[PyMOL] calculation of the contact surface between subunits

[Smith Liu]

Dear All,


Will you please tell me the pymol command for calculation of the contact 
surface between subunits of a protein complex? And what is the command for 
calculation of the cavity volume surrounded by the protein complex?


Smith--
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Re: [PyMOL] The Wiki appears outdated or in error

[James Kress]

Bob,

 

Thanks for the note.  The pdf files you generated were quite nice.  I just 
cannot get the quality of output you got using the PyMOL to dae to u3d to pdf 
path.  All I get are washed out colors.  No surface properties (shine, 
specular, etc.) at all.

 

PDF3DReportGen is the only software I have found that can give me close to the 
representation I need.  Even then, I have to use VMD, export to obj and then 
import to PDF3DReportGen to get good quality graphics.

 

Very discouraging.

 

Jim

 

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From: Robert Hanson [mailto:hans...@stolaf.edu] 
Sent: Saturday, April 02, 2016 1:14 AM
To: jimkress...@kressworks.org
Cc: Thomas Holder ; pymol-users 

Subject: Re: [PyMOL] The Wiki appears outdated or in error

 

In case you are interested, Jim, Jmol will read (most/some) PyMOL session 
files, and Jmol can then create both an idtf for generating a u3d file, and a 
small sample TeX file also that can be used to create a PDF containing it. 

I had some interest in u3d back in 2009, when I wrote this exporter. You might 
be interested in my notes at the top of 
https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/jmol/export/_IdtfExporter.java
 

Here are a few examples created using Jmol: http://chemapps.stolaf.edu/jmol/u3d/

As I recall, the TeX file is necessary in order to properly reproduce the 
viewport state.


My conclusion was that u3d is an absolutely unmanageable file format. Its 
construction is totally obtuse, and the idtf->u3d converter has bugs that will 
probably never be fixed. I could be wrong, and in the intervening years it has 
improved, but my impression at the time was that it was an experimental format 
out of Adobe's research labs that never really made it and hasn't been 
developed much since then. 

Its inclusion in PDF file quite frankly takes the "P" out of "PDF."

Bob Hanson

​

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Re: [PyMOL] Problem with isomesh without map

[Thomas Holder]

Hi Filip,

This is a bug, we'll fix that (probably by next week, looks like an easy fix).

Cheers,
  Thomas

On 01 Apr 2016, at 16:16, Filip Leonarski  
wrote:

> Hi,
> 
>I'm struggling with making compact PSE files with Pymol state for ribosome 
> structures with electron density maps. In general these maps are huge in 
> 200-500 MB range. In previous versions of PyMol (1.7.x) a following trick 
> worked:
> a) make isomesh
> b) delete map
> c) save pse
> PSE was of a decent size. Currently PyMol crashes when trying to do that.
> 
> Is it possible to fix this one?
> 
> Best,
> Filip
> 
> 
> -- 
> Filip Leonarski, PhD
> IBMC/CNRS
> 15 rue René Descartes
> 67084 Strasbourg Cedex

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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[PyMOL] Problem with isomesh without map

[Filip Leonarski]

Hi,

   I'm struggling with making compact PSE files with Pymol state for
ribosome structures with electron density maps. In general these maps are
huge in 200-500 MB range. In previous versions of PyMol (1.7.x) a following
trick worked:
a) make isomesh
b) delete map
c) save pse
PSE was of a decent size. Currently PyMol crashes when trying to do that.

Is it possible to fix this one?

Best,
Filip


-- 
Filip Leonarski, PhD
IBMC/CNRS
15 rue René Descartes
67084 Strasbourg Cedex
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