pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Jim,

There is a beta version of Incentive PyMOL available for download from http://pymol.org/download/1811/ (version 1.8.1.1 BETA).

Cheers,
  Thomas

On 29 Mar 2016, at 23:30, James Kress <jim...@kr...> wrote:

> Does that mean it is in the pay version now?  If yes, how do I get it,
> through the normal download link?
> 
> Jim
> 
> James Kress Ph.D., President
> The KressWorks® Foundation 
> An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization
> “ENGINEERING THE CURE” ©
> (248) 605-8770
> 
> Learn More and Donate At:
> Website: http://www.kressworks.org
> Facebook: https://www.facebook.com/KressWorks.Foundation/
> Twitter: @KressWorksFnd
> 
> Confidentiality Notice | This e-mail message, including any attachments, is
> for the sole use of the intended recipient(s) and may contain confidential
> or proprietary information. Any unauthorized review, use, disclosure or
> distribution is prohibited. If you are not the intended recipient,
> immediately contact the sender by reply e-mail and destroy all copies of the
> original message.
> 
> -----Original Message-----
> From: Thomas Holder [mailto:tho...@sc...] 
> Sent: Sunday, March 27, 2016 4:10 PM
> To: pymol-users <pym...@li...>
> Subject: Re: [PyMOL] The Wiki appears outdated or in error
> 
> Hi Jared,
> 
> Thanks a lot for the patch. Applied to SVN rev 4154.
> 
> Cheers,
>  Thomas
> 
> On 25 Mar 2016, at 20:03, Sampson, Jared M. <jm...@cu...>
> wrote:
> 
>> 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.
> <jm...@cu...> 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>-----------------

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Dear Pymol users,

a quick google search returned empty regarding the ability of Pymol to 
autosave the session at a specified time interval.
The feature is available in different programs from text to vector 
editors etc.
I would find it useful to have the ability to automatically save a 
couple of recent checkpoints while I am using Pymol.

My question is if this would be interesting/useful for anybody and a 
question to the developers if this can be implemented?

Best regards,
Matic

Dear All,
I was wondering if there is a way to select faces, vertices and/or edges
from a CGO either using the mouse or the command line. How difficult
would be to add this, and how would you do that?

It would be very useful for us if we could get that working.

Thanks,
Albert



-- 
---------------------------------
  Dr Albert Solernou
  EPSRC Research Fellow,
  Department of Physics and Astronomy,
  University of Leeds
  Tel: +44 (0)1133 431451

Does that mean it is in the pay version now?  If yes, how do I get it,
through the normal download link?

Jim

James Kress Ph.D., President
The KressWorks® Foundation 
An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization
“ENGINEERING THE CURE” ©
(248) 605-8770

Learn More and Donate At:
Website: http://www.kressworks.org
Facebook: https://www.facebook.com/KressWorks.Foundation/
Twitter: @KressWorksFnd

Confidentiality Notice | This e-mail message, including any attachments, is
for the sole use of the intended recipient(s) and may contain confidential
or proprietary information. Any unauthorized review, use, disclosure or
distribution is prohibited. If you are not the intended recipient,
immediately contact the sender by reply e-mail and destroy all copies of the
original message.

-----Original Message-----
From: Thomas Holder [mailto:tho...@sc...] 
Sent: Sunday, March 27, 2016 4:10 PM
To: pymol-users <pym...@li...>
Subject: Re: [PyMOL] The Wiki appears outdated or in error

Hi Jared,

Thanks a lot for the patch. Applied to SVN rev 4154.

Cheers,
  Thomas

On 25 Mar 2016, at 20:03, Sampson, Jared M. <jm...@cu...>
wrote:

> 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.
<jm...@cu...> 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>----------------------------------------------
-----------------------

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Hi Jared,

Thanks a lot for the patch. Applied to SVN rev 4154.

Cheers,
  Thomas

On 25 Mar 2016, at 20:03, Sampson, Jared M. <jm...@cu...> wrote:

> 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. <jm...@cu...> 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>---------------------------------------------------------------------

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

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 <vij...@gm...> 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 = 0.00000 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/

Thanks!

 

Jim

 

James Kress Ph.D., President

The KressWorksR Foundation 

An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization

"Engineering The Cure" C

(248) 605-8770

 

Learn More and Donate At:

Website:  <" rel="nofollow">http://www.kressworks.org/> http://www.kressworks.org

Facebook: https://www.facebook.com/KressWorks.Foundation/

Twitter: @KressWorksFnd

 

Confidentiality Notice | This e-mail message, including any attachments, is
for the sole use of the intended recipient(s) and may contain confidential
or proprietary information. Any unauthorized review, use, disclosure or
distribution is prohibited. If you are not the intended recipient,
immediately contact the sender by reply e-mail and destroy all copies of the
original message.

 

From: Sampson, Jared M. [mailto:jm...@cu...] 
Sent: Friday, March 25, 2016 3:03 PM
To: jim...@kr...
Cc: pymol-users <pym...@li...>
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. <jm...@cu...
<mailto:jm...@cu...> > 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

 

 

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. <jm...@cu...<mailto:jm...@cu...>> 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

Hi Jared,

 

Thanks for the information.  There was no screen shot attached, however.

 

Jim

 

James Kress Ph.D., President

The KressWorks® Foundation 

An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization

“Engineering The Cure” ©

(248) 605-8770

 

Learn More and Donate At:

Website:  <" rel="nofollow">http://www.kressworks.org/> http://www.kressworks.org

Facebook: https://www.facebook.com/KressWorks.Foundation/

Twitter: @KressWorksFnd

 

Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message.

 

From: Sampson, Jared M. [mailto:jm...@cu...] 
Sent: Thursday, March 24, 2016 2:26 PM
To: jim...@kr...
Cc: Sampson, Jared M. <jm...@cu...>; pymol-users <pym...@li...>
Subject: Re: [PyMOL] The Wiki appears outdated or in error

 

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

 

On Mar 24, 2016, at 1:05 PM, James Kress <jim...@kr... <mailto:jim...@kr...> > wrote:

 

Hi Jared,

 

When I 

 

set geometry_export_mode, 1

 

in PyMOL, then save myfile.dae, then import into MeshLab, MeshLab hangs.  Is there an alternative to MeshLab I can use to generate the u3d file?

 

Thanks.

 

Jim

 

James Kress Ph.D., President

The KressWorks® Foundation 

An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization

“Engineering The Cure” ©

(248) 605-8770

 

Learn More and Donate At:

Website:  <" rel="nofollow">http://www.kressworks.org/> http://www.kressworks.org

Facebook:  <" rel="nofollow">https://www.facebook.com/KressWorks.Foundation/> https://www.facebook.com/KressWorks.Foundation/

Twitter: @KressWorksFnd

 

Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message.

 

From: Sampson, Jared M. [mailto:jm...@cu...] 
Sent: Wednesday, March 23, 2016 10:53 PM
To: jim...@kr... <mailto:jim...@kr...> 
Cc: pymol-users <pym...@li... <mailto:pym...@li...> >
Subject: Re: [PyMOL] The Wiki appears outdated or in error

 

Hi Jim -  

 

This is something we've been talking about changing.  The entire scene as viewed within PyMOL is inside that block, including the camera position.   (The interior surface of the block itself provides the background color of the scene.)  Some viewers, e.g. Mac Preview.app, default to displaying from the camera position, but others, including MeshLab, don't, which is understandably confusing. 

 

To export only the geometry without any of the scene information, you can `set geometry_export_mode, 1` in PyMOL before saving the .dae.

 

Hope that helps!

