Re: [PyMOL] The Wiki appears outdated or in error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

 

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/> http://www.kressworks.org

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

Twitter: @KressWorksFnd

 

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contact the sender by reply e-mail and destroy all copies of the original 
message.

 

From: Robert Hanson [mailto:hans...@stolaf.edu] 
Sent: Saturday, April 02, 2016 1:14 AM
To: jimkress...@kressworks.org
Cc: Thomas Holder <thomas.hol...@schrodinger.com>; pymol-users 
<pymol-users@lists.sourceforge.net>
Subject: Re: [PyMOL] The Wiki appears outdated or in error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] The Wiki appears outdated or in error

[Robert Hanson]

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] The Wiki appears outdated or in error

[James Kress]

Thanks.  It works much better.  I just wish I could find an alternative to
MeshLab.  The surfaces it generates in the u3d file are really poor.

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
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-Original Message-
From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] 
Sent: Thursday, March 31, 2016 10:55 AM
To: jimkress...@kressworks.org
Cc: pymol-users <pymol-users@lists.sourceforge.net>
Subject: Re: [PyMOL] The Wiki appears outdated or in error

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 <jimkress...@kressworks.org> 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:thomas.hol...@schrodinger.com]
> Sent: Sunday, March 27, 2016 4:10 PM
> To: pymol-users <pymol-users@lists.sourceforge.net>
> 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. 
> <jms2...@cumc.columbia.edu>
> 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.
> <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
>>> 
>> 
>> 
> -

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] The Wiki appears outdated or in error

[Thomas Holder]

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 <jimkress...@kressworks.org> 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:thomas.hol...@schrodinger.com] 
> Sent: Sunday, March 27, 2016 4:10 PM
> To: pymol-users <pymol-users@lists.sourceforge.net>
> 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. <jms2...@cumc.columbia.edu>
> 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.
> <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
>>> 
>> 
>> 
> -

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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

[James Kress]

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:thomas.hol...@schrodinger.com] 
Sent: Sunday, March 27, 2016 4:10 PM
To: pymol-users <pymol-users@lists.sourceforge.net>
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. <jms2...@cumc.columbia.edu>
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.
<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
>> 
> 
>
--
---

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.



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

[Thomas Holder]

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.  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.  
>> 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
>> 
> 
> -

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


--
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Intel Data Analytics Acceleration Library.
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Re: [PyMOL] The Wiki appears outdated or in error

[James Kress]

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:  <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:jms2...@cumc.columbia.edu] 
Sent: Friday, March 25, 2016 3:03 PM
To: jimkress...@kressworks.org
Cc: pymol-users <pymol-users@lists.sourceforge.net>
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. <jms2...@cumc.columbia.edu
<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

 

 

--
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
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Re: [PyMOL] The Wiki appears outdated or in error

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

[James Kress]

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:  <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:jms2...@cumc.columbia.edu] 
Sent: Thursday, March 24, 2016 2:26 PM
To: jimkress...@kressworks.org
Cc: Sampson, Jared M. <jms2...@cumc.columbia.edu>; pymol-users 
<pymol-users@lists.sourceforge.net>
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 <jimkress...@kressworks.org 
<mailto:jimkress...@kressworks.org> > 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/> http://www.kressworks.org

Facebook:  <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:jms2...@cumc.columbia.edu] 
Sent: Wednesday, March 23, 2016 10:53 PM
To: jimkress...@kressworks.org <mailto:jimkress...@kressworks.org> 
Cc: pymol-users <pymol-users@lists.sourceforge.net 
<mailto:pymol-users@lists.sourceforge.net> >
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:jimkress...@kressworks.org> 
jimkress...@kressworks.org> 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 O

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

[Sampson, Jared M.]

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 
<jimkress...@kressworks.org<mailto:jimkress...@kressworks.org>> 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<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:jms2...@cumc.columbia.edu]
Sent: Wednesday, March 23, 2016 10:53 PM
To: jimkress...@kressworks.org<mailto:jimkress...@kressworks.org>
Cc: pymol-users <pymol-users@lists.sourceforge.net>
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 
<jimkress...@kressworks.org<mailto:jimkress...@kressworks.org>> 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<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:jms2...@cumc.columbia.edu]
Sent: Tuesday, March 22, 2016 1:40 PM
To: jimkress...@kressworks.org<mailto:jimkress...@kressworks.org>
Cc: pymol-users 
<pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>>
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.

