Re: [PyMOL] Displaying sticks on RNA bases only

[Thomas Holder]

Hi Maria,

The following shows filled rings and sticks for the nucleosides:

set cartoon_ring_finder, 1
set cartoon_ring_mode, 3
as cartoon

To not show filled rings for the nucleobases, you can hide cartoon for the 
sidechain selection, and show sticks instead (the sidechain selection keyword 
was introduced in PyMOL 1.7.0):

hide cartoon, sidechain
show sticks, sidechain extend 1

See also:
http://pymolwiki.org/index.php/Overview_of_nucleic_acid_cartoons

Hope that helps.

Cheers,
  Thomas

On 20 Jan 2016, at 10:10, COSTA Maria  wrote:

> Hello,
> 
> I am using Pymol to visualize nucleic acid structures ( I'm a new user) and I 
> would like to be able to display the functional groups of bases A, G, T/U, C 
> with sticks while using the cartoon mode : cartoon_ring_finder, 1 or 2 for 
> the ribose_phosphate backbone of the molecule. Can you please tell me how to 
> achieve that ? 
> For the moment the only thing I found was to display the 'cartoon' and the 
> 'stick' modes at the same time to get the sticks corresponding to the 
> functional groups of the bases but then I also visualize all the sticks of 
> the riboses and phosphates which makes my drawings 'overloaded'. I hope I was 
> clear enough. 
> 
> Many thanks in advance for your answers,
> 
> Maria
> 
> CNRS
> France

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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[PyMOL] Ray tracing max_threads

[Jesper Lykkegaard Karlsen]

Hi,

I am doing some heavy duty ray tracing in PyMOL.

I realize spreading the job over multiple nodes in a PBS requires MPI 
integration in PyMOL, but this is run on a single machine with 36 
physical CPU cores and 72 logical threads.
Although, during PyMOL ray tracing CPU usage maxes-out at 32 treads.

I have even tried setting max_treads to 72, but PyMOL refuses to use any 
more than 32 threads.

Why this limitation? and is the a way to overcome it?

Thanks

Jesper

-- 
Jesper Lykkegaard Karlsen
Scientific Computing
Centre for Structural Biology
Department of Molecular Biology and Genetics
Aarhus University
Gustav Wieds Vej 10C
8000 Aarhus C

E-mail: je...@mbg.au.dk


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