 

Cheers,

Jared

 

P.S. if you are able to work out a protocol/workflow for generating 3D PDFs that is better than what's on the wiki, I hope you will consider updating the wiki to help others who might try it in the future.

 

Jared Sampson

Columbia University

 

On Mar 23, 2016, at 8:26 PM, James Kress < <mailto:jim...@kr...> jim...@kr...> wrote:

 

I installed v 1.8.0.6  

 

When I save ‘myfile.dae’ and then import into MeshLab, all I get is a solid gray block.

 

What do I need to do in PyMOL to export my DNA structure?

 

Thanks.

 

Jim

 

James Kress Ph.D., President

The KressWorks® Foundation 

An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization

“Engineering The Cure” ©

(248) 605-8770

 

Learn More and Donate At:

Website:  <" rel="nofollow">http://www.kressworks.org/> http://www.kressworks.org

Facebook:  <" rel="nofollow">https://www.facebook.com/KressWorks.Foundation/> https://www.facebook.com/KressWorks.Foundation/

Twitter: @KressWorksFnd

 

Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message.

 

From: Sampson, Jared M. [ <mailto:jm...@cu...> mailto:jm...@cu...] 
Sent: Tuesday, March 22, 2016 1:40 PM
To:  <mailto:jim...@kr...> jim...@kr...
Cc: pymol-users < <mailto:pym...@li...> pym...@li...>
Subject: Re: [PyMOL] The Wiki appears outdated or in error

 

Hi Jim -  

 

The COLLADA exporting code was incorporated into Open Source PyMOL starting with 1.7.3.2 (SVN 4097), but I'm not sure when it made it into Incentive PyMOL, so if that's what you're using, 1.7.4 might be just barely too early to have that capability.  You could try saving as VRML2, (`save myfile.wrl`) and use MeshLab to convert that instead of the COLLADA file--I think VRML output is more complete than IDTF.

 

Alternatively, you could install a more recent open source PyMOL using instructions available on the wiki:  <" rel="nofollow">http://www.pymolwiki.org/index.php/Category:Installation> http://www.pymolwiki.org/index.php/Category:Installation. 

 

Cheers,

Jared

 

--

Jared Sampson

Columbia University

 

On Mar 21, 2016, at 5:46 PM, James Kress < <mailto:jim...@kr...> jim...@kr...> wrote:

 

Hi Jared,

 

The version of PyMOL I am using (1.7.4.0) does not recognize the dae file type.  

 

Here is the message PyMOL generates:

 

PyMOL>save output_no_H2O.dae

Save-Warning: Unrecognized file type -- defaulting to PDB format.

Save: wrote "output_no_H2O.dae".

 

I get the same error message if I use the command ‘save output_no_H2O.dae’

 

Jim

 

 

James Kress Ph.D., President

The KressWorks® Foundation 

An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization

“Engineering The Cure” ©

(248) 605-8770

 

Learn More and Donate At:

Website:  <" rel="nofollow">http://www.kressworks.org/> http://www.kressworks.org

Facebook:  <" rel="nofollow">https://www.facebook.com/KressWorks.Foundation/> https://www.facebook.com/KressWorks.Foundation/

Twitter: @KressWorksFnd

 

Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message.

 

From: Sampson, Jared M. [ <mailto:jm...@cu...> mailto:jm...@cu...] 
Sent: Wednesday, March 16, 2016 2:28 PM
To:  <mailto:jim...@kr...> jim...@kr...
Cc:  <mailto:pym...@li...> pym...@li...
Subject: Re: [PyMOL] The Wiki appears outdated or in error

 

Hi James -  

 

If I remember correctly, PyMOL's IDTF output currently only supports triangles meshes (not cylinders or spheres, e.g.), so unfortunately you're basically limited to surface representations for output directly into that format.   

 

As a workaround, you could try saving your scene in COLLADA format (`save myfile.dae`), and use an external program (e.g. Blender, Meshlab) to convert to IDTF or U3D.  When doing so, please note that you'll probably need to `set collada_geometry_mode=1` to specifically use the subset of COLLADA elements supported by those two programs (they only allow <polylist> elements to describe the triangles, which are a more general, verbose description than the more concise <triangles> and <tristrips> output generated with the default setting).

 

Hope that helps.

 

Cheers,

Jared

 

-- 

Jared Sampson

Columbia University

 

On Mar 12, 2016, at 11:24 PM, James Kress < <mailto:jim...@kr...> jim...@kr...> wrote:

 

Among the export functions, a particular interest of mine is the as a

idtf file as "precursor" for a 3d pdf mentioned at

 

 <" rel="nofollow">http://www.pymolwiki.org/index.php/3d_pdf> http://www.pymolwiki.org/index.php/3d_pdf

 

where I experience difficulties I want to address here.

 

   While the export via the CLI works fine for creating a *.png picture

or a VRML *.wrl-geometry, the similar export as *.idtf creates only a

header to describe the scenery, but not the (expected) spheres and tubes

to represent atoms and molecular bonds.  The file generated is the same,

regardless if I request the data export via

 

save /home/user directory/target directory/test.idtf

 

or the recommended

 

save /home/user directory/target directory/test.idtf,*

 

Marking/highlighting the molecule in question does not alter the situation.

 

   The relative orientation of the model in regard to the observer is

provided, however, in the programs command line, like

 

3Daac=20.0, 3Droll=0, 3Dc2c=0 0 1, 3Droo=50.00, 3Dcoo=0 0 -50.00

 

  In addition, there is no *.tex file written -- well in contrast to the

pymol-wiki page -- that I would expect to be created in the very same

directory, too.  (This is contrast to jmol offering export as *.idtf

while simultaneously writing a *.tex file, too.)  Should I look up in a

different directory instead?  May be a mistake during the installation

be a reason why I do not obtain (yet) a functional *.idtf?  Do I need to

load another / an additional plugin to enlarge the export functions?

 

Thanks.

 

Jim

 

James Kress Ph.D., President

The KressWorks® Foundation 

An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization

“Engineering The Cure” ©

(248) 605-8770

 

Learn More and Donate At:

Website:  <" rel="nofollow">http://www.kressworks.org/> http://www.kressworks.org

Facebook:  <" rel="nofollow">https://www.facebook.com/KressWorks.Foundation/> https://www.facebook.com/KressWorks.Foundation/

Twitter: @KressWorksFnd

 

Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message.

 

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Archives:  <" rel="nofollow">http://www.mail-archive.com/pym...@li...> http://www.mail-archive.com/pym...@li...

 

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

On Mar 24, 2016, at 1:05 PM, James Kress <jim...@kr...<mailto:jim...@kr...>> wrote:

Hi Jared,

When I

set geometry_export_mode, 1

in PyMOL, then save myfile.dae, then import into MeshLab, MeshLab hangs.  Is there an alternative to MeshLab I can use to generate the u3d file?

Thanks.

Jim

James Kress Ph.D., President
The KressWorks® Foundation
An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization
“Engineering The Cure” ©
(248) 605-8770

Learn More and Donate At:
Website: http://www.kressworks.org<" rel="nofollow">http://www.kressworks.org/>
Facebook: https://www.facebook.com/KressWorks.Foundation/
Twitter: @KressWorksFnd

Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message.

From: Sampson, Jared M. [mailto:jm...@cu...]
Sent: Wednesday, March 23, 2016 10:53 PM
To: jim...@kr...<mailto:jim...@kr...>
Cc: pymol-users <pym...@li...>
Subject: Re: [PyMOL] The Wiki appears outdated or in error

Hi Jim -

This is something we've been talking about changing.  The entire scene as viewed within PyMOL is inside that block, including the camera position.   (The interior surface of the block itself provides the background color of the scene.)  Some viewers, e.g. Mac Preview.app, default to displaying from the camera position, but others, including MeshLab, don't, which is understandably confusing.

