Re: [PyMOL] get_bond bond counting in PyMol

2016-03-25 Thread Vijay Masand 
Dear PyMol Users,

I found an easy way to count total number of bonds in a molecule,
which has been loaded in PyMol viewer:

from chempy import stored, Bond
m = cmd.get_model()
print “number of total bonds:”, len(m.bond)

I hope it will be useful.

Cheers
Vijay


On 3/22/16, Vijay Masand  wrote:
> Dear PyMol Users
>
> While working with a ligand in a pdb file, which I saved in .mol2 file
> format, I used following command:
>
>   get_bond stick_transparency, *
>  I observed following outcome in Pymol.
>  Getting: stick_transparency for 63 bonds in
> object "testing".
>  stick_transparency = 0.0 for object testing
>
> I know that PyMol can count atoms; the above command is providing
> counting of bonds in a molecule. It will be a great help if someone
> can tell me the pymol command or API for counting of Bonds in an
> object loaded in pymol viewer.
>
> Thanks in advance.
>
> From
> Vijay
>
>
> --
> Assistant Professor
> Department of Chemistry,
> Vidya Bharati College, Amravati, 444 602
> Maharashtra, India.
> Phone number- +91-9403312628
> https://sites.google.com/site/vijaymasand/
>


-- 
Assistant Professor
Department of Chemistry,
Vidya Bharati College, Amravati, 444 602
Maharashtra, India.
Phone number- +91-9403312628
https://sites.google.com/site/vijaymasand/

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Re: [PyMOL] The Wiki appears outdated or in error

2016-03-25 Thread James Kress 
Thanks!

 

Jim

 

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From: Sampson, Jared M. [mailto:jms2...@cumc.columbia.edu] 
Sent: Friday, March 25, 2016 3:03 PM
To: jimkress...@kressworks.org
Cc: pymol-users 
Subject: Re: [PyMOL] The Wiki appears outdated or in error

 

Hi Jim -  

 

Here's a patch for Open Source PyMOL (rev4153) that adds the
"collada_background_box" setting (default=0).  If you're using Open Source
PyMOL and are up to applying it and rebuilding, feel free to use it.
Otherwise, I already sent it to Thomas, so hopefully it will be incorporated
into SVN and Incentive PyMOL soon.

 

Cheers,

Jared

 

--

Jared Sampson

Columbia University

 

On Mar 24, 2016, at 2:26 PM, Sampson, Jared M. mailto:jms2...@cumc.columbia.edu> > wrote:

 

Hi Jim -  

 

When I 

 

set geometry_export_mode, 1

 

in PyMOL, then save myfile.dae, then import into MeshLab, MeshLab hangs.

 

I can confirm that this happens for me, too.  I guess maybe Meshlab requires
the camera? 

 

As a workaround, you can go back to the previous version with
collada_geometry_mode=1 and simply delete the box.  You can do this within
Meshlab by using the "Select Connected Components in a region" tool to
select a corner the box, then clicking the "Delete the current set of
selected faces and all the vertices surrounded by that faces" button (see
attached screenshot).  Then, if you zoom in (the box is 100x larger than the
largest dimension of the scene), your scene will be there. 

 

I'm working on a patch right now to exclude the bounding background box from
default COLLADA output and make it optional via a new
`collada_background_box` setting.  

 

Sorry for the confusion, hope this clears it up.

 

Cheers,

Jared

 

--

Jared Sampson

Columbia University

 

 

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

2016-03-25 Thread Sampson, Jared M. 
Hi Jim -

Here's a patch for Open Source PyMOL (rev4153) that adds the 
"collada_background_box" setting (default=0).  If you're using Open Source 
PyMOL and are up to applying it and rebuilding, feel free to use it.  
Otherwise, I already sent it to Thomas, so hopefully it will be incorporated 
into SVN and Incentive PyMOL soon.

Cheers,
Jared

--
Jared Sampson
Columbia University

On Mar 24, 2016, at 2:26 PM, Sampson, Jared M. 
mailto:jms2...@cumc.columbia.edu>> wrote:

Hi Jim -

When I

set geometry_export_mode, 1

in PyMOL, then save myfile.dae, then import into MeshLab, MeshLab hangs.

I can confirm that this happens for me, too.  I guess maybe Meshlab requires 
the camera?

As a workaround, you can go back to the previous version with 
collada_geometry_mode=1 and simply delete the box.  You can do this within 
Meshlab by using the "Select Connected Components in a region" tool to select a 
corner the box, then clicking the "Delete the current set of selected faces and 
all the vertices surrounded by that faces" button (see attached screenshot).  
Then, if you zoom in (the box is 100x larger than the largest dimension of the 
scene), your scene will be there.

I'm working on a patch right now to exclude the bounding background box from 
default COLLADA output and make it optional via a new `collada_background_box` 
setting.

Sorry for the confusion, hope this clears it up.

Cheers,
Jared

--
Jared Sampson
Columbia University




collada_background_box.patch
Description: collada_background_box.patch
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