Re: [PyMOL] Ray tracing transparent sticks

[Jarrett Johnson]

Hello,

Which version are you using? We had this regression in 2.3.0 but was fixed
in the 2.3.2 patch update.

On Thu, Jan 30, 2020 at 9:34 AM Ioannis Riziotis  wrote:

> Hello!
>
> I have been trying to ray trace stick representations with transparency
> (i.e. stick_transparency = 0.5). Although surface transparency is visible
> in ray tracing, transparent sticks always appear opaque in the rendered
> image.
>
> Is there a way to resolve this? Note that in OpenGL, stick transparency
> appears normal; the problem is only in ray tracing.
>
> Thank you very much.
>
> All the best,
> Yannis
>
> ___
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>


-- 

*Jarrett Johnson* | Senior Developer
[image: Schrodinger Logo] 
___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Re. Pymol Ray problem

[Jared Sampson]

Hi Changdev - 

Try the following command, which will save a ray-traced PNG image with 
transparent background (which is what is represented by the checkerboard 
pattern):

    png myfigure.png, ray=1

Alternatively, you can adjust the ray background setting:

    set ray_opaque_background, 1

Hope that helps.

Cheers,
Jared

On November 13, 2019 at 7:08:16 AM, Gadhe Changdev Gorakshnath 
(chang...@1stbio.com) wrote:

Hello there,

When I do ray, it shows brown and white square in the background.

I want to capture image directly from screen but squares also get copied.

Is there any way to remove these squares and capture image directly from the 
screen.

 

Regards,

Changdev

___  
PyMOL-users mailing list  
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net  
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Re. Pymol Ray problem

[Gadhe Changdev Gorakshnath]

Hello there,
When I do ray, it shows brown and white square in the background.
I want to capture image directly from screen but squares also get copied.
Is there any way to remove these squares and capture image directly from the 
screen.

Regards,
Changdev
___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Ray tracing after morphing

[ahoneg]

  1. Ray tracing after morphing (Pascal Egea)

Which version of PyMOL are you using? In the free edu version, Raytracing is 
suppressed.
In the incentive version, you find under the movie menu the option “ray trace 
frames” which you need to check.
You may also want to first set your viewport 
(https://pymolwiki.org/index.php/Viewport)  to a larger size to get a better 
resolution.

Of course, both of these actions will increase the time it takes to render your 
movie




Dr. Annemarie Honegger
Dept. of Biochemistry
Zürich University
Winterthurerstrasse 190
8057 Zürich
Switzerland

e-mail:   honeg...@bioc.uzh.ch
phone:   +41 44 635 55 62
fax:+41 44 635 57 12 



> On 22 Apr 2019, at 14:00, pymol-users-requ...@lists.sourceforge.net wrote:
> 
> Send PyMOL-users mailing list submissions to
>   pymol-users@lists.sourceforge.net
> 
> To subscribe or unsubscribe via the World Wide Web, visit
>   https://lists.sourceforge.net/lists/listinfo/pymol-users
> or, via email, send a message with subject or body 'help' to
>   pymol-users-requ...@lists.sourceforge.net
> 
> You can reach the person managing the list at
>   pymol-users-ow...@lists.sourceforge.net
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of PyMOL-users digest..."
> 
> 
> Today's Topics:
> 
>   1. Ray tracing after morphing (Pascal Egea)
> 
> 
> --
> 
> Message: 1
> Date: Sun, 21 Apr 2019 08:58:52 -0700
> From: Pascal Egea 
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Ray tracing after morphing
> Message-ID:
>   
> Content-Type: text/plain; charset="utf-8"
> 
> Dear All,
> 
> I have been making a morph in pymol and saved the different states using
> the mpng command in the active window. However, I cannot figure out how to
> get ray-traced images to make a high quality movie in quicktime, right now
> it is quite pixelated.
> Is there a way to ray0trace each state of the morph?
> Thanks in advance.
> -- 
> Pascal F. Egea, PhD
> Assistant Professor
> UCLA, David Geffen School of Medicine
> Department of Biological Chemistry
> Boyer Hall room 356
> 611 Charles E Young Drive East
> Los Angeles CA 90095
> office (310)-983-3515
> lab  (310)-983-3516
> email pegea at mednet.ucla.edu
> -- next part --
> An HTML attachment was scrubbed...
> 
> --
> 
> 
> 
> --
> 
> Subject: Digest Footer
> 
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> Unsubscribe: 
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
> 
> --
> 
> End of PyMOL-users Digest, Vol 155, Issue 9
> ***



___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe: 
https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] ray 2400 (NOT ray_trace) each frame of a movie

[Thomas Holder]

Hi AC,

In PyMOL 1.8.6 we added width and height arguments to the mpng command. So this 
is now possible:

  set ray_trace_frames
  mpng imageprefix, width=2400

With older PyMOL versions, you have two options:

1) Run PyMOL headless (pymol -c script.pml) so that the display doesn't limit 
the viewport size, and put in the script:

  viewport 2400, 1800
  mpng imageprefix

2) Write your own export loop:

python
for frame in range(1, cmd.count_frames() + 1):
cmd.frame(frame)
cmd.png('imageprefix%04d.png' % frame, width=2400, ray=1)
python end

Cheers,
  Thomas

> On Jun 29, 2017, at 8:55 PM, Academic Research  wrote:
> 
> So far there is only info about how to "ray_trace" each frame of a movie 
> while exporting to .png images.
> 
> My question: How can I "ray 2400" each image (regardless of my computer 
> screen size - because I have a small computer) so i can get very high 
> resolution images that i can combine together into a high resolution movie.
> Regards,
> 
> AC Research

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] ray command

[Tsjerk Wassenaar]

Hi Mohsen,

So raytracing is indeed not available in the educational version. I find
this a bit strange, as I regarded the educational version the
least-changed-with-respect-to-the-original (say 0.99), which did have
raytracing available. Also, I like students to give me reports with pretty
pictures, and would argue that 'educational' should also allow some basic
raytracing.

Alternatives are:

- getting an academic license
- compile from source (or get from a repository)
- export the scene and ray trace in a different program.

Hope it helps,

Tsjerk

On Tue, Jul 12, 2016 at 10:16 AM, Mohsen Chitsaz <
mohsen.chit...@flinders.edu.au> wrote:

> Hi Pymol users,
>
>
>
> The “ray command” is not working in my Educational version of Pymol. It
> seems that educational version does not allow to use this command.
>
>
>
> Does anyone have a solution for this please?
>
>
>
> Your reply is very much appreciated.
>
>
>
> Cheers
>
> Mohsen
>
>
> --
> What NetFlow Analyzer can do for you? Monitors network bandwidth and
> traffic
> patterns at an interface-level. Reveals which users, apps, and protocols
> are
> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
> J-Flow, sFlow and other flows. Make informed decisions using capacity
> planning
> reports.http://sdm.link/zohodev2dev
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>



-- 
Tsjerk A. Wassenaar, Ph.D.
--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] ray command

[Tsjerk Wassenaar]

Hi Mohsen,

What happens? What error do you get?

Best,

Tsjerk
On Jul 12, 2016 10:46 AM, "Mohsen Chitsaz" 
wrote:

Hi Pymol users,



The “ray command” is not working in my Educational version of Pymol. It
seems that educational version does not allow to use this command.



Does anyone have a solution for this please?



Your reply is very much appreciated.



Cheers

Mohsen

--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning
reports.http://sdm.link/zohodev2dev
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Ray tracing max_threads

[Thomas Holder]

Hi all,

Quick summary after off-line discussion with Jesper: The max of 32 threads was 
hard coded in PyMOL. The latest SVN update increases this limit to 125.

If you ever need a higher limit, look for PYMOL_MAX_THREADS in the code.

Cheers,
  Thomas

On 22 Jan 2016, at 03:27, Jesper Lykkegaard Karlsen  wrote:

> Hi,
> 
> I am doing some heavy duty ray tracing in PyMOL.
> 
> I realize spreading the job over multiple nodes in a PBS requires MPI 
> integration in PyMOL, but this is run on a single machine with 36 
> physical CPU cores and 72 logical threads.
> Although, during PyMOL ray tracing CPU usage maxes-out at 32 treads.
> 
> I have even tried setting max_treads to 72, but PyMOL refuses to use any 
> more than 32 threads.
> 
> Why this limitation? and is the a way to overcome it?
> 
> Thanks
> 
> Jesper
> 
> -- 
> Jesper Lykkegaard Karlsen
> Scientific Computing
> Centre for Structural Biology
> Department of Molecular Biology and Genetics
> Aarhus University
> Gustav Wieds Vej 10C
> 8000 Aarhus C
> 
> E-mail: je...@mbg.au.dk

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


--
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
Monitor end-to-end web transactions and take corrective actions now
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Ray tracing on PBS queue with multiple cores?

[Schubert, Carsten [JRDUS]]

Dan,

pymol has a setting “max_threads” which (AFIK) controls the number of CPUs on a 
multicore machine used during rendering. The program tries to set these to a 
reasonable default value, but if that fails you can try to do this yourself. I 
don’t think it is possible to spread the same job over multiple CPUs when these 
are located on different boxes.

HTH

Carsten

From: Dan Lin [mailto:dh...@caltech.edu]
Sent: Monday, August 31, 2015 8:29 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Ray tracing on PBS queue with multiple cores?

Hello all:

I'm trying to ray trace some large movies and I have access to a cluster that 
uses PBS queues. However, I am having difficulty getting pymol to render with 
more than 1 CPU. Has anybody encountered this problem and found a solution?

Thanks in advance!

-Dan
--
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Ray Trace of Icosahedral Viral Capsids using NVIDIA GE Force

[Osvaldo Martin]

Hi,

Did you try with this recipe
? Did you try doing the
ray-traicing from a script (and not using the GUI)?

Cheers,
Osvaldo.

On Tue, Apr 28, 2015 at 11:46 AM, Rallapalli, Pavithra <
pavithra.rallapalli...@ucl.ac.uk> wrote:

 Hi all
>
>
>
> I am trying to ray trace my icosahedram viral capsid, a 75 MB .pse file.
>
> I am running this on a 16 GB windows 64 bit machine with 2 GB NVIDEA
> GEFORCE graphics.
>
>
>
> But the memory still seems to be low as for some reason PyMOL’s virtual
> memory is still low.
>
> I have tried set hash_max but does not make a difference.
>
>
>
> Does any one have any suggestions on changing the settings so PyMOL uses
> the full power of the machine?
>
>
>
>
>
> Many Thanks
>
> Pavithra Rallapalli, PhD
>
>
>
>
>
>
> --
> One dashboard for servers and applications across Physical-Virtual-Cloud
> Widest out-of-the-box monitoring support with 50+ applications
> Performance metrics, stats and reports that give you Actionable Insights
> Deep dive visibility with transaction tracing using APM Insight.
> http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
​
--
One dashboard for servers and applications across Physical-Virtual-Cloud 
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] ray trace mode 1 playing up pymol 1.7.4?

[Andreas Warnecke]

Hi,

This may also be related to the setting:
ray_trace_mode

Try:
set ray_trace_mode, 0

This will deactivate outlines (ray_trace_color) during ray tracing. The
wiki page has some examples.

Cheers,

Andreas
On Dec 16, 2014 6:05 PM, "H. Adam Steinberg" 
wrote:

> The thickness, or weight of the black outline is related to the size of
> the viewport or the ray command.
>
> If you ray the image larger, the thickness of the black outline will be
> greatly reduced. This will improve the clarity of colored sphere surface by
> reducing the amount of black in those areas.
>
> I would try using surface instead of spheres to make the black outline
> work in a more cleaner style. If you want to stick with spheres, remove the
> black outline and use ambient occlusion lighting:
>
> set light_count,8set spec_count,1set shininess, 10set specular, 0.25set 
> ambient,0set direct,0set reflect,1.5set ray_shadow_decay_factor, 0.1set 
> ray_shadow_decay_range, 2
> unset depth_cue
>
>
>
> On Dec 15, 2014, at 4:33 AM, Jacob Lewis  wrote:
>
> Hi,
>
> I have a very complicated image to render in pymol and everytime I go to
> render it in colour with a black outline in spheres I get the render below
> whereby all the spheres have messing black lines in them? How do I
> circumvent this?
> 
>
> Cheers,
>
> Jacob
>
> --
> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
> with Interactivity, Sharing, Native Excel Exports, App Integration & more
> Get technology previously reserved for billion-dollar corporations, FREE
>
> http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
>
> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/592-2366
>
>
>
> --
> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
> with Interactivity, Sharing, Native Excel Exports, App Integration & more
> Get technology previously reserved for billion-dollar corporations, FREE
>
> http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
--
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] ray trace mode 1 playing up pymol 1.7.4?

[H. Adam Steinberg]

The thickness, or weight of the black outline is related to the size of the 
viewport or the ray command.

If you ray the image larger, the thickness of the black outline will be greatly 
reduced. This will improve the clarity of colored sphere surface by reducing 
the amount of black in those areas.

I would try using surface instead of spheres to make the black outline work in 
a more cleaner style. If you want to stick with spheres, remove the black 
outline and use ambient occlusion lighting:

set light_count,8
set spec_count,1
set shininess, 10
set specular, 0.25
set ambient,0
set direct,0
set reflect,1.5
set ray_shadow_decay_factor, 0.1
set ray_shadow_decay_range, 2
unset depth_cue


> On Dec 15, 2014, at 4:33 AM, Jacob Lewis  wrote:
> 
> Hi, 
> 
> I have a very complicated image to render in pymol and everytime I go to 
> render it in colour with a black outline in spheres I get the render below 
> whereby all the spheres have messing black lines in them? How do I circumvent 
> this? 
> 
> 
> Cheers, 
> 
> Jacob
> --
> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
> with Interactivity, Sharing, Native Excel Exports, App Integration & more
> Get technology previously reserved for billion-dollar corporations, FREE
> http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

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

--
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Ray trace mode 1 outline thickness

[Sampson, Jared]

Hi Martin -

Try increasing the `ray_trace_gain` setting.  Default value is 0.12, so maybe 
try 1 or 2.  If you go much higher, you’ll start to see additional lines or 
spots.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On May 14, 2014, at 9:36 AM, Martin Hediger 
mailto:ma@bluewin.ch>> wrote:

Hi guys

I wonder if you could help, I'm rendering this image:

http://qmviews.blogspot.ch/2014/05/illustrating-protein-structures.html

and I wonder if and how I could increase the thickness of the black
outlines?

Thanks for help
Martin

--
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.
Get unparalleled scalability from the best Selenium testing platform available
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net


This email message, including any attachments, is for the sole use of the 
intended recipient(s) and may contain information that is proprietary, 
confidential, and exempt from disclosure under applicable law. Any unauthorized 
review, use, disclosure, or distribution is prohibited. If you have received 
this email in error please notify the sender by return email and delete the 
original message. Please note, the recipient should check this email and any 
attachments for the presence of viruses. The organization accepts no liability 
for any damage caused by any virus transmitted by this email.
=
--
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.
Get unparalleled scalability from the best Selenium testing platform available
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Ray tracing with no GUI yields segmentation fault

[Ricardo O. S. Soares]

Hello Thomas , 

you're right, now everything runs smoothly. 

Thanks for your help! 

Best regards, 

Ricardo. 