To export only the geometry without any of the scene information, you can `set geometry_export_mode, 1` in PyMOL before saving the .dae.

Hope that helps!

Cheers,
Jared

P.S. if you are able to work out a protocol/workflow for generating 3D PDFs that is better than what's on the wiki, I hope you will consider updating the wiki to help others who might try it in the future.

Jared Sampson
Columbia University

On Mar 23, 2016, at 8:26 PM, James Kress <jim...@kr...<mailto:jim...@kr...>> wrote:

I installed v 1.8.0.6

When I save ‘myfile.dae’ and then import into MeshLab, all I get is a solid gray block.

What do I need to do in PyMOL to export my DNA structure?

Thanks.

Jim

James Kress Ph.D., President
The KressWorks® Foundation
An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization
“Engineering The Cure” ©
(248) 605-8770

Learn More and Donate At:
Website: http://www.kressworks.org<" rel="nofollow">http://www.kressworks.org/>
Facebook: https://www.facebook.com/KressWorks.Foundation/
Twitter: @KressWorksFnd

Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message.

From: Sampson, Jared M. [mailto:jm...@cu...]
Sent: Tuesday, March 22, 2016 1:40 PM
To: jim...@kr...<mailto:jim...@kr...>
Cc: pymol-users <pym...@li...<mailto:pym...@li...>>
Subject: Re: [PyMOL] The Wiki appears outdated or in error

Hi Jim -

The COLLADA exporting code was incorporated into Open Source PyMOL starting with 1.7.3.2 (SVN 4097), but I'm not sure when it made it into Incentive PyMOL, so if that's what you're using, 1.7.4 might be just barely too early to have that capability.  You could try saving as VRML2, (`save myfile.wrl`) and use MeshLab to convert that instead of the COLLADA file--I think VRML output is more complete than IDTF.

Alternatively, you could install a more recent open source PyMOL using instructions available on the wiki: http://www.pymolwiki.org/index.php/Category:Installation.

Cheers,
Jared

--
Jared Sampson
Columbia University

On Mar 21, 2016, at 5:46 PM, James Kress <jim...@kr...<mailto:jim...@kr...>> wrote:

Hi Jared,

The version of PyMOL I am using (1.7.4.0) does not recognize the dae file type.

Here is the message PyMOL generates:

PyMOL>save output_no_H2O.dae
Save-Warning: Unrecognized file type -- defaulting to PDB format.
Save: wrote "output_no_H2O.dae".

I get the same error message if I use the command ‘save output_no_H2O.dae’

Jim


James Kress Ph.D., President
The KressWorks® Foundation
An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization
“Engineering The Cure” ©
(248) 605-8770

Learn More and Donate At:
Website: http://www.kressworks.org<" rel="nofollow">http://www.kressworks.org/>
Facebook: https://www.facebook.com/KressWorks.Foundation/
Twitter: @KressWorksFnd

Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message.

From: Sampson, Jared M. [mailto:jm...@cu...]
Sent: Wednesday, March 16, 2016 2:28 PM
To: jim...@kr...<mailto:jim...@kr...>
Cc: pym...@li...<mailto:pym...@li...>
Subject: Re: [PyMOL] The Wiki appears outdated or in error

Hi James -

If I remember correctly, PyMOL's IDTF output currently only supports triangles meshes (not cylinders or spheres, e.g.), so unfortunately you're basically limited to surface representations for output directly into that format.

As a workaround, you could try saving your scene in COLLADA format (`save myfile.dae`), and use an external program (e.g. Blender, Meshlab) to convert to IDTF or U3D.  When doing so, please note that you'll probably need to `set collada_geometry_mode=1` to specifically use the subset of COLLADA elements supported by those two programs (they only allow <polylist> elements to describe the triangles, which are a more general, verbose description than the more concise <triangles> and <tristrips> output generated with the default setting).

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Columbia University

On Mar 12, 2016, at 11:24 PM, James Kress <jim...@kr...<mailto:jim...@kr...>> wrote:

Among the export functions, a particular interest of mine is the as a
idtf file as "precursor" for a 3d pdf mentioned at

http://www.pymolwiki.org/index.php/3d_pdf

where I experience difficulties I want to address here.

   While the export via the CLI works fine for creating a *.png picture
or a VRML *.wrl-geometry, the similar export as *.idtf creates only a
header to describe the scenery, but not the (expected) spheres and tubes
to represent atoms and molecular bonds.  The file generated is the same,
regardless if I request the data export via

save /home/user directory/target directory/test.idtf

or the recommended

save /home/user directory/target directory/test.idtf,*

Marking/highlighting the molecule in question does not alter the situation.

   The relative orientation of the model in regard to the observer is
provided, however, in the programs command line, like

3Daac=20.0, 3Droll=0, 3Dc2c=0 0 1, 3Droo=50.00, 3Dcoo=0 0 -50.00

  In addition, there is no *.tex file written -- well in contrast to the
pymol-wiki page -- that I would expect to be created in the very same
directory, too.  (This is contrast to jmol offering export as *.idtf
while simultaneously writing a *.tex file, too.)  Should I look up in a
different directory instead?  May be a mistake during the installation
be a reason why I do not obtain (yet) a functional *.idtf?  Do I need to
load another / an additional plugin to enlarge the export functions?

Thanks.

Jim

James Kress Ph.D., President
The KressWorks® Foundation
An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization
“Engineering The Cure” ©
(248) 605-8770

Learn More and Donate At:
Website: http://www.kressworks.org<" rel="nofollow">http://www.kressworks.org/>
Facebook: https://www.facebook.com/KressWorks.Foundation/
Twitter: @KressWorksFnd

Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message.

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Hi Jared,

 

When I 

 

set geometry_export_mode, 1

 

in PyMOL, then save myfile.dae, then import into MeshLab, MeshLab hangs.  Is there an alternative to MeshLab I can use to generate the u3d file?

 

Thanks.

 

Jim

 

James Kress Ph.D., President

The KressWorks® Foundation 

An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization

“Engineering The Cure” ©

(248) 605-8770

 

Learn More and Donate At:

Website:  <" rel="nofollow">http://www.kressworks.org/> http://www.kressworks.org

Facebook: https://www.facebook.com/KressWorks.Foundation/

Twitter: @KressWorksFnd

 

Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message.

 

From: Sampson, Jared M. [mailto:jm...@cu...] 
Sent: Wednesday, March 23, 2016 10:53 PM
To: jim...@kr...
Cc: pymol-users <pym...@li...>
Subject: Re: [PyMOL] The Wiki appears outdated or in error

 

Hi Jim -  

 

This is something we've been talking about changing.  The entire scene as viewed within PyMOL is inside that block, including the camera position.   (The interior surface of the block itself provides the background color of the scene.)  Some viewers, e.g. Mac Preview.app, default to displaying from the camera position, but others, including MeshLab, don't, which is understandably confusing. 

 

To export only the geometry without any of the scene information, you can `set geometry_export_mode, 1` in PyMOL before saving the .dae.

 

Hope that helps!

 

Cheers,

Jared

 

P.S. if you are able to work out a protocol/workflow for generating 3D PDFs that is better than what's on the wiki, I hope you will consider updating the wiki to help others who might try it in the future.