Alternat

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

[James Kress]

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/> 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:jms2...@cumc.columbia.edu] 
Sent: Wednesday, March 23, 2016 10:53 PM
To: jimkress...@kressworks.org
Cc: pymol-users <pymol-users@lists.sourceforge.net>
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 <jimkress...@kressworks.org 
<mailto:jimkress...@kressworks.org> > 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/> http://www.kressworks.org

Facebook:  <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:jms2...@cumc.columbia.edu] 
Sent: Tuesday, March 22, 2016 1:40 PM
To: jimkress...@kressworks.org <mailto:jimkress...@kressworks.org> 
Cc: pymol-users <pymol-users@lists.sourceforge.net 
<mailto:pymol-users@lists.sourceforge.net> >
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> 
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:jimkress...@kressworks.org> 
jimkress...@kressworks.org> 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 D

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

[Sampson, Jared M.]

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 
<jimkress...@kressworks.org<mailto:jimkress...@kressworks.org>> 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<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:jms2...@cumc.columbia.edu]
Sent: Tuesday, March 22, 2016 1:40 PM
To: jimkress...@kressworks.org<mailto:jimkress...@kressworks.org>
Cc: pymol-users <pymol-users@lists.sourceforge.net>
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 
<jimkress...@kressworks.org<mailto:jimkress...@kressworks.org>> 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<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:jms2...@cumc.columbia.edu]
Sent: Wednesday, March 16, 2016 2:28 PM
To: jimkress...@kressworks.org<mailto:jimkress...@kressworks.org>
Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>
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  elements to 
describe the triangles, which are a more g

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

[James Kress]

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/> 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:jms2...@cumc.columbia.edu] 
Sent: Tuesday, March 22, 2016 1:40 PM
To: jimkress...@kressworks.org
Cc: pymol-users <pymol-users@lists.sourceforge.net>
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 <jimkress...@kressworks.org 
<mailto:jimkress...@kressworks.org> > 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/> http://www.kressworks.org

Facebook:  <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:jms2...@cumc.columbia.edu] 
Sent: Wednesday, March 16, 2016 2:28 PM
To: jimkress...@kressworks.org <mailto:jimkress...@kressworks.org> 
Cc: pymol-users@lists.sourceforge.net 
<mailto:pymol-users@lists.sourceforge.net> 
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  elements to 
describe the triangles, which are a more general, verbose description than the 
more concise  and  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:jimkress...@kressworks.org> 
jimkress...@kressworks.org> 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> 
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) s

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

[Sampson, Jared M.]

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 
<jimkress...@kressworks.org<mailto:jimkress...@kressworks.org>> 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<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:jms2...@cumc.columbia.edu]
Sent: Wednesday, March 16, 2016 2:28 PM
To: jimkress...@kressworks.org<mailto:jimkress...@kressworks.org>
Cc: pymol-users@lists.sourceforge.net
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  elements to 
describe the triangles, which are a more general, verbose description than the 
more concise  and  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 
<jimkress...@kressworks.org<mailto:jimkress...@kressworks.org>> 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<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 i

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

[James Kress]

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/> 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:jms2...@cumc.columbia.edu] 
Sent: Wednesday, March 16, 2016 2:28 PM
To: jimkress...@kressworks.org
Cc: pymol-users@lists.sourceforge.net
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  elements to 
describe the triangles, which are a more general, verbose description than the 
more concise  and  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 <jimkress...@kressworks.org 
<mailto:jimkress...@kressworks.org> > 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> 
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/> 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.

 

--
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=278785111=/4140__

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

[Sampson, Jared M.]

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  elements to 
describe the triangles, which are a more general, verbose description than the 
more concise  and  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 
> 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
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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Accelerate data analysis in your applications with
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Re: [PyMOL] The Wiki appears outdated or in error

[James Kress]

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:  <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:jms2...@cumc.columbia.edu] 
Sent: Wednesday, March 16, 2016 2:28 PM
To: jimkress...@kressworks.org
Cc: pymol-users@lists.sourceforge.net
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  elements to 
describe the triangles, which are a more general, verbose description than the 
more concise  and  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 <jimkress...@kressworks.org 
<mailto:jimkress...@kressworks.org> > 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> 
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/> 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.

 

--
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=278785111=/4140___>
 
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