pymol-users Mailing List for PyMOL Molecular Graphics System

Gergori,

> 1) what is the difference between LINES, LINE_LOOP,=20
> LINE_STRIP. If I understood correctly, LINES is to build single lines,
>=20
> LINE_LOOP will connect the first and the last point (VERTEX),=20
> but no clue about LINE_STRIP.
>=20
> 2) what is the difference between TRIANGLES, TRIANGLES_STRIP=20
> and TRIANGLE_FAN

Consult OpenGL docs (GL_LINES, GL_LINE_LOOP, etc.) -- CGOs are =
essentially
just OpenGL rendering streams.
=20
> 3) is it possible to render a plain polygon (I suppose I can=20
> build a succession of triangles, but is there another way to do it?)

Not with CGOs.  The ray tracer only has triangle, cylinder, and spheres
primitives, which is why CGOs are limited to just triangles, spheres, =
and
cylinders.

> 1) in the Pymol manual, I read that LINEWIDTH was for=85=20
> line-width, and WIDTHSCALE was for ray-tracing;
> but what I observed is that LINEWIDTH do not change the line=20
> thickness (always 1 pixel) in the normal view but in=20
> ray-traced images, and when I use WIDTHSCALE Pymol simply=20
> crashes during ray-tracing=85 Is this a bug? I use the latest=20
> version of Pymol with WinXP Pro SP2 and my graphic card is an=20
> ATI Radeon 9700 with the latest drivers.

Not sture, but I think WIDTHSCALE is basically broken and should be
deprecated.  LINEWIDTH should work, but if it doesn=92t, then I suggest =
using
the  cgo_line_width setting to control line widths for now.

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Gr=E9gori Gerebtzoff
> Sent: Monday, May 30, 2005 6:08 AM
> To: pym...@li...
> Subject: [PyMOL] Questions & comments about CGO objects
>=20
> Hi list !
>=20
> I was just building (successfully) my first CGO object, and I=20
> have three questions and two comment:
>=20
> =20
>=20
> Questions:
>=20
> 1) what is the difference between LINES, LINE_LOOP,=20
> LINE_STRIP. If I understood correctly, LINES is to build single lines,
>=20
> LINE_LOOP will connect the first and the last point (VERTEX),=20
> but no clue about LINE_STRIP.
>=20
> 2) what is the difference between TRIANGLES, TRIANGLES_STRIP=20
> and TRIANGLE_FAN
>=20
> 3) is it possible to render a plain polygon (I suppose I can=20
> build a succession of triangles, but is there another way to do it?)
>=20
> =20
>=20
> Comments:
>=20
> 1) in the Pymol manual, I read that LINEWIDTH was for=85=20
> line-width, and WIDTHSCALE was for ray-tracing;
>=20
> but what I observed is that LINEWIDTH do not change the line=20
> thickness (always 1 pixel) in the normal view but in=20
> ray-traced images, and when I use WIDTHSCALE Pymol simply=20
> crashes during ray-tracing=85 Is this a bug? I use the latest=20
> version of Pymol with WinXP Pro SP2 and my graphic card is an=20
> ATI Radeon 9700 with the latest drivers.
>=20
> 2) when you use the COLOR command in a CGO object, this color=20
> cannot be overridden with the color menu in Pymol, so simply
>=20
> don=92t use the COLOR command if you want to be able to change=20
> the color of your object within Pymol!
>=20
> =20
>=20
> Many thanks for your answer(s)!
>=20
> =20
>=20
> =20
>=20
> Gr=E9gori Gerebtzoff
>=20
> =20
>=20
> Division of Biophysical Chemistry
>=20
> Biozentrum, University of Basel
>=20
> Klingelbergstrasse 70
>=20
> CH-4056 Basel / Switzerland
>=20
> =20
>=20
> Tel: +41 61 267 21 92
>=20
> Fax: +41 61 267 21 89
>=20
> e-mail: gre...@un...
>=20
>=20

Simply type

show surface
set transparency=0.5, my_object


This syntax is true for most Pymol commands...