 

Jared Sampson

Columbia University

 

On Mar 23, 2016, at 8:26 PM, James Kress <jim...@kr... <mailto:jim...@kr...> > wrote:

 

I installed v 1.8.0.6  

 

When I save ‘myfile.dae’ and then import into MeshLab, all I get is a solid gray block.

 

What do I need to do in PyMOL to export my DNA structure?

 

Thanks.

 

Jim

 

James Kress Ph.D., President

The KressWorks® Foundation 

An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization

“Engineering The Cure” ©

(248) 605-8770

 

Learn More and Donate At:

Website:  <" rel="nofollow">http://www.kressworks.org/> http://www.kressworks.org

Facebook:  <" rel="nofollow">https://www.facebook.com/KressWorks.Foundation/> https://www.facebook.com/KressWorks.Foundation/

Twitter: @KressWorksFnd

 

Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message.

 

From: Sampson, Jared M. [mailto:jm...@cu...] 
Sent: Tuesday, March 22, 2016 1:40 PM
To: jim...@kr... <mailto:jim...@kr...> 
Cc: pymol-users <pym...@li... <mailto:pym...@li...> >
Subject: Re: [PyMOL] The Wiki appears outdated or in error

 

Hi Jim -  

 

The COLLADA exporting code was incorporated into Open Source PyMOL starting with 1.7.3.2 (SVN 4097), but I'm not sure when it made it into Incentive PyMOL, so if that's what you're using, 1.7.4 might be just barely too early to have that capability.  You could try saving as VRML2, (`save myfile.wrl`) and use MeshLab to convert that instead of the COLLADA file--I think VRML output is more complete than IDTF.

 

Alternatively, you could install a more recent open source PyMOL using instructions available on the wiki:  <" rel="nofollow">http://www.pymolwiki.org/index.php/Category:Installation> http://www.pymolwiki.org/index.php/Category:Installation. 

 

Cheers,

Jared

 

--

Jared Sampson

Columbia University

 

On Mar 21, 2016, at 5:46 PM, James Kress < <mailto:jim...@kr...> jim...@kr...> wrote:

 

Hi Jared,

 

The version of PyMOL I am using (1.7.4.0) does not recognize the dae file type.  

 

Here is the message PyMOL generates:

 

PyMOL>save output_no_H2O.dae

Save-Warning: Unrecognized file type -- defaulting to PDB format.

Save: wrote "output_no_H2O.dae".

 

I get the same error message if I use the command ‘save output_no_H2O.dae’

 

Jim

 

 

James Kress Ph.D., President

The KressWorks® Foundation 

An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization

“Engineering The Cure” ©

(248) 605-8770

 

Learn More and Donate At:

Website:  <" rel="nofollow">http://www.kressworks.org/> http://www.kressworks.org

Facebook:  <" rel="nofollow">https://www.facebook.com/KressWorks.Foundation/> https://www.facebook.com/KressWorks.Foundation/

Twitter: @KressWorksFnd

 

Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message.

 

From: Sampson, Jared M. [ <mailto:jm...@cu...> mailto:jm...@cu...] 
Sent: Wednesday, March 16, 2016 2:28 PM
To:  <mailto:jim...@kr...> jim...@kr...
Cc:  <mailto:pym...@li...> pym...@li...
Subject: Re: [PyMOL] The Wiki appears outdated or in error

 

Hi James -  

 

If I remember correctly, PyMOL's IDTF output currently only supports triangles meshes (not cylinders or spheres, e.g.), so unfortunately you're basically limited to surface representations for output directly into that format.   

 

As a workaround, you could try saving your scene in COLLADA format (`save myfile.dae`), and use an external program (e.g. Blender, Meshlab) to convert to IDTF or U3D.  When doing so, please note that you'll probably need to `set collada_geometry_mode=1` to specifically use the subset of COLLADA elements supported by those two programs (they only allow <polylist> elements to describe the triangles, which are a more general, verbose description than the more concise <triangles> and <tristrips> output generated with the default setting).

 

Hope that helps.

 

Cheers,

Jared

 

-- 

Jared Sampson

Columbia University

 

On Mar 12, 2016, at 11:24 PM, James Kress < <mailto:jim...@kr...> jim...@kr...> wrote:

 

Among the export functions, a particular interest of mine is the as a

idtf file as "precursor" for a 3d pdf mentioned at

 

 <" rel="nofollow">http://www.pymolwiki.org/index.php/3d_pdf> http://www.pymolwiki.org/index.php/3d_pdf

 

where I experience difficulties I want to address here.

 

   While the export via the CLI works fine for creating a *.png picture

or a VRML *.wrl-geometry, the similar export as *.idtf creates only a

header to describe the scenery, but not the (expected) spheres and tubes

to represent atoms and molecular bonds.  The file generated is the same,

regardless if I request the data export via

 

save /home/user directory/target directory/test.idtf

 

or the recommended

 

save /home/user directory/target directory/test.idtf,*

 

Marking/highlighting the molecule in question does not alter the situation.

 

   The relative orientation of the model in regard to the observer is

provided, however, in the programs command line, like

 

3Daac=20.0, 3Droll=0, 3Dc2c=0 0 1, 3Droo=50.00, 3Dcoo=0 0 -50.00

 

  In addition, there is no *.tex file written -- well in contrast to the

pymol-wiki page -- that I would expect to be created in the very same

directory, too.  (This is contrast to jmol offering export as *.idtf

while simultaneously writing a *.tex file, too.)  Should I look up in a

different directory instead?  May be a mistake during the installation

be a reason why I do not obtain (yet) a functional *.idtf?  Do I need to

load another / an additional plugin to enlarge the export functions?

 

Thanks.

 

Jim

 

James Kress Ph.D., President

The KressWorks® Foundation 

An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization

“Engineering The Cure” ©

(248) 605-8770

 

Learn More and Donate At:

Website:  <" rel="nofollow">http://www.kressworks.org/> http://www.kressworks.org

Facebook:  <" rel="nofollow">https://www.facebook.com/KressWorks.Foundation/> https://www.facebook.com/KressWorks.Foundation/

Twitter: @KressWorksFnd

 

Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message.

 

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Click to learn more.
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Hello,
I have an issue with displaying structures in Sticks using pymol. My version is 1.7.4.5 Edu on windows 10. The structure I tried to open is 3une. When I use command "show sticks", the display became completely empty. Even if I select a residue and tried to show in sticks, the residue just disappeared. It is likely because the structure file is too complex. I don't have such issue when I opened small structure file. Can anyone help? Thanks so much!
Best.Chen

Hi Jim -

This is something we've been talking about changing.  The entire scene as viewed within PyMOL is inside that block, including the camera position.   (The interior surface of the block itself provides the background color of the scene.)  Some viewers, e.g. Mac Preview.app, default to displaying from the camera position, but others, including MeshLab, don't, which is understandably confusing.

To export only the geometry without any of the scene information, you can `set geometry_export_mode, 1` in PyMOL before saving the .dae.

Hope that helps!

Cheers,
Jared

P.S. if you are able to work out a protocol/workflow for generating 3D PDFs that is better than what's on the wiki, I hope you will consider updating the wiki to help others who might try it in the future.

Jared Sampson
Columbia University

On Mar 23, 2016, at 8:26 PM, James Kress <jim...@kr...<mailto:jim...@kr...>> wrote:

I installed v 1.8.0.6

When I save ‘myfile.dae’ and then import into MeshLab, all I get is a solid gray block.

What do I need to do in PyMOL to export my DNA structure?

Thanks.

