Re: [PyMOL] The Wiki appears outdated or in error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

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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
Cc: pymol-users 
Subject: Re: [PyMOL] The Wiki appears outdated or in error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 
> 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
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 
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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 

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

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 
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  > 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

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> 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,

Re: [PyMOL] color an isosurface with a rainbow

[Sampson, Jared M.]

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 
> 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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[PyMOL] color an isosurface with a rainbow

[harold steinberg]

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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[PyMOL] Reminder, CCP4 crystallographic summer school at the APS, June 21 - 29, 2016

[Sanishvili, Ruslan]

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
rsanishv...@anl.gov


From: Sanishvili, Ruslan [rsanishv...@anl.gov]
Sent: Tuesday, February 23, 2016 7:37 AM
To: pymol-users@lists.sourceforge.net
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
rsanishv...@anl.gov

--
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