--- 
Biological Chemistry and Physics 
Faculty of Pharmaceutical Sciences at Ribeirão Preto 
University of São Paulo - Brazil 
- Mensagem original -

> De: "Thomas Holder" 
> Para: "Ricardo O. S. Soares" 
> Cc: "pymol-users" 
> Enviadas: Quarta-feira, 15 de Janeiro de 2014 17:32:00
> Assunto: Re: [PyMOL] Ray tracing with no GUI yields segmentation
> fault

> Hi Ricardo,

> you didn't mention that you launch pymol from a script (with
> "finish_launching"), which is not very well supported. The
> recommended mode for GUI-less scripts is to run pymol like that:

> pymol -cqr yourscript.py

> Cheers,
> Thomas

> On 15 Jan 2014, at 13:48, Ricardo O. S. Soares 
> wrote:

> > Hello Thomas,
> > thanks for your reply.
> >
> > You are right, I unintentionally switched the antialias and angle
> > parameters, sorry about that.
> > But that does not change mush the outcome, any cmd.ray gives me the
> > segmentation fault.
> > I'm getting no output from cmd.png unless I use the ray command
> > first (which works fine only with loaded GUI), and that seems to
> > be a rather common issue in GUI-less mode
> > (http://pymolwiki.org/index.php/Png).
> > You said you weren't getting a seg. fault with the latest SVN code,
> > did you ran it GUI-less?
> > The representations I'm using are surfaces, however I get the same
> > error with any of them, and in different machines.
> >
> > Here's a example of script that gives me the error:
> >
> > import __main__
> > #__main__.pymol_argv = [ 'pymol', '-qc'] # Quiet and no GUI
> > __main__.pymol_argv = [ 'pymol', '-q' ]
> > import pymol, time
> >
> > pymol.finish_launching()
> > pymol.cmd.load("temp.pdb")
> > pymol.cmd.ray() -> this line gives segmentation fault
> > pymol.cmd.png("image.png", 640, 640, 300,1) -> this wont work
> > without loaded GUI
> >
> > pymol.cmd.quit()
> >
> > Cheers,
> >
> > Ricardo.
> >
> > ---
> > Biological Chemistry and Physics
> > Faculty of Pharmaceutical Sciences at Ribeirão Preto
> > University of São Paulo - Brazil
> > De: "Thomas Holder" 
> > Para: "Ricardo O. S. Soares" 
> > Cc: "pymol-users" 
> > Enviadas: Terça-feira, 14 de Janeiro de 2014 18:18:37
> > Assunto: Re: [PyMOL] Ray tracing with no GUI yields segmentation
> > fault
> >
> > Hi Ricardo,
> >
> > you probably want to do this, without calling the ray command:
> >
> > cmd.png("image.png", 640, 640, dpi=300, ray=1)
> >
> > Also, your ray command sets antialias=300 and angle=-1, which I
> > guess was not your intention. I'm not getting a segmentation fault
> > with the latest SVN code using your command, though. Do you have
> > any volume representation? Volume is not fully supported with ray
> > tracing.
> >
> > Cheers,
> > Thomas
> >
> > On 14 Jan 2014, at 13:36, Ricardo O. S. Soares
> >  wrote:
> >
> > > Hello everyone,
> > >
> > > I wrote a python script where pymol performs some color changes,
> > > ray tracing and image export.
> > > The script works perfectly if I enable the GUI, however if I load
> > > pymol without the GUI (-c flag) I receive a segmentation fault
> > > error.
> > > I found out that this issue is resolved by commenting the line
> > > "pymol.cmd.ray(640,640,300,-1)".
> > > I'd like to solve this, so the script can run in a loop without
> > > opening the GUI every time.
> > > It may help to clarify that I'm running a LinuxMint14 machine
> > > (AMD64), with GCC compiler version 4.7.2.
> > >
> > > I appreciate any help.
> > >
> > > Ricardo.
> > > ---
> > > Biological Chemistry and Physics
> > > Faculty of Pharmaceutical Sciences at Ribeirão Preto
> > > University of São Paulo - Brazil
> >
> > --
> > Thomas Holder
> > PyMOL Developer

> --
> Thomas Holder
> PyMOL Developer
--
CenturyLink Cloud: The Leader in Enterprise Cloud Services.
Learn Why More Businesses Are Choosing CenturyLink Cloud For
Critical Workloads, Development Environments & Everything In Between.
Get a Quote or Start a Free Trial Today. 
http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Ray tracing with no GUI yields segmentation fault

[Thomas Holder]

Hi Ricardo,

you didn't mention that you launch pymol from a script (with 
"finish_launching"), which is not very well supported. The recommended mode for 
GUI-less scripts is to run pymol like that:

pymol -cqr yourscript.py

Cheers,
  Thomas

On 15 Jan 2014, at 13:48, Ricardo O. S. Soares  wrote:

> Hello Thomas,
> thanks for your reply.
> 
> You are right, I unintentionally switched the antialias and angle parameters, 
> sorry about that.
> But that does not change mush the outcome, any cmd.ray gives me the 
> segmentation fault.
> I'm getting no output from cmd.png unless I use the ray command first (which 
> works fine only with loaded GUI), and that seems to be a rather common issue 
> in GUI-less mode (http://pymolwiki.org/index.php/Png).
> You said you weren't getting a seg. fault with the latest SVN code, did you 
> ran it GUI-less?
> The representations I'm using are surfaces, however I get the same error with 
> any of them, and in different machines. 
> 
> Here's a example of script that gives me the error:
> 
> import __main__
> #__main__.pymol_argv = [ 'pymol', '-qc'] # Quiet and no GUI
> __main__.pymol_argv = [ 'pymol', '-q' ]
> import pymol, time
>  
> pymol.finish_launching()
> pymol.cmd.load("temp.pdb")
> pymol.cmd.ray()-> this 
> line gives segmentation fault
> pymol.cmd.png("image.png", 640, 640, 300,1)  -> this wont work without 
> loaded GUI
> 
> pymol.cmd.quit()
> 
> Cheers,
> 
> Ricardo.
> 
> ---
> Biological Chemistry and Physics
> Faculty of Pharmaceutical Sciences at Ribeirão Preto
> University of São Paulo - Brazil
> De: "Thomas Holder" 
> Para: "Ricardo O. S. Soares" 
> Cc: "pymol-users" 
> Enviadas: Terça-feira, 14 de Janeiro de 2014 18:18:37
> Assunto: Re: [PyMOL] Ray tracing with no GUI yields segmentation fault
> 
> Hi Ricardo,
> 
> you probably want to do this, without calling the ray command:
> 
> cmd.png("image.png", 640, 640, dpi=300, ray=1)
> 
> Also, your ray command sets antialias=300 and angle=-1, which I guess was not 
> your intention. I'm not getting a segmentation fault with the latest SVN code 
> using your command, though. Do you have any volume representation? Volume is 
> not fully supported with ray tracing.
> 
> Cheers,
>   Thomas
> 
> On 14 Jan 2014, at 13:36, Ricardo O. S. Soares  wrote:
> 
> > Hello everyone,
> > 
> > I wrote a python script where pymol performs some color changes, ray 
> > tracing and image export.
> > The script works perfectly if I enable the GUI, however if I load pymol 
> > without the GUI (-c flag) I receive a segmentation fault error.
> > I found out that this issue is  resolved by commenting the line 
> > "pymol.cmd.ray(640,640,300,-1)".
> > I'd like to solve this, so the script can run in a loop without opening the 
> > GUI every time.
> > It may help to clarify that I'm running a LinuxMint14 machine (AMD64), with 
> > GCC compiler version 4.7.2.
> > 
> > I appreciate any help.
> > 
> > Ricardo.
> > ---
> > Biological Chemistry and Physics
> > Faculty of Pharmaceutical Sciences at Ribeirão Preto
> > University of São Paulo - Brazil
> 
> -- 
> Thomas Holder
> PyMOL Developer

-- 
Thomas Holder
PyMOL Developer


--
CenturyLink Cloud: The Leader in Enterprise Cloud Services.
Learn Why More Businesses Are Choosing CenturyLink Cloud For
Critical Workloads, Development Environments & Everything In Between.
Get a Quote or Start a Free Trial Today. 
http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Ray tracing with no GUI yields segmentation fault

[Ricardo O. S. Soares]

Hello Thomas, 
thanks for your reply. 

You are right, I unintentionally switched the antialias and angle parameters, 
sorry about that. 
But that does not change mush the outcome, any cmd.ray gives me the 
segmentation fault. 
I'm getting no output from cmd.png unless I use the ray command first (which 
works fine only with loaded GUI), and that seems to be a rather common issue in 
GUI-less mode (http://pymolwiki.org/index.php/Png). 
You said you weren't getting a seg. fault with the latest SVN code, did you ran 
it GUI-less? 
The representations I'm using are surfaces, however I get the same error with 
any of them, and in different machines. 

Here's a example of script that gives me the error: 

import __main__ 
#__main__.pymol_argv = [ 'pymol', '-qc'] # Quiet and no GUI 
__main__.pymol_argv = [ 'pymol', '-q' ] 
import pymol, time 

pymol.finish_launching() 
pymol.cmd.load("temp.pdb") 
pymol.cmd.ray() -> this line gives segmentation fault 
pymol.cmd.png("image.png", 640, 640, 300,1) -> this wont work without 
loaded GUI 

pymol.cmd.quit() 

Cheers, 

Ricardo. 

--- 
Biological Chemistry and Physics 
Faculty of Pharmaceutical Sciences at Ribeirão Preto 
University of São Paulo - Brazil 
- Mensagem original -

> De: "Thomas Holder" 
> Para: "Ricardo O. S. Soares" 
> Cc: "pymol-users" 
> Enviadas: Terça-feira, 14 de Janeiro de 2014 18:18:37
> Assunto: Re: [PyMOL] Ray tracing with no GUI yields segmentation
> fault

> Hi Ricardo,

> you probably want to do this, without calling the ray command:

> cmd.png("image.png", 640, 640, dpi=300, ray=1)

> Also, your ray command sets antialias=300 and angle=-1, which I guess
> was not your intention. I'm not getting a segmentation fault with
> the latest SVN code using your command, though. Do you have any
> volume representation? Volume is not fully supported with ray
> tracing.

> Cheers,
> Thomas

> On 14 Jan 2014, at 13:36, Ricardo O. S. Soares 
> wrote:

> > Hello everyone,
> >
> > I wrote a python script where pymol performs some color changes,
> > ray tracing and image export.
> > The script works perfectly if I enable the GUI, however if I load
> > pymol without the GUI (-c flag) I receive a segmentation fault
> > error.
> > I found out that this issue is resolved by commenting the line
> > "pymol.cmd.ray(640,640,300,-1)".
> > I'd like to solve this, so the script can run in a loop without
> > opening the GUI every time.
> > It may help to clarify that I'm running a LinuxMint14 machine
> > (AMD64), with GCC compiler version 4.7.2.
> >
> > I appreciate any help.
> >
> > Ricardo.
> > ---
> > Biological Chemistry and Physics
> > Faculty of Pharmaceutical Sciences at Ribeirão Preto
> > University of São Paulo - Brazil

> --
> Thomas Holder
> PyMOL Developer
--
CenturyLink Cloud: The Leader in Enterprise Cloud Services.
Learn Why More Businesses Are Choosing CenturyLink Cloud For
Critical Workloads, Development Environments & Everything In Between.
Get a Quote or Start a Free Trial Today. 
http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Ray tracing with no GUI yields segmentation fault

[Thomas Holder]

Hi Ricardo,

you probably want to do this, without calling the ray command:

cmd.png("image.png", 640, 640, dpi=300, ray=1)

Also, your ray command sets antialias=300 and angle=-1, which I guess was not 
your intention. I'm not getting a segmentation fault with the latest SVN code 
using your command, though. Do you have any volume representation? Volume is 
not fully supported with ray tracing.

Cheers,
  Thomas

On 14 Jan 2014, at 13:36, Ricardo O. S. Soares  wrote:

> Hello everyone,
> 
> I wrote a python script where pymol performs some color changes, ray tracing 
> and image export.
> The script works perfectly if I enable the GUI, however if I load pymol 
> without the GUI (-c flag) I receive a segmentation fault error.
> I found out that this issue is  resolved by commenting the line 
> "pymol.cmd.ray(640,640,300,-1)".
> I'd like to solve this, so the script can run in a loop without opening the 
> GUI every time.
> It may help to clarify that I'm running a LinuxMint14 machine (AMD64), with 
> GCC compiler version 4.7.2.
> 
> I appreciate any help.
> 
> Ricardo.
> ---
> Biological Chemistry and Physics
> Faculty of Pharmaceutical Sciences at Ribeirão Preto
> University of São Paulo - Brazil

-- 
Thomas Holder
PyMOL Developer


--
CenturyLink Cloud: The Leader in Enterprise Cloud Services.
Learn Why More Businesses Are Choosing CenturyLink Cloud For
Critical Workloads, Development Environments & Everything In Between.
Get a Quote or Start a Free Trial Today. 
http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] ray-tracing cones

[Thomas Holder]

Hi Robert,

this looks like a bug, none of the closed CGOs is rendered on the
inside, even with two_sided_lighting=on.

I filed a bug report: https://sourceforge.net/p/pymol/bugs/134/

Cheers,
  Thomas

Bryn Fenwick wrote, On 08/20/13 00:42:
> 
> Hi All,
> 
> I am trying to ray trace an empty cone. I can find no way to get an image of 
> the inside of the cone. Does anyone have a work around. Example attached.
> 
> run test.py
> cone
> ray
> 
> when the ray command is issued the cone disappears from view.
> 
> robert
> 
> 
> #
> # test.py
> #
> 
> 
> from pymol import cmd
> from pymol.cgo import *
> 
> 
> def cone(name='cone'):
> 
> o = []
> 
> o.extend( [ CONE,
>   0.0, 0.0, 0.0,# XYZ 1
>   0.0, 0.0, 1.5,# XYZ 2
>   0.0,  # Radius 1
>   0.3,  # Radius 2
>   1.0, 0.0, 0.0,# RGB Color 1
>   0.0, 0.0, 1.0,# RGB Color 2
>   0.0, 0.0, # Caps 1 & 2
> ] )
> 
> 
> cmd.load_cgo(o, name)
> 
> cmd.extend('cone', cone)

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

--
Introducing Performance Central, a new site from SourceForge and 
AppDynamics. Performance Central is your source for news, insights, 
analysis and resources for efficient Application Performance Management. 
Visit us today!
http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Ray-trace of volume visualization

[Per Larsson]

Hi Jason

Great, it works, but as you say there is not much difference really.

And thanks - we're talking about right now how to include this in an upcoming 
publication. When and if it is published, I can send you an image.

Cheers
/Per

2 nov 2012 kl. 22:50 skrev Jason Vertrees:

> Hi Per,
> 
> set ray_volume, 1
> 
> We disabled this feature because it wasn't of high enough quality to
> be used. Once we fix this, we'll change PyMOL to automatically ray
> trace the volumes. Until then, you can try the trick I noted above.
> 
> If you feel like sharing I'd love to see what you came up with.
> 
> Cheers,
> 
> -- Jason
> 
> On Fri, Nov 2, 2012 at 1:19 PM, Per Larsson  wrote:
>> Hi!
>> 
>> Following up on my earlier post 
>> http://sourceforge.net/mailarchive/message.php?msg_id=30017929, I have 
>> managed to make some very nice volume visualizations in Pymol.
>> 
>> I now wonder about the possibilities of ray-tracing the volume? I should add 
>> that I'm not a graphics guru, so maybe this does not make sense at all.
>> Essentially, I have my volume, and also in the same view a protein. When I 
>> type 'ray' to ray-trace everything, only the protein is visible. I also 
>> tried exporting everything to a .wml file (save myscene.wml) and converting 
>> that file to a .pov for ray-tracing in povray, but again only the protein is 
>> visible.
>> 
>> So, my question is if it is possible to somehow improve the (already very 
>> nice) volume visualization, or is what you see on screen also the "only" 
>> thing you can get when saving a png-image?
>> 
>> Many thanks
>> /Per
>> --
>> LogMeIn Central: Instant, anywhere, Remote PC access and management.
>> Stay in control, update software, and manage PCs from one command center
>> Diagnose problems and improve visibility into emerging IT issues
>> Automate, monitor and manage. Do more in less time with Central
>> http://p.sf.net/sfu/logmein12331_d2d
>> ___
>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> 
> 
> 
> -- 
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrödinger, Inc.
> 
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120


--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_nov
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Ray-trace of volume visualization

[Jason Vertrees]

Hi Per,

set ray_volume, 1

We disabled this feature because it wasn't of high enough quality to
be used. Once we fix this, we'll change PyMOL to automatically ray
trace the volumes. Until then, you can try the trick I noted above.