Jim

James Kress Ph.D., President
The KressWorks® Foundation
An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization
“Engineering The Cure” ©
(248) 605-8770

Learn More and Donate At:
Website: http://www.kressworks.org<" rel="nofollow">http://www.kressworks.org/>
Facebook: https://www.facebook.com/KressWorks.Foundation/
Twitter: @KressWorksFnd

Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message.

From: Sampson, Jared M. [mailto:jm...@cu...]
Sent: Tuesday, March 22, 2016 1:40 PM
To: jim...@kr...<mailto:jim...@kr...>
Cc: pymol-users <pym...@li...>
Subject: Re: [PyMOL] The Wiki appears outdated or in error

Hi Jim -

The COLLADA exporting code was incorporated into Open Source PyMOL starting with 1.7.3.2 (SVN 4097), but I'm not sure when it made it into Incentive PyMOL, so if that's what you're using, 1.7.4 might be just barely too early to have that capability.  You could try saving as VRML2, (`save myfile.wrl`) and use MeshLab to convert that instead of the COLLADA file--I think VRML output is more complete than IDTF.

Alternatively, you could install a more recent open source PyMOL using instructions available on the wiki: http://www.pymolwiki.org/index.php/Category:Installation.

Cheers,
Jared

--
Jared Sampson
Columbia University

On Mar 21, 2016, at 5:46 PM, James Kress <jim...@kr...<mailto:jim...@kr...>> wrote:

Hi Jared,

The version of PyMOL I am using (1.7.4.0) does not recognize the dae file type.

Here is the message PyMOL generates:

PyMOL>save output_no_H2O.dae
Save-Warning: Unrecognized file type -- defaulting to PDB format.
Save: wrote "output_no_H2O.dae".

I get the same error message if I use the command ‘save output_no_H2O.dae’

Jim


James Kress Ph.D., President
The KressWorks® Foundation
An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization
“Engineering The Cure” ©
(248) 605-8770

Learn More and Donate At:
Website: http://www.kressworks.org<" rel="nofollow">http://www.kressworks.org/>
Facebook: https://www.facebook.com/KressWorks.Foundation/
Twitter: @KressWorksFnd

Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message.

From: Sampson, Jared M. [mailto:jm...@cu...]
Sent: Wednesday, March 16, 2016 2:28 PM
To: jim...@kr...<mailto:jim...@kr...>
Cc: pym...@li...<mailto:pym...@li...>
Subject: Re: [PyMOL] The Wiki appears outdated or in error

Hi James -

If I remember correctly, PyMOL's IDTF output currently only supports triangles meshes (not cylinders or spheres, e.g.), so unfortunately you're basically limited to surface representations for output directly into that format.

As a workaround, you could try saving your scene in COLLADA format (`save myfile.dae`), and use an external program (e.g. Blender, Meshlab) to convert to IDTF or U3D.  When doing so, please note that you'll probably need to `set collada_geometry_mode=1` to specifically use the subset of COLLADA elements supported by those two programs (they only allow <polylist> elements to describe the triangles, which are a more general, verbose description than the more concise <triangles> and <tristrips> output generated with the default setting).

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Columbia University

On Mar 12, 2016, at 11:24 PM, James Kress <jim...@kr...<mailto:jim...@kr...>> wrote:

Among the export functions, a particular interest of mine is the as a
idtf file as "precursor" for a 3d pdf mentioned at

http://www.pymolwiki.org/index.php/3d_pdf

where I experience difficulties I want to address here.

   While the export via the CLI works fine for creating a *.png picture
or a VRML *.wrl-geometry, the similar export as *.idtf creates only a
header to describe the scenery, but not the (expected) spheres and tubes
to represent atoms and molecular bonds.  The file generated is the same,
regardless if I request the data export via

save /home/user directory/target directory/test.idtf

or the recommended

save /home/user directory/target directory/test.idtf,*

Marking/highlighting the molecule in question does not alter the situation.

   The relative orientation of the model in regard to the observer is
provided, however, in the programs command line, like

3Daac=20.0, 3Droll=0, 3Dc2c=0 0 1, 3Droo=50.00, 3Dcoo=0 0 -50.00

  In addition, there is no *.tex file written -- well in contrast to the
pymol-wiki page -- that I would expect to be created in the very same
directory, too.  (This is contrast to jmol offering export as *.idtf
while simultaneously writing a *.tex file, too.)  Should I look up in a
different directory instead?  May be a mistake during the installation
be a reason why I do not obtain (yet) a functional *.idtf?  Do I need to
load another / an additional plugin to enlarge the export functions?

Thanks.

Jim

James Kress Ph.D., President
The KressWorks® Foundation
An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization
“Engineering The Cure” ©
(248) 605-8770

Learn More and Donate At:
Website: http://www.kressworks.org<" rel="nofollow">http://www.kressworks.org/>
Facebook: https://www.facebook.com/KressWorks.Foundation/
Twitter: @KressWorksFnd

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I installed v 1.8.0.6  

 

When I save ‘myfile.dae’ and then import into MeshLab, all I get is a solid gray block.

 

What do I need to do in PyMOL to export my DNA structure?

 

Thanks.

 

Jim

 

James Kress Ph.D., President

The KressWorks® Foundation 

An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization

“Engineering The Cure” ©

(248) 605-8770

 

Learn More and Donate At:

Website:  <" rel="nofollow">http://www.kressworks.org/> http://www.kressworks.org

Facebook: https://www.facebook.com/KressWorks.Foundation/

Twitter: @KressWorksFnd

 

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From: Sampson, Jared M. [mailto:jm...@cu...] 
Sent: Tuesday, March 22, 2016 1:40 PM
To: jim...@kr...
Cc: pymol-users <pym...@li...>
Subject: Re: [PyMOL] The Wiki appears outdated or in error

 

Hi Jim -  

 

The COLLADA exporting code was incorporated into Open Source PyMOL starting with 1.7.3.2 (SVN 4097), but I'm not sure when it made it into Incentive PyMOL, so if that's what you're using, 1.7.4 might be just barely too early to have that capability.  You could try saving as VRML2, (`save myfile.wrl`) and use MeshLab to convert that instead of the COLLADA file--I think VRML output is more complete than IDTF.

 

Alternatively, you could install a more recent open source PyMOL using instructions available on the wiki: http://www.pymolwiki.org/index.php/Category:Installation. 

 

Cheers,

Jared

 

--

Jared Sampson

Columbia University

 

On Mar 21, 2016, at 5:46 PM, James Kress <jim...@kr... <mailto:jim...@kr...> > wrote:

 

Hi Jared,

 

The version of PyMOL I am using (1.7.4.0) does not recognize the dae file type.  

 

Here is the message PyMOL generates:

 

PyMOL>save output_no_H2O.dae

Save-Warning: Unrecognized file type -- defaulting to PDB format.

Save: wrote "output_no_H2O.dae".

 

I get the same error message if I use the command ‘save output_no_H2O.dae’

 

Jim

 

 

James Kress Ph.D., President

The KressWorks® Foundation 

An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization

“Engineering The Cure” ©

(248) 605-8770

 

Learn More and Donate At:

Website:  <" rel="nofollow">http://www.kressworks.org/> http://www.kressworks.org

Facebook:  <" rel="nofollow">https://www.facebook.com/KressWorks.Foundation/> https://www.facebook.com/KressWorks.Foundation/

Twitter: @KressWorksFnd

 

Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message.

 

From: Sampson, Jared M. [mailto:jm...@cu...] 
Sent: Wednesday, March 16, 2016 2:28 PM
To: jim...@kr... <mailto:jim...@kr...> 
Cc: pym...@li... <mailto:pym...@li...> 
Subject: Re: [PyMOL] The Wiki appears outdated or in error

 

Hi James -  

 

If I remember correctly, PyMOL's IDTF output currently only supports triangles meshes (not cylinders or spheres, e.g.), so unfortunately you're basically limited to surface representations for output directly into that format.   

