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Subject: Re: [PyMOL] The Wiki appears outdated or in error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