If you feel like sharing I'd love to see what you came up with.

Cheers,

-- Jason

On Fri, Nov 2, 2012 at 1:19 PM, Per Larsson  wrote:
> Hi!
>
> Following up on my earlier post 
> http://sourceforge.net/mailarchive/message.php?msg_id=30017929, I have 
> managed to make some very nice volume visualizations in Pymol.
>
> I now wonder about the possibilities of ray-tracing the volume? I should add 
> that I'm not a graphics guru, so maybe this does not make sense at all.
> Essentially, I have my volume, and also in the same view a protein. When I 
> type 'ray' to ray-trace everything, only the protein is visible. I also tried 
> exporting everything to a .wml file (save myscene.wml) and converting that 
> file to a .pov for ray-tracing in povray, but again only the protein is 
> visible.
>
> So, my question is if it is possible to somehow improve the (already very 
> nice) volume visualization, or is what you see on screen also the "only" 
> thing you can get when saving a png-image?
>
> Many thanks
> /Per
> --
> LogMeIn Central: Instant, anywhere, Remote PC access and management.
> Stay in control, update software, and manage PCs from one command center
> Diagnose problems and improve visibility into emerging IT issues
> Automate, monitor and manage. Do more in less time with Central
> http://p.sf.net/sfu/logmein12331_d2d
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, Inc.

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

--
LogMeIn Central: Instant, anywhere, Remote PC access and management.
Stay in control, update software, and manage PCs from one command center
Diagnose problems and improve visibility into emerging IT issues
Automate, monitor and manage. Do more in less time with Central
http://p.sf.net/sfu/logmein12331_d2d
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Ray tracing transparent Isopotential surfaces

[Jason Vertrees]

Hi Warren,

What commands did you use? I just tested the following on PyMOL
v1.5.0.4 and everything worked as advertised:

fetch 1rx1, async=0
fetch 1rx1, type=2fofc, async=0
isosurface mySurf, 1rx1_2fofc, 1.0, (organic)
orient organic
set transparency, 0.5
ray

Can you try the above code and let me know what you get?

Cheers,

-- Jason

On Thu, Sep 27, 2012 at 12:02 PM, Warren Gallin  wrote:
> Hi,
>
> I have generated isopotential surfaces for a protein that completely 
> enclose the basic structure using the APBS plugin.
>
> I can increase the transparency so I can visualize an underlying 
> cartoon representation of the structure.
>
> However, when I do a ray tracing to get a publication quality image, 
> I only get the isopotential surface - the ray tracing seems to view the 
> surface as 0% transparent, contrary to the settings that were used to 
> visualize the image in the first place.
>
> Is this a bug, or am I missing some step that allows the ray tracing 
> to handle a partially transparent surface?
>
> Thanks in advance for any advice.
>
> Warren Gallin
> --
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://ad.doubleclick.net/clk;258768047;13503038;j?
> http://info.appdynamics.com/FreeJavaPerformanceDownload.html
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, Inc.

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://ad.doubleclick.net/clk;258768047;13503038;j?
http://info.appdynamics.com/FreeJavaPerformanceDownload.html
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] ray - volume

[Jason Vertrees]

Hi David,

> Since I happen to be playing with volumes right now, I tried that and
> it causes my sticks to pop out of the volumes (see attached).  This is
> on a build of the latest open source code in SVN.

You have found the reason why this isn't turned on by default. There
are still some problems with calculating depth that we haven't yet
fixed.

The way around this is to use the "draw" command with a very large
image size that you can scale down later to high-res.

Cheers,

-- Jason


> On Tue, Nov 29, 2011 at 10:34 AM, Jason Vertrees
>  wrote:
>> Hi Lina,
>>
>> set ray_volume, on
>>
>> Cheers,
>>
>> -- Jason
>>
>> On Tue, Nov 29, 2011 at 10:27 AM, lina  wrote:
>>> Hi,
>>>
>>> a quick question, how to keep the volume during ray.
>>>
>>> the volume is here,
>>>
>>> but after ray,
>>>
>>> it's gone,
>>>
>>> what's kinda of special settings I need to take care?
>>>
>>> Thanks with best regards,
>>>
>>> --
>>> All the data continuously generated in your IT infrastructure
>>> contains a definitive record of customers, application performance,
>>> security threats, fraudulent activity, and more. Splunk takes this
>>> data and makes sense of it. IT sense. And common sense.
>>> http://p.sf.net/sfu/splunk-novd2d
>>> ___
>>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>>
>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrodinger, LLC
>>
>> (e) jason.vertr...@schrodinger.com
>> (o) +1 (603) 374-7120
>>
>> --
>> All the data continuously generated in your IT infrastructure
>> contains a definitive record of customers, application performance,
>> security threats, fraudulent activity, and more. Splunk takes this
>> data and makes sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-novd2d
>> ___
>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

--
All the data continuously generated in your IT infrastructure 
contains a definitive record of customers, application performance, 
security threats, fraudulent activity, and more. Splunk takes this 
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] ray - volume

[lina]

On Wed, Nov 30, 2011 at 12:25 AM, Jason Vertrees
 wrote:
> Hi David,
>
> Are your data and color ramp points correct? If you send me the data,
> I can double-check what we've done.

I am also confusing how to put the quasi-center of volume on some certain atom.

Even I only chose one atom, but the volume still shifted away from
this certain atom,

The way I tried based on this page:
 http://www.pymolwiki.org/index.php/Isomesh

might I understand volume totally wrong.

Thanks ahead for pointing out.

p.s frankly speaking, I am interested in "volumn" simply cause the
representation looks fantastic.
>
> Cheers,
>
> -- Jason
>
> On Tue, Nov 29, 2011 at 10:56 AM, David Hall  wrote:
>> Since I happen to be playing with volumes right now, I tried that and
>> it causes my sticks to pop out of the volumes (see attached).  This is
>> on a build of the latest open source code in SVN.
>>
>> Thanks,
>> David
>>
>> On Tue, Nov 29, 2011 at 10:34 AM, Jason Vertrees
>>  wrote:
>>> Hi Lina,
>>>
>>> set ray_volume, on
>>>
>>> Cheers,
>>>
>>> -- Jason
>>>
>>> On Tue, Nov 29, 2011 at 10:27 AM, lina  wrote:
 Hi,

 a quick question, how to keep the volume during ray.

 the volume is here,

 but after ray,

 it's gone,

 what's kinda of special settings I need to take care?

 Thanks with best regards,

 --
 All the data continuously generated in your IT infrastructure
 contains a definitive record of customers, application performance,
 security threats, fraudulent activity, and more. Splunk takes this
 data and makes sense of it. IT sense. And common sense.
 http://p.sf.net/sfu/splunk-novd2d
 ___
 PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
 Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

>>>
>>>
>>>
>>> --
>>> Jason Vertrees, PhD
>>> PyMOL Product Manager
>>> Schrodinger, LLC
>>>
>>> (e) jason.vertr...@schrodinger.com
>>> (o) +1 (603) 374-7120
>>>
>>> --
>>> All the data continuously generated in your IT infrastructure
>>> contains a definitive record of customers, application performance,
>>> security threats, fraudulent activity, and more. Splunk takes this
>>> data and makes sense of it. IT sense. And common sense.
>>> http://p.sf.net/sfu/splunk-novd2d
>>> ___
>>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120

--
All the data continuously generated in your IT infrastructure 
contains a definitive record of customers, application performance, 
security threats, fraudulent activity, and more. Splunk takes this 
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] ray - volume

[Jason Vertrees]

Hi David,

Are your data and color ramp points correct? If you send me the data,
I can double-check what we've done.

Cheers,

-- Jason

On Tue, Nov 29, 2011 at 10:56 AM, David Hall  wrote:
> Since I happen to be playing with volumes right now, I tried that and
> it causes my sticks to pop out of the volumes (see attached).  This is
> on a build of the latest open source code in SVN.
>
> Thanks,
> David
>
> On Tue, Nov 29, 2011 at 10:34 AM, Jason Vertrees
>  wrote:
>> Hi Lina,
>>
>> set ray_volume, on
>>
>> Cheers,
>>
>> -- Jason
>>
>> On Tue, Nov 29, 2011 at 10:27 AM, lina  wrote:
>>> Hi,
>>>
>>> a quick question, how to keep the volume during ray.
>>>
>>> the volume is here,
>>>
>>> but after ray,
>>>
>>> it's gone,
>>>
>>> what's kinda of special settings I need to take care?
>>>
>>> Thanks with best regards,
>>>
>>> --
>>> All the data continuously generated in your IT infrastructure
>>> contains a definitive record of customers, application performance,
>>> security threats, fraudulent activity, and more. Splunk takes this
>>> data and makes sense of it. IT sense. And common sense.
>>> http://p.sf.net/sfu/splunk-novd2d
>>> ___
>>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>>
>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrodinger, LLC
>>
>> (e) jason.vertr...@schrodinger.com
>> (o) +1 (603) 374-7120
>>
>> --
>> All the data continuously generated in your IT infrastructure
>> contains a definitive record of customers, application performance,
>> security threats, fraudulent activity, and more. Splunk takes this
>> data and makes sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-novd2d
>> ___
>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

--
All the data continuously generated in your IT infrastructure 
contains a definitive record of customers, application performance, 
security threats, fraudulent activity, and more. Splunk takes this 
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] ray - volume

[lina]

On Tue, Nov 29, 2011 at 11:56 PM, David Hall  wrote:
> Since I happen to be playing with volumes right now, I tried that and
> it causes my sticks to pop out of the volumes (see attached).  This is
> on a build of the latest open source code in SVN.

Thanks for confirmation.

There are some unmet dependencies on my box, so I have to stick to 1.4
for a while and will try again in future.

Thanks and best regards,

>
> Thanks,
> David
>
> On Tue, Nov 29, 2011 at 10:34 AM, Jason Vertrees
>  wrote:
>> Hi Lina,
>>
>> set ray_volume, on
>>
>> Cheers,
>>
>> -- Jason
>>
>> On Tue, Nov 29, 2011 at 10:27 AM, lina  wrote:
>>> Hi,
>>>
>>> a quick question, how to keep the volume during ray.
>>>
>>> the volume is here,
>>>
>>> but after ray,
>>>
>>> it's gone,
>>>
>>> what's kinda of special settings I need to take care?
>>>
>>> Thanks with best regards,
>>>
>>> --
>>> All the data continuously generated in your IT infrastructure
>>> contains a definitive record of customers, application performance,
>>> security threats, fraudulent activity, and more. Splunk takes this
>>> data and makes sense of it. IT sense. And common sense.
>>> http://p.sf.net/sfu/splunk-novd2d
>>> ___
>>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>>
>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrodinger, LLC
>>
>> (e) jason.vertr...@schrodinger.com
>> (o) +1 (603) 374-7120
>>
>> --
>> All the data continuously generated in your IT infrastructure
>> contains a definitive record of customers, application performance,
>> security threats, fraudulent activity, and more. Splunk takes this
>> data and makes sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-novd2d
>> ___
>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

--
All the data continuously generated in your IT infrastructure 
contains a definitive record of customers, application performance, 
security threats, fraudulent activity, and more. Splunk takes this 
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] ray - volume

[lina]

On Tue, Nov 29, 2011 at 11:34 PM, Jason Vertrees
 wrote:
> Hi Lina,
>
> set ray_volume, on
Thanks,

is the ray_volume some new feature in latest version?

seems Version 1.4. no ray_volume feature.

Best regards,
>
> Cheers,
>
> -- Jason
>
> On Tue, Nov 29, 2011 at 10:27 AM, lina  wrote:
>> Hi,
>>
>> a quick question, how to keep the volume during ray.
>>
>> the volume is here,
>>
>> but after ray,
>>
>> it's gone,
>>
>> what's kinda of special settings I need to take care?
>>
>> Thanks with best regards,
>>
>> --
>> All the data continuously generated in your IT infrastructure
>> contains a definitive record of customers, application performance,
>> security threats, fraudulent activity, and more. Splunk takes this
>> data and makes sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-novd2d
>> ___
>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120

--
All the data continuously generated in your IT infrastructure 
contains a definitive record of customers, application performance, 
security threats, fraudulent activity, and more. Splunk takes this 
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] ray - volume

[Jason Vertrees]

Hi Lina,

set ray_volume, on

Cheers,

-- Jason

On Tue, Nov 29, 2011 at 10:27 AM, lina  wrote:
> Hi,
>
> a quick question, how to keep the volume during ray.
>
> the volume is here,
>
> but after ray,
>
> it's gone,
>
> what's kinda of special settings I need to take care?
>
> Thanks with best regards,
>
> --
> All the data continuously generated in your IT infrastructure
> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
> data and makes sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-novd2d
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

--
All the data continuously generated in your IT infrastructure 
contains a definitive record of customers, application performance, 
security threats, fraudulent activity, and more. Splunk takes this 
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Ray Trace Mode 1 and Labels

[Thomas Holder]

Hi Jack,

you could render the labels to a separate image and assemble both images 
using Photoshop, Gimp, etc.

set ray_trace_mode, 1
hide labels
png image1.png, ray=1

set ray_trace_mode, 0
as labels
set label_font_id, 7
set label_size, 20
set label_color, black
set label_outline_color, white
png image2.png, ray=1

Cheers,
   Thomas

Tsjerk Wassenaar wrote, On 10/15/11 08:13:
> Hi Jack,
> 
> Unfortunately, that is not possible. The ray-trace mode affects the
> behaviour/display of edges during raytracing, It's basically doing
> edge detection, similar to what can be done in image processing
> afterwards. So, it's similar to having an image and wanting to enhance
> edges on some, but not on other objects, using photoshop or so. It's
> impossible to do that automatically.
> 
> In principle, it would be possible to modify the behaviour of the
> raytracer, though. But I think it would require quite a bit of effort
> coding that. But it could be interesting, also to use different line
> colors for different selections :)
> 
> Sorry,
> 
> Tsjerk
> 
> On Fri, Oct 14, 2011 at 3:38 PM, Jack Orford  wrote:
>> Is there a way to stop ray_trace_mode 1 putting an outline on labels?  
>> Although the outline looks quite good for the graphics, especially once they 
>> are printed, it makes the text look like blocky typewriter font.  Any advice 
>> appreciated.
>>
>> Thanks

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

--
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2d-oct
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Ray Trace Mode 1 and Labels

[Tsjerk Wassenaar]

Hi Jack,

Unfortunately, that is not possible. The ray-trace mode affects the
behaviour/display of edges during raytracing, It's basically doing
edge detection, similar to what can be done in image processing
afterwards. So, it's similar to having an image and wanting to enhance
edges on some, but not on other objects, using photoshop or so. It's
impossible to do that automatically.

In principle, it would be possible to modify the behaviour of the
raytracer, though. But I think it would require quite a bit of effort
coding that. But it could be interesting, also to use different line
colors for different selections :)

Sorry,

Tsjerk

On Fri, Oct 14, 2011 at 3:38 PM, Jack Orford  wrote:
> Is there a way to stop ray_trace_mode 1 putting an outline on labels?  
> Although the outline looks quite good for the graphics, especially once they 
> are printed, it makes the text look like blocky typewriter font.  Any advice 
> appreciated.
>
> Thanks
> --
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2d-oct
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

--
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2d-oct
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Ray tracing - distinction between inside and outside of binding pocket

[Ben Roberts]

On 23/8/2011, at 11:02 a.m., Jason Vertrees wrote:

> Hi Ben,
> 
> This isn't yet available. PyMOL only support inside and outside color
> on surface objects (surfaces from maps), not surface representations
> (what we typically consider a surface).
> 
> I'll let you know if this changes.