 

As a workaround, you could try saving your scene in COLLADA format (`save myfile.dae`), and use an external program (e.g. Blender, Meshlab) to convert to IDTF or U3D.  When doing so, please note that you'll probably need to `set collada_geometry_mode=1` to specifically use the subset of COLLADA elements supported by those two programs (they only allow <polylist> elements to describe the triangles, which are a more general, verbose description than the more concise <triangles> and <tristrips> output generated with the default setting).

 

Hope that helps.

 

Cheers,

Jared

 

-- 

Jared Sampson

Columbia University

 

On Mar 12, 2016, at 11:24 PM, James Kress < <mailto:jim...@kr...> jim...@kr...> wrote:

 

Among the export functions, a particular interest of mine is the as a

idtf file as "precursor" for a 3d pdf mentioned at

 

 <" rel="nofollow">http://www.pymolwiki.org/index.php/3d_pdf> http://www.pymolwiki.org/index.php/3d_pdf

 

where I experience difficulties I want to address here.

 

   While the export via the CLI works fine for creating a *.png picture

or a VRML *.wrl-geometry, the similar export as *.idtf creates only a

header to describe the scenery, but not the (expected) spheres and tubes

to represent atoms and molecular bonds.  The file generated is the same,

regardless if I request the data export via

 

save /home/user directory/target directory/test.idtf

 

or the recommended

 

save /home/user directory/target directory/test.idtf,*

 

Marking/highlighting the molecule in question does not alter the situation.

 

   The relative orientation of the model in regard to the observer is

provided, however, in the programs command line, like

 

3Daac=20.0, 3Droll=0, 3Dc2c=0 0 1, 3Droo=50.00, 3Dcoo=0 0 -50.00

 

  In addition, there is no *.tex file written -- well in contrast to the

pymol-wiki page -- that I would expect to be created in the very same

directory, too.  (This is contrast to jmol offering export as *.idtf

while simultaneously writing a *.tex file, too.)  Should I look up in a

different directory instead?  May be a mistake during the installation

be a reason why I do not obtain (yet) a functional *.idtf?  Do I need to

load another / an additional plugin to enlarge the export functions?

 

Thanks.

 

Jim

 

James Kress Ph.D., President

The KressWorks® Foundation 

An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization

“Engineering The Cure” ©

(248) 605-8770

 

Learn More and Donate At:

Website:  <" rel="nofollow">http://www.kressworks.org/> http://www.kressworks.org

Facebook:  <" rel="nofollow">https://www.facebook.com/KressWorks.Foundation/> https://www.facebook.com/KressWorks.Foundation/

Twitter: @KressWorksFnd

 

Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message.

 

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 <" rel="nofollow">http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140_______________________________________________> http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140_______________________________________________
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Hi H. Adam -

Try the http://pymolwiki.org/index.php/Distancetoatom script by Andreas Warnecke and use it to set b (or your own custom property in recent Incentive PyMOL versions) based on the distance from a point.

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Columbia University

On Mar 23, 2016, at 5:20 PM, harold steinberg <h.a...@gm...<mailto:h.a...@gm...>> wrote:

I have a pdb ‘xyz1’ and create a mapA, then create a surfA.

set surface_quality, 1
alter all, b=50
alter all, q=1
set gaussian_resolution,5
map_new mapA, gaussian, 1, sele or pdb, 6
isosurface surfA, mapA

I can then color that surfA with any solid color.

How can one color the surfA with a rainbow affect that radiates out from the center, or similar.

This is easy to do with a protein (pdb) but I cannot get a ramp to work with a surf.


H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

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I have a pdb ‘xyz1’ and create a mapA, then create a surfA.

set surface_quality, 1
alter all, b=50
alter all, q=1
set gaussian_resolution,5
map_new mapA, gaussian, 1, sele or pdb, 6
isosurface surfA, mapA

I can then color that surfA with any solid color.

How can one color the surfA with a rainbow affect that radiates out from the center, or similar.

This is easy to do with a protein (pdb) but I cannot get a ramp to work with a surf.


H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

Dear Colleagues,

This is a reminder that the application deadline for the 9th annual CCP4/APS crystallographic school is on April 21, 2016. Applications received after this date will not be considered.
The school will take place from June 21 through June 29, 2016 at the Advanced Photon Source, Argonne National Laboratory, near Chicago.
All aspects of macromolecular crystallography from data collection to structure refinement and validation, as well as functional assessment, will be covered. Instructions and hands-on assistance will be provided by the authors and developers of the represented software, and/or by other premier experts.

>From our past experience, the majority of participants bring with them the crystallographic problems they cannot resolve independently and almost all these problems are resolved at the school.
Some of the publications, acknowledging the contribution of the school, are listed here:
http://www.ccp4.ac.uk/schools/APS-school/publications.php

Each registered participant will be provided with a Linux computer with all covered software already installed and configured. Lodging is on-campus and all meals and refreshments will be provided at the venue.

These and other details, such as the fees, the on-line application, the program, the contact information etc. can be found here: http://www.ccp4.ac.uk/schools/APS-2016/index.php

We are looking forward to meeting you in Argonne this summer.
Garib, Ronan and Nukri


Ruslan Sanishvili (Nukri), Ph.D.
Macromolecular Crystallographer
GM/CA@APS
X-ray Science Division, ANL
9700 S. Cass Ave.
Lemont, IL 60439

Tel: (630)252-0665
Fax: (630)252-0667
rsa...@an...

________________________________
From: Sanishvili, Ruslan [rsa...@an...]
Sent: Tuesday, February 23, 2016 7:37 AM
To: pym...@li...
Subject: [PyMOL] [ccp4bb] CCP4 crystallographic summer school at the APS, June 21 - 29, 2016

Dear Colleagues,

We are pleased to announce the 9th annual CCP4 crystallographic summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2016/index.php

Title: CCP4 crystallographic school: From data collection to structure refinement and beyond

Dates: June 21 through 29, 2016

Site: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA

The school comprises
Data collection workshop the first three days: beamline training and data collection on GM/CA@APS beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used.
Crystallographic computation workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on, interactive trouble-shooting.
There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions.

Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level, along with commercial/industrial researchers are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops.

Application: Application deadline is April 21. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2016/index.php

Registration fees: The registration fee for the selected participants is $400 for the academic and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making the reservations at economical lodging at the Argonne Guest House. The workshop will cover all other expenses.

We hope to see you at the school,
Garib, Ronan and Nukri

Ruslan Sanishvili (Nukri), Ph.D.
Macromolecular Crystallographer
GM/CA@APS
X-ray Science Division, ANL
9700 S. Cass Ave.
Lemont, IL 60439

Tel: (630)252-0665
Fax: (630)252-0667
rsa...@an...

Hi Jim -

The COLLADA exporting code was incorporated into Open Source PyMOL starting with 1.7.3.2 (SVN 4097), but I'm not sure when it made it into Incentive PyMOL, so if that's what you're using, 1.7.4 might be just barely too early to have that capability.  You could try saving as VRML2, (`save myfile.wrl`) and use MeshLab to convert that instead of the COLLADA file--I think VRML output is more complete than IDTF.

Alternatively, you could install a more recent open source PyMOL using instructions available on the wiki: http://www.pymolwiki.org/index.php/Category:Installation.

