax etc.

I am wanting to easily show where a mutation is located in  cartoon model. I’ve 
tried to label the residues with spheres but it generates more than one dot and 
that’s not what I want. I just want one single sphere/circle/dot localised to 
an atom on the structure for me to label myself.

Basically like figure 2A in this paper >> 
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1326319/

Thanks,
Laura


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[PyMOL] Making movies with PyMol

[COSTA Maria]

Hello everyone,

I know how to use PyMOL to do different types of figures, rather simple ones. 
Now, I would like to learn how to make movies with PyMol. Not only rotations of 
an object but also movies showing how two residues come into interaction or how 
a residue moves from one position to the other. I would like to have your 
advice about how to get started (tutorials, documents to read, etc).

Many thanks in advance for your insights

Maria
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[PyMOL] Pymol Command window not displaying

[Srikanth Gumma]

Hi,

I recently installed pymol from source using python-2.7.12 in my cluster. I
have to install python, tcl in a non standard location as this is a
cluster.

After successful installation of pymol, I'm facing an issue while opening
pymol. I'm not able to see pymol command window, and receiving the below
error on the console.

PyMOL(TM) Molecular Graphics System, Version 1.8.2.0.
 Copyright (c) Schrodinger, LLC.
 All Rights Reserved.

Created by Warren L. DeLano, Ph.D.

PyMOL is user-supported open-source software.  Although some versions
are freely available, PyMOL is not in the public domain.

If PyMOL is helpful in your work or study, then please volunteer
support for our ongoing efforts to create open and affordable scientific
software by purchasing a PyMOL Maintenance and/or Support subscription.

More information can be found at "http://www.pymol.org";.

Enter "help" for a list of commands.
Enter "help " for information on a specific command.

 Hit ESC anytime to toggle between text and graphics.

 Detected OpenGL version prior to 2.0. Shaders and volumes unavailable.
 OpenGL graphics engine:
  GL_VENDOR:   Intel
  GL_RENDERER: Intel(R) HD Graphics 4600
  GL_VERSION:  1.4 (4.0.0 - Build 9.18.10.3272)
Traceback (most recent call last):
  File "/app/python/intel/pymol/lib/python/pmg_tk/__init__.py", line 35, in
run
PMGApp(pymol_instance,skin).run(poll)
  File "/app/python/intel/pymol/lib/python/pmg_tk/PMGApp.py", line 323, in
__init__
self.root = Tk() # creates the root window for the application
  File "/app/python/intel/2.7.12/lib/python2.7/lib-tk/Tkinter.py", line
1815, in __init__
self.tk = _tkinter.create(screenName, baseName, className, interactive,
wantobjects, useTk, sync, use)
TclError: invalid command name "tcl_findLibrary"
 Detected 24 CPU cores.  Enabled multithreaded rendering.


Appreciate any help to resolve the issue.

-srikanth
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