Thanks Jason. In this case, I managed to get much of what I wanted by dint of 
applying a fierce ray trace fog (I think about 0.8 units).

Cheers,
Ben
-- 
For greater security, I support S/MIME encryption.



smime.p7s
Description: S/MIME cryptographic signature
--
EMC VNX: the world's simplest storage, starting under $10K
The only unified storage solution that offers unified management 
Up to 160% more powerful than alternatives and 25% more efficient. 
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Ray tracing - distinction between inside and outside of binding pocket

[Jason Vertrees]

Hi Ben,

This isn't yet available. PyMOL only support inside and outside color
on surface objects (surfaces from maps), not surface representations
(what we typically consider a surface).

I'll let you know if this changes.

Cheers,

-- Jason

On Mon, Aug 22, 2011 at 5:57 PM, Ben Roberts  wrote:
> Hi,
>
> Having prepared and superimposed the binding pockets that I spoke of in my 
> earlier email, I'm now trying to come up with a way of producing high 
> resolution images of them.
>
> The problem I'm now facing is that I can't seem to come up with a high-res 
> rendering that clearly distinguishes between the inside and outside of the 
> binding pocket. Well, that's not quite accurate. But I have three options 
> I've been able to identify, all of which are less than ideal.
>
> My first option is to use the standard rendering engine (i.e., no ray 
> tracing). Problem: That severely limits my resolution and image quality.
>
> My second option is to use ray tracing with double-sided lighting. Problem: 
> The ray tracing, even more than the standard rendering, makes it all but 
> impossible for the viewer to distinguish between the inside and the outside 
> of the binding pocket.
>
> My third option is to use ray tracing with single-sided lighting. Problem: 
> The "protein" side of the binding pocket then comes out as an unsightly solid 
> black colour.
>
> I've tried to install POV-Ray on my Mac, to no avail. I downloaded and 
> installed version 3.6 from the POV-Ray web site, but when I tried to run the 
> executable, it unceremoniously carked it. Also, it didn't place an x-povray 
> on my command line, nor in the POV-Ray directory, that I could find. So 
> unless I've overlooked something, that avenue is closed to me. I'm loath to 
> try compiling POV-Ray from source.
>
> Having said all that, is there a known way to generate images that are (a) 
> high-resolution, (b) lit up (at least to an extent) from both sides, and (c) 
> in such a style that it's easy for a casual viewer to distinguish the inside 
> from the outside?
>
> Thanks,
> Ben
>
> --
> For greater security, I support S/MIME encryption.
>
>
> --
> uberSVN's rich system and user administration capabilities and model
> configuration take the hassle out of deploying and managing Subversion and
> the tools developers use with it. Learn more about uberSVN and get a free
> download at:  http://p.sf.net/sfu/wandisco-dev2dev
>
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

--
Get a FREE DOWNLOAD! and learn more about uberSVN rich system, 
user administration capabilities and model configuration. Take 
the hassle out of deploying and managing Subversion and the 
tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Ray Trace Triangles

[Robert Campbell]

Hi Sean,

On Fri, 09 Jul 2010 11:05:09 -0400 Sean Law  wrote:

> I have been tackling this problem (on and off) for quite some time now but
> without any luck.  I have been trying to create CGO triangles using the
> following simple sample script:
> 
> 
> ###
> 
> from pymol.cgo import *
> from math import *
> from pymol import cmd
> 
> def triangle ():
> name="test";
> obj=[ BEGIN, TRIANGLES ]
> obj.extend([COLOR,1.0,0.0,0.0,VERTEX,0.0,0.0,0.0])
> obj.extend([COLOR,1.0,0.0,0.0,VERTEX,2.0,0.0,0.0])
> obj.extend([COLOR,1.0,0.0,0.0,VERTEX,0.0,2.0,0.0])
> obj.extend([END])
> cmd.delete("test")
> cmd.load_cgo(obj,"test")
> 
> return
> cmd.extend("triangle",triangle)
> 
> ###
> 
> 
> This creates a nice red triangle for me in the viewing window.  However,
> when I move it around and then ray trace the image, I end up getting either
> a triangle with the original bright red color, a black triangle, or a dark
> red triangle.  What I'm looking for is to be able to get the same bright
> red triangle no matter how I manipulate the object.  I've tried playing
> around with the "NORMAL" value but, if I recall correctly, ray tracing
> produced a blank image.
> 
> Any help or suggestion would be greatly appreciated.  Thanks!

I can't find any way to have a CGO object that is not "lit" in the normal
sense especially when ray traced.  When you leave out the NORMAL vector, then
your triangle is fully lit no matter it's orientation, until you ray trace it.

If you do include a normal vector then its brightness will vary with
orientation both in normal viewing and when ray traced.  You can at least
avoid the problem of having one side completely black when ray traced by
turning on two-sided lighting (in the "Display" menu).

I guess this doesn't really answer your question, though!

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821Fax: 613-533-2497
http://pldserver1.biochem.queensu.ca/~rlc

--
This SF.net email is sponsored by Sprint
What will you do first with EVO, the first 4G phone?
Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] ray with cuda

[Jason Vertrees]

Quyen,

Something like this may appear in alpha-form in a PyMOL 1.x release
(this year or early next) and in full in the PyMOL 2.0 release
(later).  My guess is this will take time to do well.  We'd most
likely be targeting the more generic openCL over CUDA in particular.

As for implementation, check out NVidia's openCL and CUDA developer
zone (http://www.nvidia.com/object/cuda_opencl_new.html).

Cheers,

-- Jason

On Sun, Apr 4, 2010 at 12:01 AM, QT  wrote:
> Dear Jason,
>
> Oh I see...In the mean time, do you have any advice as how to accomplish
> such a thing?  What about a forecast of when an official implementation of
> such thing in pymol framework?
>
> Best,
> Quyen
>
> On Fri, Apr 2, 2010 at 4:08 PM, Jason Vertrees
>  wrote:
>>
>> Quyen,
>>
>> No, not yet.  It's something I very excited to get done though.
>>
>> -- Jason
>>
>> On Fri, Apr 2, 2010 at 4:44 PM, QT  wrote:
>> > Dear all,
>> >
>> > Is it possible to ray using cuda?  I know VMD has some plugin that
>> > allows
>> > cuda integration and was wondering if Pymol has a similar thing.
>> >
>> > Best,
>> > Quyen
>> >
>> >
>> > --
>> > Download Intel® Parallel Studio Eval
>> > Try the new software tools for yourself. Speed compiling, find bugs
>> > proactively, and fine-tune applications for parallel performance.
>> > See why Intel Parallel Studio got high marks during beta.
>> > http://p.sf.net/sfu/intel-sw-dev
>> > ___
>> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>> >
>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrodinger, LLC
>>
>> (e) jason.vertr...@schrodinger.com
>> (o) +1 (603) 374-7120
>
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] ray with cuda

[QT]

Dear Jason,

Oh I see...In the mean time, do you have any advice as how to accomplish
such a thing?  What about a forecast of when an official implementation of
such thing in pymol framework?

Best,
Quyen

On Fri, Apr 2, 2010 at 4:08 PM, Jason Vertrees <
jason.vertr...@schrodinger.com> wrote:

> Quyen,
>
> No, not yet.  It's something I very excited to get done though.
>
> -- Jason
>
> On Fri, Apr 2, 2010 at 4:44 PM, QT  wrote:
> > Dear all,
> >
> > Is it possible to ray using cuda?  I know VMD has some plugin that allows
> > cuda integration and was wondering if Pymol has a similar thing.
> >
> > Best,
> > Quyen
> >
> >
> --
> > Download Intel® Parallel Studio Eval
> > Try the new software tools for yourself. Speed compiling, find bugs
> > proactively, and fine-tune applications for parallel performance.
> > See why Intel Parallel Studio got high marks during beta.
> > http://p.sf.net/sfu/intel-sw-dev
> > ___
> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> >
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
>
--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] ray with cuda

[Jason Vertrees]

Quyen,

No, not yet.  It's something I very excited to get done though.

-- Jason

On Fri, Apr 2, 2010 at 4:44 PM, QT  wrote:
> Dear all,
>
> Is it possible to ray using cuda?  I know VMD has some plugin that allows
> cuda integration and was wondering if Pymol has a similar thing.
>
> Best,
> Quyen
>
> --
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Ray Tracing A Protein Gallery

[Warren DeLano]

> 1. Use the grid_mode option (only available in the compiled from
> source pymols)

FYI: grid_mode and many other enhancements will be present in the
soon-to-be-available PyMOL 1.2 BETA builds.  The annual PyMOL release
cycle for "official" PyMOL builds has settled down as follows:

- Summer:  The major annual release is cut in June/July, followed by any
necessary patch/updates during the summer so that we enter the academic
cycle with a robust build intended for widespread adoption.

- Fall:  We hunker down and tackle the toughest development challenges
for the year, issuing few releases since the code at its most unstable
and incompatible condition.  

- Winter:  Starting in January, we begin issuing a series of routine
beta builds with all the new stuff, so that the bold and the daring can
try things out and begin reporting any issues.

- Spring:  We freeze the feature set then stabilize and test everything
as much as possible in anticipation of the robust major release at the
start of summer.

Of course, the open-source "trunk" is available to developers at any
time of the year :).

Cheers,
Warren

> -Original Message-
> From: Buz Barstow [mailto:b...@mac.com]
> Sent: Thursday, December 18, 2008 3:27 PM
> To: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] Ray Tracing A Protein Gallery
> 
> Dear All,
> 
> Thanks for all your suggestions on ray tracing the protein gallery.
> 
> In the end, I used several of the techniques suggested, and everything
> worked out really well!
> 
> To summarize:
> 
> 1. Use the grid_mode option (only available in the compiled from
> source pymols)
> 2. Make a fake .pdb that has the corners and centers of a 3D box to
> use for alignment
> 3. Use the set_view command to apply the same viewing matrix
> 4. Use the zoom command with a center and a distance specified.
> 
> Also, the cealign package is really helpful for aligning and
> translating very dissimilar molecules.
> 
> Thanks! and all the best,
> 
> --Buz
> 
> 
> 
> 
> On Dec 16, 2008, at 4:05 PM, DeLano Scientific wrote:
> 
> > Hi Buz,
> >
> > You can use "center" as a selection name for input with zoom, along
> > with a
> > distance value.
> >
> > zoom center, distance
> >
> > e.g.
> >
> > # first, get the object you want in the center of the screen
> >
> > orient
> >
> > # then zoom the viewer by a fixed amount about the center point
> >
> > zoom center, 10
> >
> > # you may also wish to move the clipping planes in/out to avoid
> > cutting into
> > any of the molecular representations:
> >
> > clip atoms, 4, selection=all
> >
> > # also, depending upon the application, you might want to disable
> > perspective
> >
> > set orthoscopic
> >
> > # get rid of background pixels
> >
> > unset opaque_background
> >
> > # render
> >
> > ray
> >
> > # and save
> >
> > save struct001.png
> >
> > Cheers,
> > Warren
> >
> >
> > --
> > DeLano Scientific LLC
> > Subscriber Support Services
> > mailto:supp...@delsci.com
> >
> >
> >
> >> -Original Message-
> >> From: Buz Barstow [mailto:b...@mac.com]
> >> Sent: Monday, December 15, 2008 11:42 AM
> >> To: pymol-users@lists.sourceforge.net
> >> Subject: [PyMOL] Ray Tracing A Protein Gallery
> >>
> >> Dear All,
> >>
> >> I'm making a gallery of protein molecules for my PhD thesis.
> >> I'd like to find an automatic way to ensure that all of the
> >> ray traced images have the same scale. Is there an easy way
> >> to do this?
> >>
> >> Thanks! and all the best,
> >>
> >> --Buz
> >>
> >> --
> >> 
> >> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las
> >> Vegas, Nevada.
> >> The future of the web can't happen without you.  Join us at
> >> MIX09 to help pave the way to the Next Web now. Learn more
> >> and register at
> >> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009
> > .visitmix.com/
> >> ___
> >> PyMOL-users mailing list
> >> PyMOL-users@lists.sourceforge.net
> >> https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> >
> >

> --
> > SF.Net email is Sponsored by MIX09, March 18-20, 20

Re: [PyMOL] Ray Tracing A Protein Gallery

[Buz Barstow]

Dear All,

Thanks for all your suggestions on ray tracing the protein gallery.

In the end, I used several of the techniques suggested, and everything  
worked out really well!


To summarize:

1. Use the grid_mode option (only available in the compiled from  
source pymols)
2. Make a fake .pdb that has the corners and centers of a 3D box to  
use for alignment

3. Use the set_view command to apply the same viewing matrix
4. Use the zoom command with a center and a distance specified.

Also, the cealign package is really helpful for aligning and  
translating very dissimilar molecules.


Thanks! and all the best,

--Buz




On Dec 16, 2008, at 4:05 PM, DeLano Scientific wrote:


Hi Buz,

You can use "center" as a selection name for input with zoom, along  
with a

distance value.

zoom center, distance

e.g.

# first, get the object you want in the center of the screen

orient

# then zoom the viewer by a fixed amount about the center point

zoom center, 10

# you may also wish to move the clipping planes in/out to avoid  
cutting into

any of the molecular representations:

clip atoms, 4, selection=all

# also, depending upon the application, you might want to disable
perspective

set orthoscopic

# get rid of background pixels

unset opaque_background

# render

ray

# and save

save struct001.png

Cheers,
Warren


--
DeLano Scientific LLC
Subscriber Support Services
mailto:supp...@delsci.com




-Original Message-
From: Buz Barstow [mailto:b...@mac.com]
Sent: Monday, December 15, 2008 11:42 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Ray Tracing A Protein Gallery

Dear All,

I'm making a gallery of protein molecules for my PhD thesis.
I'd like to find an automatic way to ensure that all of the
ray traced images have the same scale. Is there an easy way
to do this?

Thanks! and all the best,

--Buz

--

SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las
Vegas, Nevada.
The future of the web can't happen without you.  Join us at
MIX09 to help pave the way to the Next Web now. Learn more
and register at
http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009

.visitmix.com/

___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users



--
SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas,  
Nevada.
The future of the web can't happen without you.  Join us at MIX09 to  
help

pave the way to the Next Web now. Learn more and register at
http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/
___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users

Re: [PyMOL] Ray Tracing A Protein Gallery

[DeLano Scientific]

Hi Buz,

You can use "center" as a selection name for input with zoom, along with a
distance value.

zoom center, distance

e.g.

# first, get the object you want in the center of the screen

orient

# then zoom the viewer by a fixed amount about the center point

zoom center, 10

# you may also wish to move the clipping planes in/out to avoid cutting into
any of the molecular representations:

clip atoms, 4, selection=all

# also, depending upon the application, you might want to disable
perspective

set orthoscopic

# get rid of background pixels

unset opaque_background

# render

ray

# and save

save struct001.png

Cheers,
Warren


--
DeLano Scientific LLC
Subscriber Support Services
mailto:supp...@delsci.com

 

> -Original Message-
> From: Buz Barstow [mailto:b...@mac.com] 
> Sent: Monday, December 15, 2008 11:42 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Ray Tracing A Protein Gallery
> 
> Dear All,
> 
> I'm making a gallery of protein molecules for my PhD thesis. 
> I'd like to find an automatic way to ensure that all of the 
> ray traced images have the same scale. Is there an easy way 
> to do this?
> 
> Thanks! and all the best,
> 
> --Buz
> 
> --
> 
> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las 
> Vegas, Nevada.
> The future of the web can't happen without you.  Join us at 
> MIX09 to help pave the way to the Next Web now. Learn more 
> and register at 
> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009
.visitmix.com/
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Re: [PyMOL] Ray Tracing A Protein Gallery

[Nathaniel Echols]

On Mon, Dec 15, 2008 at 11:41 AM, Buz Barstow  wrote:

> I'm making a gallery of protein molecules for my PhD thesis. I'd like
> to find an automatic way to ensure that all of the ray traced images
> have the same scale. Is there an easy way to do this?
>

Translate every model so that the center is at the origin, then use the
set_view command to apply the same viewing matrix for each model.  (You can
still rotate the models, just don't zoom.)  I'm not sure if there's already
a simple way to do the translation from within PyMOL, but it should be quite
straightforward using cctbx or CNS or something similar.