Cheers,
Jared

--
Jared Sampson
Columbia University

On Mar 21, 2016, at 5:46 PM, James Kress <jim...@kr...<mailto:jim...@kr...>> wrote:

Hi Jared,

The version of PyMOL I am using (1.7.4.0) does not recognize the dae file type.

Here is the message PyMOL generates:

PyMOL>save output_no_H2O.dae
Save-Warning: Unrecognized file type -- defaulting to PDB format.
Save: wrote "output_no_H2O.dae".

I get the same error message if I use the command ‘save output_no_H2O.dae’

Jim


James Kress Ph.D., President
The KressWorks® Foundation
An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization
“Engineering The Cure” ©
(248) 605-8770

Learn More and Donate At:
Website: http://www.kressworks.org<" rel="nofollow">http://www.kressworks.org/>
Facebook: https://www.facebook.com/KressWorks.Foundation/
Twitter: @KressWorksFnd

Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message.

From: Sampson, Jared M. [mailto:jm...@cu...]
Sent: Wednesday, March 16, 2016 2:28 PM
To: jim...@kr...<mailto:jim...@kr...>
Cc: pym...@li...
Subject: Re: [PyMOL] The Wiki appears outdated or in error

Hi James -

If I remember correctly, PyMOL's IDTF output currently only supports triangles meshes (not cylinders or spheres, e.g.), so unfortunately you're basically limited to surface representations for output directly into that format.

As a workaround, you could try saving your scene in COLLADA format (`save myfile.dae`), and use an external program (e.g. Blender, Meshlab) to convert to IDTF or U3D.  When doing so, please note that you'll probably need to `set collada_geometry_mode=1` to specifically use the subset of COLLADA elements supported by those two programs (they only allow <polylist> elements to describe the triangles, which are a more general, verbose description than the more concise <triangles> and <tristrips> output generated with the default setting).

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Columbia University

On Mar 12, 2016, at 11:24 PM, James Kress <jim...@kr...<mailto:jim...@kr...>> wrote:

Among the export functions, a particular interest of mine is the as a
idtf file as "precursor" for a 3d pdf mentioned at

http://www.pymolwiki.org/index.php/3d_pdf

where I experience difficulties I want to address here.

   While the export via the CLI works fine for creating a *.png picture
or a VRML *.wrl-geometry, the similar export as *.idtf creates only a
header to describe the scenery, but not the (expected) spheres and tubes
to represent atoms and molecular bonds.  The file generated is the same,
regardless if I request the data export via

save /home/user directory/target directory/test.idtf

or the recommended

save /home/user directory/target directory/test.idtf,*

Marking/highlighting the molecule in question does not alter the situation.

   The relative orientation of the model in regard to the observer is
provided, however, in the programs command line, like

3Daac=20.0, 3Droll=0, 3Dc2c=0 0 1, 3Droo=50.00, 3Dcoo=0 0 -50.00

  In addition, there is no *.tex file written -- well in contrast to the
pymol-wiki page -- that I would expect to be created in the very same
directory, too.  (This is contrast to jmol offering export as *.idtf
while simultaneously writing a *.tex file, too.)  Should I look up in a
different directory instead?  May be a mistake during the installation
be a reason why I do not obtain (yet) a functional *.idtf?  Do I need to
load another / an additional plugin to enlarge the export functions?

Thanks.

Jim

James Kress Ph.D., President
The KressWorks® Foundation
An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization
“Engineering The Cure” ©
(248) 605-8770

Learn More and Donate At:
Website: http://www.kressworks.org<" rel="nofollow">http://www.kressworks.org/>
Facebook: https://www.facebook.com/KressWorks.Foundation/
Twitter: @KressWorksFnd

Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message.

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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 = 0.00000 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/

Thanks for the help Christoph, it was my mistake, I had installed the 32bit
version of python. Everything worked now and pymol is working properly.
Best regards
Sergio
El 21/3/2016 18:34, "Christoph Gohlke" <cg...@uc...> escribió:

> Make sure you are using the 64-bit version of Python 2.7:
> python-2.7.11.amd64.msi.
>
> If that does not help, please list the contents of %CD%: dir "%CD%"\*.whl
>
> Christoph
>
>
>
> On 3/21/2016 3:31 AM, Bondurant wrote:
> > Hi everybody,
> > I recently restored my laptop to factory settings and I am trying now to
> > install latest precompiled pymol version  following the instructions
> > from http://www.pymolwiki.org/index.php/Windows_Install.
> > I have installed python 2.7.11 and put in a Pymol_installation folder
> > pip 8.0.3, numpy 1.10.4+mkl, pmw 2.0.1, pymol 1.8.1.0 and pymol_launcher
> > 1.0 whl files, all of them downloaded from the  Christoph Gohlke
> > webpage. However, after typing in the command prompt
> >
> > C:\Python27\python.exe  pip-8.0.3-py2.py3-none-any.whl/pip  install
> --no-index  --find-links="%CD%"  pymol_launcher
> >
> > I get the following error:
> >
> >   "Could not find  a version that satifisfies the requirement
> > pymol-launcher (from versions: )
> > No matching distribution found for pymol launcher"
> >
> >
> > Could you provide me any help? Am i doing anything wrong? Have i skipped
> > any step in the installation process?
> >
> > Thanks
> >
> > Sergio
> >
> >
> >
> ------------------------------------------------------------------------------
> > Transform Data into Opportunity.
> > Accelerate data analysis in your applications with
> > Intel Data Analytics Acceleration Library.
> > Click to learn more.
> > http://pubads.g.doubleclick.net/gampad/clk?id=278785351&iu=/4140
> >
> >
> >
> > _______________________________________________
> > PyMOL-users mailing list (PyM...@li...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pym...@li...
> >
>
>
> ------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785351&iu=/4140
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hi Jared,

 

The version of PyMOL I am using (1.7.4.0) does not recognize the dae file type.  

 

Here is the message PyMOL generates:

 

PyMOL>save output_no_H2O.dae

Save-Warning: Unrecognized file type -- defaulting to PDB format.

Save: wrote "output_no_H2O.dae".

 

I get the same error message if I use the command ‘save output_no_H2O.dae’

 

Jim

 

 

James Kress Ph.D., President

The KressWorks® Foundation 

An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization

“Engineering The Cure” ©

(248) 605-8770

 

Learn More and Donate At:

Website:  <" rel="nofollow">http://www.kressworks.org/> http://www.kressworks.org

Facebook: https://www.facebook.com/KressWorks.Foundation/

Twitter: @KressWorksFnd

 

Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message.

 

From: Sampson, Jared M. [mailto:jm...@cu...] 
Sent: Wednesday, March 16, 2016 2:28 PM
To: jim...@kr...
Cc: pym...@li...
Subject: Re: [PyMOL] The Wiki appears outdated or in error

 

Hi James -  

 

If I remember correctly, PyMOL's IDTF output currently only supports triangles meshes (not cylinders or spheres, e.g.), so unfortunately you're basically limited to surface representations for output directly into that format.   

 

As a workaround, you could try saving your scene in COLLADA format (`save myfile.dae`), and use an external program (e.g. Blender, Meshlab) to convert to IDTF or U3D.  When doing so, please note that you'll probably need to `set collada_geometry_mode=1` to specifically use the subset of COLLADA elements supported by those two programs (they only allow <polylist> elements to describe the triangles, which are a more general, verbose description than the more concise <triangles> and <tristrips> output generated with the default setting).

 

Hope that helps.

 

Cheers,

Jared

 

-- 

Jared Sampson

Columbia University

 

On Mar 12, 2016, at 11:24 PM, James Kress <jim...@kr... <mailto:jim...@kr...> > wrote:

 

Among the export functions, a particular interest of mine is the as a

idtf file as "precursor" for a 3d pdf mentioned at

 

 <" rel="nofollow">http://www.pymolwiki.org/index.php/3d_pdf> http://www.pymolwiki.org/index.php/3d_pdf

 

where I experience difficulties I want to address here.

 

   While the export via the CLI works fine for creating a *.png picture

or a VRML *.wrl-geometry, the similar export as *.idtf creates only a

header to describe the scenery, but not the (expected) spheres and tubes

to represent atoms and molecular bonds.  The file generated is the same,

regardless if I request the data export via

 

save /home/user directory/target directory/test.idtf

 

or the recommended

 

save /home/user directory/target directory/test.idtf,*

 

Marking/highlighting the molecule in question does not alter the situation.

 

   The relative orientation of the model in regard to the observer is

provided, however, in the programs command line, like

 

3Daac=20.0, 3Droll=0, 3Dc2c=0 0 1, 3Droo=50.00, 3Dcoo=0 0 -50.00

 

  In addition, there is no *.tex file written -- well in contrast to the

pymol-wiki page -- that I would expect to be created in the very same

directory, too.  (This is contrast to jmol offering export as *.idtf

while simultaneously writing a *.tex file, too.)  Should I look up in a

different directory instead?  May be a mistake during the installation

be a reason why I do not obtain (yet) a functional *.idtf?  Do I need to

load another / an additional plugin to enlarge the export functions?

 

Thanks.

 

Jim

 

James Kress Ph.D., President

The KressWorks® Foundation 

An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization

“Engineering The Cure” ©

(248) 605-8770

 

Learn More and Donate At:

Website:  <" rel="nofollow">http://www.kressworks.org/> http://www.kressworks.org

Facebook: https://www.facebook.com/KressWorks.Foundation/

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Make sure you are using the 64-bit version of Python 2.7: 
python-2.7.11.amd64.msi.

If that does not help, please list the contents of %CD%: dir "%CD%"\*.whl

Christoph



On 3/21/2016 3:31 AM, Bondurant wrote:
> Hi everybody,
> I recently restored my laptop to factory settings and I am trying now to
> install latest precompiled pymol version  following the instructions
> from http://www.pymolwiki.org/index.php/Windows_Install.
> I have installed python 2.7.11 and put in a Pymol_installation folder
> pip 8.0.3, numpy 1.10.4+mkl, pmw 2.0.1, pymol 1.8.1.0 and pymol_launcher
> 1.0 whl files, all of them downloaded from the  Christoph Gohlke
> webpage. However, after typing in the command prompt
>
> C:\Python27\python.exe  pip-8.0.3-py2.py3-none-any.whl/pip  install  --no-index  --find-links="%CD%"  pymol_launcher
>
> I get the following error:
>
>   "Could not find  a version that satifisfies the requirement
> pymol-launcher (from versions: )
> No matching distribution found for pymol launcher"
>
>
> Could you provide me any help? Am i doing anything wrong? Have i skipped
> any step in the installation process?
>
> Thanks
>
> Sergio
>
>
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> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
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>
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>

Hi everybody,
I recently restored my laptop to factory settings and I am trying now to
install latest precompiled pymol version  following the instructions from
http://www.pymolwiki.org/index.php/Windows_Install.
I have installed python 2.7.11 and put in a Pymol_installation folder pip
8.0.3, numpy 1.10.4+mkl, pmw 2.0.1, pymol 1.8.1.0 and pymol_launcher 1.0
whl files, all of them downloaded from the  Christoph Gohlke webpage.
However, after typing in the command prompt

C:\Python27\python.exe pip-8.0.3-py2.py3-none-any.whl/pip install
--no-index --find-links="%CD%" pymol_launcher

I get the following error:

 "Could not find  a version that satifisfies the requirement pymol-launcher
(from versions: )
No matching distribution found for pymol launcher"


Could you provide me any help? Am i doing anything wrong? Have i skipped
any step in the installation process?

Thanks

Sergio

Dear All,

I want to show the H bond distances in my receptor-ligand complex. I was
able to get the distances, but I don't know how to add the unit (Å) to the
end of the distance label.
Can anyone help me?

Thank you

HI Jared,

 

Thank you for your response.  I will give it a try!

 

Jim

 

James Kress Ph.D., President

The KressWorks® Foundation 

An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization

“Engineering The Cure” ©

(248) 605-8770

 

Learn More and Donate At:

Website:  <" rel="nofollow">http://www.kressworks.org/> http://www.kressworks.org

Facebook: https://www.facebook.com/KressWorks.Foundation/

Twitter: @KressWorksFnd

 

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From: Sampson, Jared M. [mailto:jm...@cu...] 
Sent: Wednesday, March 16, 2016 2:28 PM
To: jim...@kr...
Cc: pym...@li...
Subject: Re: [PyMOL] The Wiki appears outdated or in error

 

Hi James -  

 

If I remember correctly, PyMOL's IDTF output currently only supports triangles meshes (not cylinders or spheres, e.g.), so unfortunately you're basically limited to surface representations for output directly into that format.   

 

As a workaround, you could try saving your scene in COLLADA format (`save myfile.dae`), and use an external program (e.g. Blender, Meshlab) to convert to IDTF or U3D.  When doing so, please note that you'll probably need to `set collada_geometry_mode=1` to specifically use the subset of COLLADA elements supported by those two programs (they only allow <polylist> elements to describe the triangles, which are a more general, verbose description than the more concise <triangles> and <tristrips> output generated with the default setting).

 

Hope that helps.

 

Cheers,

Jared

 

-- 

Jared Sampson

Columbia University

 

On Mar 12, 2016, at 11:24 PM, James Kress <jim...@kr... <mailto:jim...@kr...> > wrote:

 

Among the export functions, a particular interest of mine is the as a

idtf file as "precursor" for a 3d pdf mentioned at

 

 <" rel="nofollow">http://www.pymolwiki.org/index.php/3d_pdf> http://www.pymolwiki.org/index.php/3d_pdf

 

where I experience difficulties I want to address here.

 

   While the export via the CLI works fine for creating a *.png picture

or a VRML *.wrl-geometry, the similar export as *.idtf creates only a

header to describe the scenery, but not the (expected) spheres and tubes

to represent atoms and molecular bonds.  The file generated is the same,

regardless if I request the data export via

 

save /home/user directory/target directory/test.idtf

 

or the recommended

 

save /home/user directory/target directory/test.idtf,*

 

Marking/highlighting the molecule in question does not alter the situation.

 

   The relative orientation of the model in regard to the observer is

provided, however, in the programs command line, like

 

3Daac=20.0, 3Droll=0, 3Dc2c=0 0 1, 3Droo=50.00, 3Dcoo=0 0 -50.00

 

  In addition, there is no *.tex file written -- well in contrast to the

pymol-wiki page -- that I would expect to be created in the very same

directory, too.  (This is contrast to jmol offering export as *.idtf

while simultaneously writing a *.tex file, too.)  Should I look up in a

different directory instead?  May be a mistake during the installation

be a reason why I do not obtain (yet) a functional *.idtf?  Do I need to

load another / an additional plugin to enlarge the export functions?

 

Thanks.

 

Jim

 

James Kress Ph.D., President

The KressWorks® Foundation 

An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization

“Engineering The Cure” ©

(248) 605-8770

 

Learn More and Donate At:

Website:  <" rel="nofollow">http://www.kressworks.org/> http://www.kressworks.org

Facebook: https://www.facebook.com/KressWorks.Foundation/

Twitter: @KressWorksFnd

 

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