-Nat

Re: [PyMOL] ray and mpng

[DeLano Scientific]

Doug,
 
set ray_trace_frames
 
before issuing the mpng command.
 
Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:supp...@delsci.com

 

  _  

From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Bailey,
Douglas (NIH/NCI) [E]
Sent: Thursday, July 24, 2008 9:20 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] ray and mpng


Hello Everyone,
 
Can the "ray" command be used to set a higher image quality before issuing
the "mpng" command to generate image files for making movies? 
 
I am trying to confirm this for someone else, but as I see it,t the "ray"
command is best for a single high quality image and that it would need to be
imbedded in a script to generate movie images.
 
Thanks,
 
Doug
 
 
 
 
 

Douglas Bailey
NCI-Frederick
1050 Boyles Street
Frederick, Maryland 21702
Ph: 301-846-5328  Fax: 301-846-6322
 

Re: [PyMOL] ray-traced stero figurea

[Dirk Kostrewa]

Hi Richard,

to change wall-eyed stereo figures to cross-eyed, you can simply 
exchange the left and right images (in wall-eyed, the left picture is 
for the left eye, the right picture for the right eye, whereas in 
cross-eyed, the left picture is for the right eye and vice versa).


Warren once explained to me the two stereo angle definitions PyMOL uses. 
Here is en excerpt of what he wrote:


" ...

stereo_shift is the separation between the two cameras observing the
image, expressed as a % of the distance from the objective.

stereo_angle is a scaling factor applied to the natural angular
difference which would occur between two eyes at that distance, both
looking at the objective.

Generally speaking stereo_shift is the main depth control parameter, and
stereo_angle should remain close to 2 in order to generate "correct"
stereo geometry.  However, adjusting stereo_angle can reduce ghosting
and change the apparent Z location of the objective.

Detting stereo_shift to zero makes you a Cyclops (you're basically
telling PyMOL that your eyes are superimposed).

...

The actual translation(+/-) and rotation(+/-) of the camera at
"distance" are:

translation = distance * (stereo_shift/100)

rotation = (stereo_angle/2) * (arctan(stereo_shift/100))
(default = ± 1.2 deg)

..."

In my ~/.pymolrc, I've put these two values for getting +/- 3 degree 
rotations for hardware (quadbuffered) stereo:

set stereo_angle = 2.0
set stereo_shift = 5.24

I hope, this helps.

Best regards,

Dirk.

Richard Baxter wrote:

Dear All,

I used the following commands to generate a nice wall-eye stereo figure
(at least it seems to work for me):

ray 600,900,-1,-3;
png stereo_right.png
ray 600,900,-1,3;
png stereo_left.png

figures are combined in photoshop at 300dpi with an extra 5mm between,
so that images are 2 inches across separated by ~55mm.

My question, how to convert this to a cross-eye stereo figure, do I just
switch the sign of the angle, or should I also multiply/divide by some
amount? I don't understand the shift argument, how I should figure out
what value to use. Any advice greatly appreciated.

sincerely,

Richard Baxter




--


Dirk Kostrewa
Paul Scherrer Institut
Biomolecular Research, OFLC/110
CH-5232 Villigen PSI, Switzerland
Phone:  +41-56-310-4722
Fax:+41-56-310-5288
E-mail: dirk.kostr...@psi.ch
http://sb.web.psi.ch

Re: [PyMOL] ray-traced stero figurea

[Tsjerk Wassenaar]

Hi Richard,

Why not set stereo_mode,3 and raytrace as it is on the screen? You can
set stereo_angle and stereo_shift to modify the scene.

Cheers,

Tsjerk

On 03 Apr 2007 10:57:36 -0500, Richard Baxter
 wrote:

Dear All,

I used the following commands to generate a nice wall-eye stereo figure
(at least it seems to work for me):

ray 600,900,-1,-3;
png stereo_right.png
ray 600,900,-1,3;
png stereo_left.png

figures are combined in photoshop at 300dpi with an extra 5mm between,
so that images are 2 inches across separated by ~55mm.

My question, how to convert this to a cross-eye stereo figure, do I just
switch the sign of the angle, or should I also multiply/divide by some
amount? I don't understand the shift argument, how I should figure out
what value to use. Any advice greatly appreciated.

sincerely,

Richard Baxter

--
Richard Baxter 


-
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT & business topics through brief surveys-and earn cash
http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users




--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Re: [PyMOL] ray trace density

[Peter Adrian Meyer]

Hi,

> We are, for the first time, using pymol to make figures that show
> electron density in addition to the model.  No problem making the
> figure, but when we go to ray-trace the image, pymol crashes.  This
> only seems to happen when electron density is present in the figure.
> We are using ccp4 style maps and have tried this on our Macs, PCs and
> Linux boxes, all of which have failed to ray trace the figure.

I've seen similar situations for both isomesh and isosurface objects that
seemed to be due to the complexity of the scene requiring more memory than
available for ray-tracing.  Isomesh doesn't require quite as much memory
as isosurface, but both are a big increase over just a model.

There are a two ways to get around this.  The easy one is to increase
memory (either physical memory or swap space; although using swap space
will dramatically increase ray-tracing time).  The other way is to
decrease the complixity of your scene, or otherwise reduce the amount of
memory pymol needs.  If it's a close up, use a map with an extent that
just barely covers the physical region you're trying to display.  Or
calculate the map using fewer gridpoints (which will give you a coarser
map, and may only be appropriate for overall views depending on the
resolution of the map).

One other trick is to make sure that you are not starting from a saved
session file (*.pse).  Loading a pse uses additional memory (there's more
details on this in the list archives), loading the same objects from a pml
script will allow for more memory available for ray-tracing.

Good luck,

Pete


Pete Meyer
Fu Lab
BMCB grad student
Cornell University

Re: [PyMOL] Ray-tracing inner surface backside

[Robert Immormino]

Paul,

I'm actually quite interested in an answer to this question as well. 
An example of what I have been able to do is this:

http://kinemage.biochem.duke.edu/~immormino/neca_new.png

I like using this type of rendering to look at a protein cavity from
inside the protein.  For me it has been helpful in presenting the VDWs
interaction of ligands in the pocket.

To render this picture:

set surface_color, slate
set ray_interior_color, grey
set transparency, .3
set transparency_mode, 0
ray

The one thing that kinda bothers me with this approach is that
transparency_mode=0 is called fast and ugly in the GUI.  But this is
the only way that i have found to get this effect. Other ( better )
suggestions would be appreciated.

-bob





On 4/4/06, Paul Wilhelm Elsinghorst  wrote:
>  Hi folks,
>
>
>  what I did for now is that I selected a subset of residues that sit around
> a cavity. Then I showed the surface of the original protein inside the
> selection to get only the inside surface of the cavity. Now it looks sort of
> like a hose with inside and outside just as I wanted.
>
>
>  Now I'd like to raytrace this and I find no texture on the outside surface,
> which is actually just the back of the inside. I put a picture on
> http://pwe.no-ip.org/other/Pymol.png to illustrate my
> problem. See how the inner surface has texture and its back doesn't!
>
>
>  How can I get this fixed? Any ideas?
>
>
>  Paul

Re: [PyMOL] Ray, png

[Matthew . Franklin]

pymol-users-ad...@lists.sourceforge.net wrote on 01/03/2006 05:32:38 PM:

> Hi,
> On the subject of larger image sizes, I had a question a while back;
> I'd like to know if it's been addressed or anyone has a quick(er)
workaround-
> Basically, is there in inverse to the viewport command?  i.e., if I
> manually resize the Pymol window to fit around the molecule I'm
> displaying, how can I get the relative dimensions of the new window?
> These dimensions are needed for the Ray command to keep proper
> perspective.  What I've done in the past is save a small image of
> what's displayed in the window, used a graphics program to determine
> the x & y dimensions, and then used these to generate a high-
> resolution ray traced image with the same x/y ratio.
> I figure I'm missing something.
>
> Regards,
>

Hi David -

I usually just write a temporary png image to get the viewport dimensions,
i.e.

PyMOL>png junk.png
 ScenePNG: wrote 640x480 pixel image to file "junk.png".

As long as you haven't just executed a raytracing, the png dimensions are
the viewport dimensions.

- Matt

--
Matthew Franklin phone:(917)606-4116
Senior Scientist, ImClone Systems  fax:(212)645-2054
180 Varick Street, 6th floor
New York, NY 10014


Confidentiality Note:  This e-mail, and any attachment to it, contains
privileged and confidential information intended only for the use of the
individual(s) or entity named on the e-mail.  If the reader of this e-mail
is not the intended recipient, or the employee or agent responsible for
delivering it to the intended recipient, you are hereby notified that
reading it is strictly prohibited.  If you have received this e-mail in
error, please immediately return it to the sender and delete it from your
system.  Thank you.

RE: [PyMOL] Ray, png

[Warren DeLano]

David,

In recent builds, you don't need to specify both dimensions for the ray
command -- just give it height or width and it will compute the other
based on the current aspect ratio.

Regardless, to get the current window, here is one way:

print cmd.get_session()['main']

Cheers,
Warren

--
Warren L. DeLano, Ph.D. 
Principal Scientist

. DeLano Scientific LLC  
. 400 Oyster Point Blvd., Suite 213   
. South San Francisco, CA 94080 USA   
. Biz:(650)-872-0942  Tech:(650)-872-0834 
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:war...@delsci.com  
 

> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net 
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
> David A. Horita
> Sent: Tuesday, January 03, 2006 2:39 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Ray, png
> 
> Hi,
> On the subject of larger image sizes, I had a question a 
> while back; I'd like to know if it's been addressed or anyone 
> has a quick(er) workaround- Basically, is there in inverse to 
> the viewport command?  i.e., if I manually resize the Pymol 
> window to fit around the molecule I'm displaying, how can I 
> get the relative dimensions of the new window?  These 
> dimensions are needed for the Ray command to keep proper 
> perspective.  What I've done in the past is save a small 
> image of what's displayed in the window, used a graphics 
> program to determine the x & y dimensions, and then used 
> these to generate a high-resolution ray traced image with the 
> same x/y ratio.
> I figure I'm missing something.
>  
> Regards,
>  
>  
> -
> David A. Horita, Ph.D.
> Department of Biochemistry
> Wake Forest University School of Medicine Winston-Salem, NC 27157-1016
> Tel: 336 713-4194
> Fax: 336 716-7671
> email:  dhor...@wfubmc.edu
> web:  http://www1.wfubmc.edu/biochem/faculty/Horita.htm 
>  
>  
> 

Re: [PyMOL] ray tracing problem

[Lari Lehtio]

Thank you Warren and Jacob,

I pressed stop and then ray tracing went fine. I don't know who pressed that 
play-button, but it wasn't me...

~Lari~ 

On Friday 02 September 2005 18:41, Lari Lehtio wrote:
> Hello,
>
> I'm in a process of making a whole bunch of figures for a paper and I have
> an irritating problem. Some of the figures just do _not_ get ray traced. It
> processes the image, but the image stays normal (=ugly).
>
> I'm running 0.98 on an amd64 box with gentoo and I've tried the binary
> distribution as well as compiled pymol from the source. If I start from
> scratch and make similar objects, it works fine again.
>
> Has anyone else seen this kind of behaviour?
>
> ~Lari~
>
> ___
> Lari Lehtiö
> University of Helsinki
> Institute of Biotechnology
> Macromolecular X-ray crystallography
> P.O.Box 65
> 00014 HY
> Finland
> http://www.biocenter.helsinki.fi/~lehtio/
> ___
>
>
> ---
> SF.Net email is Sponsored by the Better Software Conference & EXPO
> September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices
> Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA
> Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Re: [PyMOL] ray

[Christopher Colbert]

Hi Kostas,

This topic has been covered several times from a resolution stand point.
Joel has a nice hint, but be sure to set your viewport to the right aspect
ratio before using the ray command.

viewport 700, 700
(other pymol commands to make your figure the way you want)

ray 2400, 2400
png myfig.png

will give you the exact same view in your raytraced image.  Without it the
default aspect ratio from startup will be used and you will either add
extra white space to your image or you will crop your image.

Additionally, you can set the cartoon variables to improve the look of
your helices, loops, and beta strands as well.

Examples:

set cartoon_oval_width, 0.2000
set cartoon_oval_length, 1.200
set cartoon_oval_quality, 100.0
set cartoon_loop_quality, 60.0
set cartoon_rect_width, 0.2
set cartoon_rect_length, 1.2

You will find these under the Setting menu, then select edit all to find a
list of all the variables that can be modified.

Good Luck,

Chris


On Thu, 24 Feb 2005, Joel Tyndall wrote:

>Hi Kostas,
>
>I tghink generally 300 dpi is sufficient for publication but you can ray 
>trace to any sort of resolution and then down size your graphic. See 
>posts on High end graphics but this should help
>
>*To get 4in by 4in figure @600dpi
>
>ray 2400, 2400*
>
>*
>*
>
>*Then png picture.png
>
>Then resize in something like photoshop...increase resolution to that desired 
>and reduce image size so file size is similar to original
>
>Hope this helps
>
>J*
>
>
>
>Kostas Tripsianes wrote:
>
>> Dear PyMolers
>>
>> I am about to write a paper and I want your suggestions for the 
>> pictures I am going to make. First of all I will use white background
>> and the structure is a NMR one. So I need to display the backbone of 
>> the ensemble and the rest pictureswill be cartoons and sticks mainly.
>> I want to achieve nice quality pictures (resolution, depth etc.) 
>> that's why I am asking for your experience on this issue.
>> Any hints for the ray parameters it will be appreciated.
>> thanks in advance kostas
>>
>> PS: virtually no memory space limitations for any action it is to perform
>> -- 
>>
>> 
>>
>>Kostas Tripsianes, PhD student
>>Bijvoet Center for Biomolecular Research
>>NMR Spectroscopy, Utrecht University
>>Padualaan 8, 3584 CH Utrecht, The Netherlands
>>_kos...@nmr.chem.uu.nl_
>>phone: +31-30-2532875
>>fax: +31-30-2537623
>> :-) 
>>  
>>
>
>-- 
>Joel Tyndall, PhD
>
>Lecturer
>National School of Pharmacy
>University of Otago
>PO Box 913 Dunedin
>New Zealand 
>
>Pukenga
>Te Kura Taiwhanga Putaiao
>Te Whare Wananga o Otago
>Pouaka Poutapeta 913 Otepoti
>Aotearoa
>
>Ph / Waea   +64 3 4797293 
>Fax / Waeawhakaahua +64 3 4797034
>
>
>
>
>---
>SF email is sponsored by - The IT Product Guide
>Read honest & candid reviews on hundreds of IT Products from real users.
>Discover which products truly live up to the hype. Start reading now.
>http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
>___
>PyMOL-users mailing list
>PyMOL-users@lists.sourceforge.net
>https://lists.sourceforge.net/lists/listinfo/pymol-users
>

Christopher L. Colbert, Ph.D.
Research AssociatePhone: (214) 648 5002
University of Texas Southwestern Medical Center   FAX:   (214) 648 5095
5323 Harry Hines Boulevard
Dallas, TX 75390

Re: [PyMOL] ray

[Joel Tyndall]

Hi Kostas,

I tghink generally 300 dpi is sufficient for publication but you can ray 
trace to any sort of resolution and then down size your graphic. See 
posts on High end graphics but this should help


*To get 4in by 4in figure @600dpi

ray 2400, 2400*

*
*

*Then png picture.png

Then resize in something like photoshop...increase resolution to that desired 
and reduce image size so file size is similar to original

Hope this helps

J*



Kostas Tripsianes wrote:


Dear PyMolers

I am about to write a paper and I want your suggestions for the 
pictures I am going to make. First of all I will use white background
and the structure is a NMR one. So I need to display the backbone of 
the ensemble and the rest pictureswill be cartoons and sticks mainly.
I want to achieve nice quality pictures (resolution, depth etc.) 
that's why I am asking for your experience on this issue.

Any hints for the ray parameters it will be appreciated.
thanks in advance kostas

PS: virtually no memory space limitations for any action it is to perform
--



Kostas Tripsianes, PhD student
Bijvoet Center for Biomolecular Research
NMR Spectroscopy, Utrecht University
Padualaan 8, 3584 CH Utrecht, The Netherlands
_kos...@nmr.chem.uu.nl_
phone: +31-30-2532875
fax: +31-30-2537623
:-) 
 



--
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand 


Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

Ph / Waea   +64 3 4797293 
Fax / Waeawhakaahua +64 3 4797034

Re: [PyMOL] ray-trace stop button?

[Jules Jacobsen]

Mark,

You don't have to reboot, go to the process tab of windows task manager 
and end the python image underlying PyMOl.


Jules

Mark Wilke wrote:

Is there any way of stopping a ray trace once it has been started without
closing pymol?  Some of my ray trace jobs take too long and I want to stop
them.  I've also noticed that pymol doesn't close very elegently during a
ray trace job.  I'm working on a windows pc and the "end task" approach
sometimes doesn't seem to work at all, forcing me to reboot.  


-Mark



---
This SF.Net email sponsored by Black Hat Briefings & Training.
Attend Black Hat Briefings & Training, Las Vegas July 24-29 - 
digital self defense, top technical experts, no vendor pitches, 
unmatched networking opportunities. Visit www.blackhat.com

___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users

Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2

[Michael Banck]

On Thu, Feb 19, 2004 at 12:24:53PM +0100, Michael Banck wrote:
> On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund wrote:
> > For me PyMol on SuSE 8.2 crashed always when raytracing a line element. 
> 
> That seems to be identical to Debian Bug #229080
> (http://bugs.debian.org/229080)
> 
> > The stock  compiler on SuSE 8.2 is gcc 3.3 20030226 (prerelease). I
> > got the same crash with  gcc 3.3.1, but not with gcc 2.95. I have not
> > tried it on SUSE 9 yet, installing and using gcc 2.95 (for PyMol only)
> > solved the problem for me. See PyMol bugreport 806361.
> 
> Thanks for the information, I will see whether that helps on Debian,
> too.

For the record, the current gcc-3.3 in Debian testing/unstable seems to
work fine again for rendering sticks and lines, so I uploaded 0.95-1
using the standard gcc on all architectures again.


Michael

RE: [PyMOL] ray command

[Warren DeLano]

David,

There isn't currently a programmatic way of doing this, but it wouldn't be
too hard to make one.  I'll put onto the todo list support for commands
like: ray 1024; ray width=800; height=600; where the second axis is
calculated.

Note that we're currently missing an API function for getting the viewer
size (we'll need to add that), but you can rip it out of a session
dictionary constructed on-the-fly (which is grossly inefficient, but it
works):

print cmd.get_session()['main'][0:2]
[640,480]

Cheers,
Warren


> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net 
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
> David A. Horita
> Sent: Monday, April 05, 2004 11:30 AM
> To: pymol-users@lists.sourceforge.net
> Subject: RE: [PyMOL] ray command
> 
> Hi,
> Regarding the use of the ray command, is there a way to 
> automatically set either the x or y value to maintain the 
> same aspect ratio as displayed in the window?  For that 
> matter, how do you determine the number of x and y points 
> displayed (other than making a bitmap and loading that into 
> another program)?
> 
> -David Horita
> > 
> > 
> > Mohammed,
> > 
> > ray width, height
> >   png filename.png
> > 
> > for example, for a 5x4 figure at 300 dpi:
> > 
> > ray 1600,1200
> >   
> >   png hires.png
> >  (or use Save image... from the File menu after the ray command)
> > 
> > Cheers,
> > Warren
> >
> > 
> 
> 
> ---
> This SF.Net email is sponsored by: IBM Linux Tutorials Free 
> Linux tutorial presented by Daniel Robbins, President and CEO 
> of GenToo technologies. Learn everything from fundamentals to 
> system administration.http://ads.osdn.com/?ad_id70&alloc_id638&op=ick
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

RE: [PyMOL] ray command

[David A. Horita]

Hi,
Regarding the use of the ray command, is there a way to automatically set 
either the x or y value to maintain the same aspect ratio as displayed in the 
window?  For that matter, how do you determine the number of x and y points 
displayed (other than making a bitmap and loading that into another program)?

-David Horita
> 
> 
> Mohammed,
> 
>   ray width, height
>   png filename.png
> 
> for example, for a 5x4 figure at 300 dpi:
> 
>   ray 1600,1200
>   
>   png hires.png
>  (or use Save image... from the File menu after the ray command)
> 
> Cheers,
> Warren
>
> 

RE: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2

[Warren DeLano]

Morri has a good point:  

The standalone pymol-0_xx-bin-linux-libc6-i386.tgz binary builds
should be capable of running on virtually any current x86-based Linux
system: RH, SUSE, Debian, Fedora, or whatever.

So, if you're having trouble with compilation or use of
distribution-specific packages on Linux and simply want to use PyMOL as a
standalone tool, then downloading those binaries is an easy way to get
going.  Installation is trivial and you don't need root privileges.

1) tar zxvf pymol-(version)-bin-linux-libc6-i386.tgz
2) cd pymol
3) ./setup.sh
4) ./pymol.com 

Cheers,
Warren

FYI: those builds are built using GCC 2.96 under RedHat 6.2 for maximum
compatibility -- they're not the fastest PyMOL binaries in the world, but
they do run without a hassle.
 
> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net 
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
> Morri Feldman
> Sent: Thursday, February 19, 2004 3:18 PM
> To: Michael Banck
> Cc: pymol users
> Subject: Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2
> 
> Hi Michael,
> 
> I downloaded pymol-0_93-bin-linux-libc6-i386.tgz to my Debian machine.
> When I run this copy rather than the .deb version I am able 
> to ray trace lines without a crash.
> 
> Best,
> Morri
> 
>  On Thu, 19 Feb 2004, Michael Banck wrote:
> 
> > On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund wrote:
> > > For me PyMol on SuSE 8.2 crashed always when raytracing a 
> line element.
> >
> > That seems to be identical to Debian Bug #229080
> > (http://bugs.debian.org/229080)
> >
> > > The stock  compiler on SuSE 8.2 is gcc 3.3 20030226 
> (prerelease). I 
> > > got the same crash with  gcc 3.3.1, but not with gcc 2.95. I have 
> > > not tried it on SUSE 9 yet, installing and using gcc 2.95 
> (for PyMol 
> > > only) solved the problem for me. See PyMol bugreport 806361.
> >
> > Thanks for the information, I will see whether that helps 
> on Debian, 
> > too.
> >
> >
> > Michael
> >
> >
> > ---
> > SF.Net is sponsored by: Speed Start Your Linux Apps Now.
> > Build and deploy apps & Web services for Linux with a free DVD 
> > software kit from IBM. Click Now!
> > http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click
> > ___
> > PyMOL-users mailing list
> > PyMOL-users@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> 
> 
> ---
> SF.Net is sponsored by: Speed Start Your Linux Apps Now.
> Build and deploy apps & Web services for Linux with a free 
> DVD software kit from IBM. Click Now!
> http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2

[Morri Feldman]

Hi Michael,

I downloaded pymol-0_93-bin-linux-libc6-i386.tgz to my Debian machine.
When I run this copy rather than the .deb version I am able to ray trace
lines without a crash.

Best,
Morri

 On Thu, 19 Feb 2004, Michael Banck wrote:

> On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund wrote:
> > For me PyMol on SuSE 8.2 crashed always when raytracing a line element.
>
> That seems to be identical to Debian Bug #229080
> (http://bugs.debian.org/229080)
>
> > The stock  compiler on SuSE 8.2 is gcc 3.3 20030226 (prerelease). I
> > got the same crash with  gcc 3.3.1, but not with gcc 2.95. I have not
> > tried it on SUSE 9 yet, installing and using gcc 2.95 (for PyMol only)
> > solved the problem for me. See PyMol bugreport 806361.
>
> Thanks for the information, I will see whether that helps on Debian,
> too.
>
>
> Michael
>
>
> ---
> SF.Net is sponsored by: Speed Start Your Linux Apps Now.
> Build and deploy apps & Web services for Linux with
> a free DVD software kit from IBM. Click Now!
> http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2

[Robert Campbell]

Michael,

* Michael Banck  [2004-02-19 12:24] wrote:
> On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund wrote:
> > For me PyMol on SuSE 8.2 crashed always when raytracing a line element. 
> 
> That seems to be identical to Debian Bug #229080
> (http://bugs.debian.org/229080)
> 
> > The stock  compiler on SuSE 8.2 is gcc 3.3 20030226 (prerelease). I
> > got the same crash with  gcc 3.3.1, but not with gcc 2.95. I have not
> > tried it on SUSE 9 yet, installing and using gcc 2.95 (for PyMol only)
> > solved the problem for me. See PyMol bugreport 806361.
> 
> Thanks for the information, I will see whether that helps on Debian,
> too.

Just as another data point. I use the CVS version of PyMOL (currently
version 0.94) under Debian testing (using gcc-3.3.3 20040125). I haven't
seen any crashes.  (In case it makes a difference: Athlon XP+ 2500 and
Radeon 9500 Pro graphics).

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D. 
Senior Research Associatephone: 613-533-6821
Dept. of Biochemistry, Queen's University, fax: 613-533-2497
Kingston, ON K7L 3N6  Canada   http://adelie.biochem.queensu.ca/~rlc
PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2

[Michael Banck]

On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund wrote:
> For me PyMol on SuSE 8.2 crashed always when raytracing a line element. 

That seems to be identical to Debian Bug #229080
(http://bugs.debian.org/229080)

> The stock  compiler on SuSE 8.2 is gcc 3.3 20030226 (prerelease). I
> got the same crash with  gcc 3.3.1, but not with gcc 2.95. I have not
> tried it on SUSE 9 yet, installing and using gcc 2.95 (for PyMol only)
> solved the problem for me. See PyMol bugreport 806361.

Thanks for the information, I will see whether that helps on Debian,
too.


Michael

Re: [PyMOL] Ray Tracing Bug in Pymol 0.93 on SuSE Linux 8.2

[Thomas Siegmund]

Dear Buz,

> I've been using Pymol 0.93 on SuSE Linux 8.2 for a few hours now, and I'm
> having trouble ray tracing graphics.

> Each time I start the ray tracer Pymol quits with a segmentation fault
> error;


I guess you are running into a compiler bug (or a bug in PyMol which gets 
exposed only by some compiler versions).

For me PyMol on SuSE 8.2 crashed always when raytracing a line element. The 
stock  compiler on SuSE 8.2 is gcc 3.3 20030226 (prerelease). I got the same 
crash with  gcc 3.3.1, but not with gcc 2.95. I have not tried it on SUSE 9 
yet, installing and using gcc 2.95 (for PyMol only) solved the problem for 
me. See PyMol bugreport 806361.

Thomas

-- 
Thomas Siegmund, Ph.D.
DeveloGen AG
Bioinformatics and Data Management
Phone: +49(551) 505 58 651

E-Mails können unvollständig oder fehlerhaft oder manipuliert sein. Sie
dienen daher stets nur der Information. Rechtsverbindliche
Willenserklärungen müssen in Schriftform, d.h. mindestens per Telefax mit
Unterschrift des Erklärenden, abgegeben werden, um wirksam zu sein. Unsere
E-Mails sind stets vertraulich und nur für den angegebenen Adressaten
bestimmt. Andere Empfänger werden gebeten, diese Nachricht zu löschen. Jede
unberechtigte Weiterleitung ist untersagt. Trotz ergriffener
Vorsichtsmaßnahmen gegen Viren kann keine Haftung für etwaige Schäden aus
der Verwendung dieser E-Mail übernommen werden.

E-mails may be incomplete or be subject to change without notice. Therefore
the content of this E-mail is not binding unless confirmed by letter or by
telefax with signature of the author. Our E-mails are confidential and
dedicated to the intended recipient only. If you are not an intended
recipient, please delete the original message and all copies. Any
unauthorized distribution is strictly prohibited. Although precautions have
been taken to prevent the existence of viruses in this E-mail, the company
cannot accept any responsibility for any damage arising out of or from the
use of this E-mail.

Re: [PyMOL] Ray Tracing Crash

[Michael Banck]

Package: pymol
Version: 0.93-2

On Thu, Jan 22, 2004 at 08:53:37AM -0800, Morri Feldman wrote:
> On Thu, 22 Jan 2004 11:02:25 +0100 Michael Banck wrote:
> 
> > On Wed, Jan 21, 2004 at 09:11:01PM -0800, Morri Feldman wrote:
> > > Regarding my problems raytracing on my debian/testing machine.
> > 
> > What is the exact version of the pymol .deb you're using? 0.93-2?
> pymol_0.93-2_i386.deb
> 
> > What architecture are you running on? i386 or something else?
> i386, Pentium III
> 
> > Do you use pymol's internal raytracer, or povray? 
> I invoke the raytracer by typing "ray".  I assume this is the internal
> raytracer.
> 
> > Does the raytracing-demo from the demo-menu work?
> The ray tracing demo works.  But after running the raytracing-demo, pymol 
> will crash if I type either:
> hide spheres
> show sticks
> ray
> 
> or:
> hide spheres
> show lines
> ray

Indeed, I can reproduce this here. Thanks for the bug report. I'll try
to debug this during the weekend (won't have time tomorrow I guess),
please nag me if you don't here back next week.


thanks,

Michael

Re: [PyMOL] Ray Tracing Crash

[Morri Feldman]

On Thu, 22 Jan 2004 11:02:25 +0100 Michael Banck wrote:

> On Wed, Jan 21, 2004 at 09:11:01PM -0800, Morri Feldman wrote:
> > Regarding my problems raytracing on my debian/testing machine.
> 
> What is the exact version of the pymol .deb you're using? 0.93-2?
pymol_0.93-2_i386.deb

> What architecture are you running on? i386 or something else?
i386, Pentium III

> Do you use pymol's internal raytracer, or povray? 
I invoke the raytracer by typing "ray".  I assume this is the internal
raytracer.

> Does the raytracing-demo from the demo-menu work?
The ray tracing demo works.  But after running the raytracing-demo, pymol 
will crash if I type either:
hide spheres
show sticks
ray

or:
hide spheres
show lines
ray

Thanks,
Morri

>  
> 
> thanks,
> 
> Michael
> 
> 
> ---
> The SF.Net email is sponsored by EclipseCon 2004
> Premiere Conference on Open Tools Development and Integration
> See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
> http://www.eclipsecon.org/osdn
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 



Morri Feldman

Re: [PyMOL] Ray Tracing Crash

[Michael Banck]

On Wed, Jan 21, 2004 at 09:11:01PM -0800, Morri Feldman wrote:
> Regarding my problems raytracing on my debian/testing machine.

What is the exact version of the pymol .deb you're using? 0.93-2?
What architecture are you running on? i386 or something else?
Do you use pymol's internal raytracer, or povray? 
Does the raytracing-demo from the demo-menu work?
 

thanks,

Michael

Re: [PyMOL] Ray Tracing Crash

[Morri Feldman]

Regarding my problems raytracing on my debian/testing machine.

The system has 128mb of ram.

I have attached a pymol session file.  To generate the session file, I
loaded a very simple molecule into pymol.  After loading the session file 
and executing the ray command I get a segmentation fault.  The tail end
of pymols output to the shell is show below.  As you can see below, while 
pymol starts up I recieve an error complaining about 'PYMOL_PATH'.  I
don't know if this error is related to the problems I am having with ray
tracing.  Please let me know if you would like any more information.

-START OF PYMOL'S OUTPUT TO THE SHELL
 Hit ESC anytime to toggle between text and graphics.

Traceback (most recent call last):
  File "", line 1, in ?
  File "/usr/lib/python2.3/UserDict.py", line 19, in __getitem__
def __getitem__(self, key): return self.data[key]
KeyError: 'PYMOL_PATH'
 OpenGL based graphics front end:
  GL_VENDOR: VA Linux Systems, Inc.
  GL_RENDERER: Mesa GLX Indirect
  GL_VERSION: 1.2 Mesa 3.4.2
 Executive: Loading version 0.92 session...
PyMOL>ray
/usr/bin/pymol: line 7:   975 Segmentation fault  python
/usr/lib/python2.3/site-packages/pymol/__init__.py $*
-END OF PYMOL'S OUTPUT TO THE SHELL-

Best,

Morri

On Wed, 21 Jan 2004 17:24:48 +0100 Michael Banck wrote:

> On Tue, Jan 20, 2004 at 10:52:17PM -0800, Morri Feldman wrote:
> > My debian/testing system at home also has trouble ray
> > tracing, especially with sticks.  When it fails I get a
> > segmentation fault.  
> 
> What architecture are you running on? i386 or something else?
> 
> Do you use pymol's internal raytracer, or povray?
> 
> > Is my problem at home also due to an unpatched glibc?
> 
> glibc in debian/testing should be fairly recent. Perhaps it suffers from
> a different bug, but the one described earlier should be fixed by now,
> if it ever pertained to Debian.
> 
> > The error message is:
> > /usr/bin/pymol: line 7: 32460 Segmentation fault 
> > python
> > /usr/lib/python2.3/site-packages/pymol/__init__.py $*
> 
> As Warren said, a detailed description of the scene you were trying to
> raytrace would be welcomed.
> 
> 
> Michael
> 
> 
> ---
> The SF.Net email is sponsored by EclipseCon 2004
> Premiere Conference on Open Tools Development and Integration
> See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
> http://www.eclipsecon.org/osdn
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 



Morri Feldman





ray_session.pse
Description: Binary data

Re: [PyMOL] Ray Tracing Crash

[Morri Feldman]

Warren,

The RH9 Patch fixed the ray tracing problem.  Thanks for your help.

Tonight I will send you specific information about the Debian ray tracing 
problem.

Thanks,
Morri

On Wed, 21 Jan 2004 08:07:00 -0800 "Warren L. DeLano" wrote:

> Morri,
> 
> The RH9 Patch is described and published on: 
> 
> https://rhn.redhat.com/errata/RHBA-2003-136.html
> 
> I would not expect Debian to suffer from the same crash.  If it does,
> then we may be dealing with a genuine bug in PyMOL (assuming that you're
> not simply running out of RAM).
> 
> With respect to Debian, in order to debug the problem, you might want to
> send me a PyMOL session file which crashes on your system when the next
> command issued is "ray".  
> 
> Cheers,
> Warren
> 
> --
> mailto:war...@delanoscientific.com
> Warren L. DeLano, Ph.D.
> Principal Scientist
> DeLano Scientific LLC
> Voice (650)-346-1154 
> Fax   (650)-593-4020
> 
> > -Original Message-
> > From: Morri Feldman [mailto:morrifeld...@yahoo.com]
> > Sent: Tuesday, January 20, 2004 10:36 PM
> > To: Warren L. DeLano; 'Matt Franklin'; 'Morri Feldman'
> > Cc: 'pymol-users'
> > Subject: RE: [PyMOL] Ray Tracing Crash
> > 
> > Warren and Matt,
> > 
> > Thanks so much for your help.  I must be using the
> > stock glibc because "set max_threads, 1" allows me to
> > ray trace without crashing.  I will tell my system
> > administrator to patch glibc.  Do you know where I
> > should look for the patch?
> > 
> > My debian/testing system at home also has trouble ray
> > tracing especially sticks.  When it fails I get a
> > segmentation fault.  Is my problem at home also due to
> > an unpatched glibc?
> > 
> > The error message is:
> > /usr/bin/pymol: line 7: 32460 Segmentation fault
> > python
> > /usr/lib/python2.3/site-packages/pymol/__init__.py $*
> > 
> > Thanks for creating such a great program,
> > Morri
> > 
> > --- "Warren L. DeLano" 
> > wrote:
> > > Morri,
> > >
> > >   (First, thanks Matt for the great diagnostic
> > > advice!)
> > >
> > >   This sounds to me like a potential threading
> > > deadlock, possible
> > > due to the broken threading in RedHat 9.  Are you
> > > using the stock
> > > version or have you patched glibc?
> > >
> > >   If you haven't patched your RedHat 9, then one way
> > > to be sure
> > > this is the problem is to "set max_threads, 1"
> > > before issuing the ray
> > > command.  If PyMOL doesn't hang, then you've found
> > > the culprit.
> > >
> > >   If have already patched your RH9, then let's do
> > > some more work
> > > to determine what's going on...
> > >
> > > Cheers,
> > > Warren
> > >
> > > --
> > > mailto:war...@delanoscientific.com
> > > Warren L. DeLano, Ph.D.
> > > Principal Scientist
> > > DeLano Scientific LLC
> > > Voice (650)-346-1154
> > > Fax   (650)-593-4020
> > >
> > > > -Original Message-
> > > > From: pymol-users-ad...@lists.sourceforge.net
> > > [mailto:pymol-users-
> > > > ad...@lists.sourceforge.net] On Behalf Of Matt
> > > Franklin
> > > > Sent: Tuesday, January 20, 2004 6:25 PM
> > > > To: Morri Feldman
> > > > Cc: pymol-users
> > > > Subject: Re: [PyMOL] Ray Tracing Crash
> > > >
> > > > Morri Feldman wrote:
> > > > > I am running pymol .93.  When I try to ray trace
> > > a scene, the gui
> > > shows
> > > > a
> > > > > white status bar that moves halfway across the
> > > screen and then
> > > freezes.
> > > > > After this the GUI is frozen and must be killed.
> > >  No error messages
> > > are
> > > > > shown.  The computer is running RedHat 9 and has
> > > 4 processors.  Has
> > > > > anyone else experienced this problem?  Do you
> > > have any solutions?
> > > > >
> > > > > This message may double post because I
> > > accidentally tried to post it
> > > > from
> > > > > my other email account.  Sorry
> > > > >
> > > > > Thanks, Morri
> > > > >
> > > > > Morri Feldman
> > > > >
> >

Re: [PyMOL] Ray Tracing Crash

[Michael Banck]

On Tue, Jan 20, 2004 at 10:52:17PM -0800, Morri Feldman wrote:
> My debian/testing system at home also has trouble ray
> tracing, especially with sticks.  When it fails I get a
> segmentation fault.  

What architecture are you running on? i386 or something else?

Do you use pymol's internal raytracer, or povray?

> Is my problem at home also due to an unpatched glibc?

glibc in debian/testing should be fairly recent. Perhaps it suffers from
a different bug, but the one described earlier should be fixed by now,
if it ever pertained to Debian.

> The error message is:
> /usr/bin/pymol: line 7: 32460 Segmentation fault 
> python
> /usr/lib/python2.3/site-packages/pymol/__init__.py $*

As Warren said, a detailed description of the scene you were trying to
raytrace would be welcomed.


Michael

RE: [PyMOL] Ray Tracing Crash

[Warren L. DeLano]

Morri,

The RH9 Patch is described and published on: 

https://rhn.redhat.com/errata/RHBA-2003-136.html

I would not expect Debian to suffer from the same crash.  If it does,
then we may be dealing with a genuine bug in PyMOL (assuming that you're
not simply running out of RAM).

With respect to Debian, in order to debug the problem, you might want to
send me a PyMOL session file which crashes on your system when the next
command issued is "ray".  

Cheers,
Warren

--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -Original Message-
> From: Morri Feldman [mailto:morrifeld...@yahoo.com]
> Sent: Tuesday, January 20, 2004 10:36 PM
> To: Warren L. DeLano; 'Matt Franklin'; 'Morri Feldman'
> Cc: 'pymol-users'
> Subject: RE: [PyMOL] Ray Tracing Crash
> 
> Warren and Matt,
> 
> Thanks so much for your help.  I must be using the
> stock glibc because "set max_threads, 1" allows me to
> ray trace without crashing.  I will tell my system
> administrator to patch glibc.  Do you know where I
> should look for the patch?
> 
> My debian/testing system at home also has trouble ray
> tracing especially sticks.  When it fails I get a
> segmentation fault.  Is my problem at home also due to
> an unpatched glibc?
> 
> The error message is:
> /usr/bin/pymol: line 7: 32460 Segmentation fault
> python
> /usr/lib/python2.3/site-packages/pymol/__init__.py $*
> 
> Thanks for creating such a great program,
> Morri
> 
> --- "Warren L. DeLano" 
> wrote:
> > Morri,
> >
> > (First, thanks Matt for the great diagnostic
> > advice!)
> >
> > This sounds to me like a potential threading
> > deadlock, possible
> > due to the broken threading in RedHat 9.  Are you
> > using the stock
> > version or have you patched glibc?
> >
> > If you haven't patched your RedHat 9, then one way
> > to be sure
> > this is the problem is to "set max_threads, 1"
> > before issuing the ray
> > command.  If PyMOL doesn't hang, then you've found
> > the culprit.
> >
> > If have already patched your RH9, then let's do
> > some more work
> > to determine what's going on...
> >
> > Cheers,
> > Warren
> >
> > --
> > mailto:war...@delanoscientific.com
> > Warren L. DeLano, Ph.D.
> > Principal Scientist
> > DeLano Scientific LLC
> > Voice (650)-346-1154
> > Fax   (650)-593-4020
> >
> > > -Original Message-
> > > From: pymol-users-ad...@lists.sourceforge.net
> > [mailto:pymol-users-
> > > ad...@lists.sourceforge.net] On Behalf Of Matt
> > Franklin
> > > Sent: Tuesday, January 20, 2004 6:25 PM
> > > To: Morri Feldman
> > > Cc: pymol-users
> > > Subject: Re: [PyMOL] Ray Tracing Crash
> > >
> > > Morri Feldman wrote:
> > > > I am running pymol .93.  When I try to ray trace
> > a scene, the gui
> > shows
> > > a
> > > > white status bar that moves halfway across the
> > screen and then
> > freezes.
> > > > After this the GUI is frozen and must be killed.
> >  No error messages
> > are
> > > > shown.  The computer is running RedHat 9 and has
> > 4 processors.  Has
> > > > anyone else experienced this problem?  Do you
> > have any solutions?
> > > >
> > > > This message may double post because I
> > accidentally tried to post it
> > > from
> > > > my other email account.  Sorry
> > > >
> > > > Thanks, Morri
> > > >
> > > > Morri Feldman
> > > >
> > >
> > > Hi Morri -
> > >
> > > The progress bar for raytracing doesn't move
> > linearly - the first half
> > > of the bar is covered fairly quickly, then more
> > slowly, then very
> > > slowly, then the last fifth is usually covered in
> > one jump.  Are you
> > > sure you just aren't being impatient?  Try
> > raytracing a very simple
> > > scene, like a single amino acid in spheres mode,
> > to see if it hangs
> > > then.  Also try raytracing parts of your scene in
> > case some funny bit
> > of
> > > your molecule is causing this problem.  Finally,
> > try reducing the
> > > complexity of your surfaces and/or spheres: "set
> > surface_quality, -1"
> > (0
> > > is the default).
> > >
> > > Feel free

Re: [PyMOL] Ray Tracing Crash

[Morri Feldman]

Warren and Matt,

Thanks so much for your help.  I must be using the
stock glibc because "set max_threads, 1" allows me to
ray trace without crashing.  I will tell my system
administrator to patch glibc.  Do you know where I
should look for the patch?

My debian/testing system at home also has trouble ray
tracing, especially with sticks.  When it fails I get a
segmentation fault.  Is my problem at home also due to
an unpatched glibc?

The error message is:
/usr/bin/pymol: line 7: 32460 Segmentation fault 
python
/usr/lib/python2.3/site-packages/pymol/__init__.py $*

Thanks for creating such a great program,
Morri

On Tue, 20 Jan 2004 18:35:07 -0800 "Warren L. DeLano" wrote:

> Morri,
> 
>   (First, thanks Matt for the great diagnostic advice!)
> 
>   This sounds to me like a potential threading deadlock, possible
> due to the broken threading in RedHat 9.  Are you using the stock
> version or have you patched glibc?
> 
>   If you haven't patched your RedHat 9, then one way to be sure
> this is the problem is to "set max_threads, 1" before issuing the ray
> command.  If PyMOL doesn't hang, then you've found the culprit.
> 
>   If have already patched your RH9, then let's do some more work
> to determine what's going on... 
> 
> Cheers,
> Warren
> 
> --
> mailto:war...@delanoscientific.com
> Warren L. DeLano, Ph.D.
> Principal Scientist
> DeLano Scientific LLC
> Voice (650)-346-1154 
> Fax   (650)-593-4020
> 
> > -Original Message-
> > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
> > ad...@lists.sourceforge.net] On Behalf Of Matt Franklin
> > Sent: Tuesday, January 20, 2004 6:25 PM
> > To: Morri Feldman
> > Cc: pymol-users
> > Subject: Re: [PyMOL] Ray Tracing Crash
> > 
> > Morri Feldman wrote:
> > > I am running pymol .93.  When I try to ray trace a scene, the gui
> shows
> > a
> > > white status bar that moves halfway across the screen and then
> freezes.
> > > After this the GUI is frozen and must be killed.  No error messages
> are
> > > shown.  The computer is running RedHat 9 and has 4 processors.  Has
> > > anyone else experienced this problem?  Do you have any solutions?
> > >
> > > This message may double post because I accidentally tried to post it
> > from
> > > my other email account.  Sorry
> > >
> > > Thanks, Morri
> > >
> > > Morri Feldman
> > >
> > 
> > Hi Morri -
> > 
> > The progress bar for raytracing doesn't move linearly - the first half
> > of the bar is covered fairly quickly, then more slowly, then very
> > slowly, then the last fifth is usually covered in one jump.  Are you
> > sure you just aren't being impatient?  Try raytracing a very simple
> > scene, like a single amino acid in spheres mode, to see if it hangs
> > then.  Also try raytracing parts of your scene in case some funny bit
> of
> > your molecule is causing this problem.  Finally, try reducing the
> > complexity of your surfaces and/or spheres: "set surface_quality, -1"
> (0
> > is the default).
> > 
> > Feel free to contact me directly - I'm local!  (Although Warren will
> be
> > more helpful...)
> > 
> > - Matt
> > 
> > 
> > --
> > Matthew FranklinPhone:(650)225-4596
> > Postdoctoral Researcher   Fax:(650)225-3734
> > Genentech, Inc.
> > 1 DNA Way, South San Francisco, CA 94080
> > 
> > 
> > 
> > ---
> > The SF.Net email is sponsored by EclipseCon 2004
> > Premiere Conference on Open Tools Development and Integration
> > See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
> > http://www.eclipsecon.org/osdn
> > ___
> > PyMOL-users mailing list
> > PyMOL-users@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> 
> 
> 
> 
> ---
> The SF.Net email is sponsored by EclipseCon 2004
> Premiere Conference on Open Tools Development and Integration
> See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
> http://www.eclipsecon.org/osdn
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 



Morri Feldman

RE: [PyMOL] Ray Tracing Crash

[Warren L. DeLano]

Morri,

(First, thanks Matt for the great diagnostic advice!)

This sounds to me like a potential threading deadlock, possible
due to the broken threading in RedHat 9.  Are you using the stock
version or have you patched glibc?

If you haven't patched your RedHat 9, then one way to be sure
this is the problem is to "set max_threads, 1" before issuing the ray
command.  If PyMOL doesn't hang, then you've found the culprit.

If have already patched your RH9, then let's do some more work
to determine what's going on... 

Cheers,
Warren

--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
> ad...@lists.sourceforge.net] On Behalf Of Matt Franklin
> Sent: Tuesday, January 20, 2004 6:25 PM
> To: Morri Feldman
> Cc: pymol-users
> Subject: Re: [PyMOL] Ray Tracing Crash
> 
> Morri Feldman wrote:
> > I am running pymol .93.  When I try to ray trace a scene, the gui
shows
> a
> > white status bar that moves halfway across the screen and then
freezes.
> > After this the GUI is frozen and must be killed.  No error messages
are
> > shown.  The computer is running RedHat 9 and has 4 processors.  Has
> > anyone else experienced this problem?  Do you have any solutions?
> >
> > This message may double post because I accidentally tried to post it
> from
> > my other email account.  Sorry
> >
> > Thanks, Morri
> >
> > Morri Feldman
> >
> 
> Hi Morri -
> 
> The progress bar for raytracing doesn't move linearly - the first half
> of the bar is covered fairly quickly, then more slowly, then very
> slowly, then the last fifth is usually covered in one jump.  Are you
> sure you just aren't being impatient?  Try raytracing a very simple
> scene, like a single amino acid in spheres mode, to see if it hangs
> then.  Also try raytracing parts of your scene in case some funny bit
of
> your molecule is causing this problem.  Finally, try reducing the
> complexity of your surfaces and/or spheres: "set surface_quality, -1"
(0
> is the default).
> 
> Feel free to contact me directly - I'm local!  (Although Warren will
be
> more helpful...)
> 
> - Matt
> 
> 
> --
> Matthew FranklinPhone:(650)225-4596
> Postdoctoral Researcher   Fax:(650)225-3734
> Genentech, Inc.
> 1 DNA Way, South San Francisco, CA 94080
> 
> 
> 
> ---
> The SF.Net email is sponsored by EclipseCon 2004
> Premiere Conference on Open Tools Development and Integration
> See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
> http://www.eclipsecon.org/osdn
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Re: [PyMOL] Ray Tracing Crash

[Matt Franklin]

Morri Feldman wrote:
I am running pymol .93.  When I try to ray trace a scene, the gui shows a 
white status bar that moves halfway across the screen and then freezes.

After this the GUI is frozen and must be killed.  No error messages are
shown.  The computer is running RedHat 9 and has 4 processors.  Has
anyone else experienced this problem?  Do you have any solutions?

This message may double post because I accidentally tried to post it from 
my other email account.  Sorry


Thanks, Morri

Morri Feldman



Hi Morri -

The progress bar for raytracing doesn't move linearly - the first half 
of the bar is covered fairly quickly, then more slowly, then very 
slowly, then the last fifth is usually covered in one jump.  Are you 
sure you just aren't being impatient?  Try raytracing a very simple 
scene, like a single amino acid in spheres mode, to see if it hangs 
then.  Also try raytracing parts of your scene in case some funny bit of 
your molecule is causing this problem.  Finally, try reducing the 
complexity of your surfaces and/or spheres: "set surface_quality, -1" (0 
is the default).


Feel free to contact me directly - I'm local!  (Although Warren will be 
more helpful...)


- Matt


--
Matthew FranklinPhone:(650)225-4596
Postdoctoral Researcher   Fax:(650)225-3734
Genentech, Inc.
1 DNA Way, South San Francisco, CA 94080

RE: [PyMOL] Ray tracing dashed lines

[Warren L. DeLano]

Einat,

with version 0.92:

set dash_gap,0
set dash_length,1

seems to do the trick for me, raytraced or not.

Cheers,
Warren


--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net 
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
> Einat Sitbon
> Sent: Thursday, October 30, 2003 4:29 AM
> To: PyMOL-users@lists.sourceforge.net
> Subject: [PyMOL] Ray tracing dashed lines
> 
> 
> 
> Hello Pymolers,
> 
> I'm using pymol 0.92. I changes some of the dash parameters - 
> I want the 
> distance lines to look continuous. This works fine, until I 
> ray trace the 
> protein. Then the dash returns to it's default settings...
> Any suggestions?
> thanks, Einat.
> 
> Einat Sitbon
> Department of Molecular Genetics
> Weizmann Institute of Science
> 
> _
> The new MSN 8: smart spam protection and 2 months FREE*  
> http://join.msn.com/?page=features/junkmail
> 
> 
> 
> ---
> This SF.net email is sponsored by: SF.net Giveback Program. 
> Does SourceForge.net help you be more productive?  Does it
> help you create better code?   SHARE THE LOVE, and help us help
> YOU!  Click Here: http://sourceforge.net/donate/ 
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net 
> https://lists.sourceforge.net/lists/listinfo/p> ymol-users
> 

Re: [PyMOL] Ray trace is freezing...

[JP Cartailler]

the command 'ray' initiates the raytracing which is not GPU-dependent, 
i.e. your gfx drivers won't increase your raytrace time, only upgrading 
your main CPU will.

But it shouldn't freeze.  Does it crash?  Have you tried ray'ing a simple 
scene, i.e. just a few residue, stick representation, nothing special?

my 2 cents' worth :)

jp

On Mon, 18 Aug 2003, naalas wrote:

> Dear everybody,
> 
> I'm using the last version of PyMOL, which is very fast (!), but I 
> encountered a problem with ray. I found a driver for my video card which 
> makes programs like O a lot faster, and it also makes PyMOL faster in 
> all the *preparation* process. But as soon as I want to ray my picture, 
> then it freezes. I do not know if the problem is coming from my video 
> card or from PyMOL (e.g. my configuration), so if you have any 
> suggestion, I'd be thankful...
> 
> I am using Red Hat 9;
> video card= Ge Force 2.MX;
> commercial driver from NVIDIA version 1.0.4496.
> 
> Thank you in advance.
> 
> Leo
> -
> cha...@post.kek.jp
> naa...@docomo.ne.jp
> hnaa...@hotmail.com
> -
> 
> 
> 
> ---
> This SF.Net email sponsored by: Free pre-built ASP.NET sites including
> Data Reports, E-commerce, Portals, and Forums are available now.
> Download today and enter to win an XBOX or Visual Studio .NET.
> http://aspnet.click-url.com/go/psa0013ave/direct;at.aspnet_072303_01/01
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

-- 
JP Cartailler

3205 McGaugh Hall
Dept. of Molecular Biology & Biochemistry
Irvine Research Unit in Macromolecular Structure
UC Irvine
Irvine, CA 92697-3900
USA

(949) 824 4322 (T)
j...@bragg.bio.uci.edu (email)
www.cartailler.com (www)

RE: [PyMOL] ray trace stereo

[Warren L. DeLano]

Milton,

To generate stereo images, you need to separately ray-trace both
the left and right-hand images using the angle option:

ray angle=-3
png image1.png
ray angle=3
png image2.png

You can then assemble the images manually to accommodate the exact
requirement for publication.

If you need higher-quality images with a higher resolution, then provide
an explicit width and height to ray:

set antialias,1
ray 2000,1500,angle=-3
png image1.png
ray 2000,1500,angle=3
png image2.png

Cheers,
Warren


--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
> ad...@lists.sourceforge.net] On Behalf Of Milton H. Werner, Ph.D.
> Sent: Friday, August 01, 2003 5:51 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] ray trace stereo
> 
> When I ray trace with the internal renderer (default renderer), my
> rendered image is not kept in stereo, but instead snaps back to mono.
> How do I get stereo ray traced images.
> 
> Also, is there a way to increase the number of passes for the
> anti-alias smoothing function--it seems a little low for ribbons
> drawings compared to, say, Mike Carson's Ribbons program.
> 
> Milton
> --
> Associate Professor and Head, Laboratory of Molecular Biophysics
> The Rockefeller University
> 1230 York Avenue, Box 42
> New York, NY  10021
> 
> 212/327-7221
> 212/327-7222 FAX
> mwer...@portugal.rockefeller.edu
> http://www.rockefeller.edu/labheads/werner/werner-lab.html
> 
> 
> ---
> This SF.Net email sponsored by: Free pre-built ASP.NET sites including
> Data Reports, E-commerce, Portals, and Forums are available now.
> Download today and enter to win an XBOX or Visual Studio .NET.
> http://aspnet.click-
> url.com/go/psa0013ave/direct;at.aspnet_072303_01/01
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Re: [PyMOL] ray tracing of stereo figures

[Jason Thomas Maynes]

Hello:

Stereo ray-tracing is not supported yet.  Ray trace one image and then
rotate around y by 5 degrees and re-trace.

Cheers,
JTM

"We can be sure that if a detailed understanding of the molecular basis of
chemo-therapeutic activity were to be obtained, the advance of medicine
would be greatly accelerated."
  
Linus Pauling, Nobel Laureate 1954
 
"...everything that living things do can be understood in terms of the
jigglings and wigglings of atoms."
  
Richard Feynman
  
*
Jason Thomas Maynes
PhD/MD Program
Department of Biochemistry
Faculty of Medicine
University of Alberta
ja...@biochem.ualberta.ca
*



On Fri, 20 Dec 2002, cheom-gil cheong wrote:

> Dear All  :
> 
> I tried to ray trace the cross-eyed stereo figure.
> On the screen, I saw the nice stereo figure.
> However, when I opened the .png file using Adobe Illustrator after ray 
> tracing and saving the file in PyMol, I don't see the stereo figure but only 
> one image.
> Did I do something wrong?
> Did anybody successfully ray trace and make a stereo figures for the 
> publications?
> 
> Thank you very much in advance.
> 
> Sincerely Yours,
> 
> 
> 
> 
> Cheom-Gil Cheong, Ph.D.
> 
> 
> 
> _
> MSN 8 limited-time offer: Join now and get 3 months FREE*. 
> http://join.msn.com/?page=dept/dialup&xAPID=42&PS=47575&PI=7324&DI=7474&SU= 
> http://www.hotmail.msn.com/cgi-bin/getmsg&HL=1216hotmailtaglines_newmsn8ishere_3mf
> 
> 
> 
> ---
> This SF.NET email is sponsored by:  The Best Geek Holiday Gifts!
> Time is running out!  Thinkgeek.com has the coolest gifts for
> your favorite geek.   Let your fingers do the typing.   Visit Now.
> T H I N K G E E K . C O Mhttp://www.thinkgeek.com/sf/
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

"We can be sure that if a detailed understanding of the molecular basis of
chemo-therapeutic activity were to be obtained, the advance of medicine
would be greatly accelerated."

Linus Pauling, Nobel Laureate 1954

"...everything that living things do can be understood in terms of the
jigglings and wigglings of atoms."

Richard Feynman

*
Jason Thomas Maynes
PhD/MD Program
Department of Biochemistry
Faculty of Medicine
University of Alberta
ja...@biochem.ualberta.ca
*

RE: [PyMOL] ray tracing and cross-eyed stereo

[Schubert, Carsten]

Dottore Ambroggio: 

For sereo figures people usually  use a rotation angle of ~6 deg with
coinciding elements of the images spaced ca 60-65 mm apart (assuming normal
human physiology) You can either take one image then rotate the scene with
turn y,6 and take the other shot or sometimes it makes more sense to start
from the "center" and take images +- 3 degrees apart. I use the later
technique for electron density shots, gives  less artifacts.

Happy PyMol'ing

Carsten

> -Original Message-
> From: Xavier I. Ambroggio [mailto:ambro...@its.caltech.edu]
> Sent: Thursday, November 21, 2002 18:04
> To: PyMOL-users@lists.sourceforge.net
> Subject: [PyMOL] ray tracing and cross-eyed stereo
> 
> 
> Pymolers,
> 
> I am trying to make an image (png file) in cross-eyed stereo, 
> but it seems
> that I cannot make the stereo image and ray trace. Does 
> anyone know either
> how to do this or how to manually make the image by making 
> two images with
> the proper angles/distance/etc.?
> 
> Thanks,
> Xavier
> 
> 
> http://www.its.caltech.edu/~ambrosia
> 
> 
> 
> ---
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

RE: [PyMOL] Ray-tracing without display

[DeLano, Warren]

You can't raytrace it the background using threads, but if you have everything 
in a script, you can launch a separate process to do the work:

"pymol -c script.pml" 

or

"pymol -c script.py"

will run PyMOL without a Window.  You do need to like against the X11 and 
OpenGL libs though...

Cheers,
Warren


--
mailto:war...@sunesis.com
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606  FAX:(650)-266-3501



> -Original Message-
> From: Serge Cohen [mailto:co...@embl-grenoble.fr]
> Sent: Monday, September 23, 2002 11:32 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Ray-tracing without display
> 
> 
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
> 
> Hi there,
> 
> I'm just starting using PyMol, currently making some couple 
> of movies...
> I'm set to test the movies on my laptop, but I'd like to do the 
> ray-tracing rendering on a computing server, and if possible 
> to run that 
> on the background without having a X11 session... Is that possible in 
> anyway?
> 
> 
> Thanks for this very nice software.
> 
> Serge.
> 
> 
> - 
> Serge Cohen
> 
> GPG Key ID: 1024D/69B1D346
> - 
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.0.7 (Darwin)
> 
> iD8DBQE9j14OMygj1Wmx00YRAqU2AJ40IrivKH/R1SLwkBf1vAPxfZYbpwCghiQa
> YcTC3ucvZ6mWlApvww/T9VE=
> =mY7I
> -END PGP SIGNATURE-
> 
> 
> 
> ---
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

RE: [PyMOL] "ray" doubts

[DeLano, Warren]

Ricardo,

  Yes, ray makes a huge difference in quality.  You get true specular
reflections (not just OpenGL interpolations), you get perfectly round
spheres, you get shadows, you get clean transparent surfaces (without
artifacts), and you get better depth-cue fogging (although with light
backgrounds you'll probably want to set ray_trace_fog to 0).

  It renders all objects in the scene except for labels (which it is
incapable of handling at present).

  Yes, you need to render (ray-trace) again after the image is rotated.
(If you rotate an object, the shadows move).  

  Most of the figures you see in the top journals are generated using
Molscript and Raster3D (or PovScript and PovRay) using a process very
similar to the "ray" command.  PyMOL simply makes creation of such
figures much easier since you only need one program and you get to
preview the exact image before-hand (set orthoscopic=0 to get a
pixel-for-pixel match between OpenGL and the ray tracer).

  
Cheers,
Warren


--
mailto:war...@sunesis.com
Warren L. DeLano, Ph.D.

> From: Ricardo Aparicio [mailto:apari...@if.sc.usp.br]
> 
> Dear PyMol users,
> 
> as stated in the manual, command
> 
>  "ray" creates a ray traced image of the current frame. This
>can take some time (up to several minutes, depending on image
>complexity).
> 
> My question is:
> 
> - is it necessary? Does it make great difference in the final 
> quality of
> figures published (in the case of a paper)?
> 
> - does it renderize(?) all the active objects in the screen?
> 
> - after finished ray process, if the image is rotated, is it necessary
> to renderize again (I think no, just to confirm)
> 
> 
> Many thanks,
> 
> 
> Ricardo Aparicio
> PhD Student - USP 
> Sao Paulo - Brazil
> 
> ___
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>