Greg

Hi list !

I was just building (successfully) my first CGO object, and I have three
questions and two comment:

=20

Questions:

1) what is the difference between LINES, LINE_LOOP, LINE_STRIP. If I
understood correctly, LINES is to build single lines,

LINE_LOOP will connect the first and the last point (VERTEX), but no =
clue
about LINE_STRIP.

2) what is the difference between TRIANGLES, TRIANGLES_STRIP and
TRIANGLE_FAN

3) is it possible to render a plain polygon (I suppose I can build a
succession of triangles, but is there another way to do it?)

=20

Comments:

1) in the Pymol manual, I read that LINEWIDTH was for=85 line-width, and
WIDTHSCALE was for ray-tracing;

but what I observed is that LINEWIDTH do not change the line thickness
(always 1 pixel) in the normal view but in ray-traced images,
and when I use WIDTHSCALE Pymol simply crashes during ray-tracing=85 Is =
this a
bug? I use the latest version of Pymol with=20
WinXP Pro SP2 and my graphic card is an ATI Radeon 9700 with the latest
drivers.

2) when you use the COLOR command in a CGO object, this color cannot be
overridden with the color menu in Pymol, so simply

don=92t use the COLOR command if you want to be able to change the color =
of
your object within Pymol!

=20

Many thanks for your answer(s)!

=20

=20

Gr=E9gori Gerebtzoff

=20

Division of Biophysical Chemistry

Biozentrum, University of Basel

Klingelbergstrasse 70

CH-4056 Basel / Switzerland

=20

Tel: +41 61 267 21 92

Fax: +41 61 267 21 89

e-mail: gre...@un...

Hi, all,

I have several objects using surface presentation.  Is there a way to 
make the surface of one object to be transparent and the the surfaces 
of other objects still solid?

Thanks.

Jianghai

set scene_animation_duration, 5.0

Time in seconds.

--
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:wa...@de...      
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> hari jayaram
> Sent: Friday, May 27, 2005 11:55 AM
> To: pym...@li...
> Subject: Re: [PyMOL] v0.98 slow (includes: ray abort info...)
> 
> Hi , I really like the slow transitions between scenes in 
> Pymol 0.98. It is a great benefit to structure presentation.
> 
> I had just one question is there a way to slow down the 
> transitions by a custom amount. 
> 
> Any help/suggestions will be greatly appreciated Hari Jayaram 
> Brandeis University
> 
> 
> On 5/27/05, Warren DeLano <wa...@de...> wrote:
> 
> 	Mark,
> 	
> 	0.98 should rarely be more4X slower to ray-trace than 
> 0.97 unless you are
> 	running out of RAM.
> 	
> 	To get the faster but orthoscopic 0.97 raytracing behavior, "set
> 	orthoscopic" before raytracing. 
> 	
> 	> Oh yeah, please make a clean way of aborting from a
> 	> ray-trace...please.
> 	
> 	Actually, it exists...but it is not 100% general:
> 	
> 	To be able abort from ray tracing, it is necessary to 
> run it asychronously 
> 	(ray async=1).  This is the default if you press the 
> "ray" button in the
> 	Tcl/Tk GUI.
> 	
> 	Provide that a ray trace is running asychronously, then 
> you can in abort it
> 	in 0.98 by clicking on the OpenGL window to get focus 
> and then hitting the 
> 	backspace or delete keys.
> 	
> 	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:wa...@de...
> 	
> 	
> 	> -----Original Message-----
> 	> From: pym...@li... 
> <mailto:pym...@li...> 
> 	> [mailto:pym...@li...] On Behalf Of
> 	> Mark Wilke
> 	> Sent: Friday, May 27, 2005 11:08 AM 
> 	> To: pym...@li...
> 	> Subject: [PyMOL] v0.98 slow
> 	>
> 	> I last used pymol about a year ago (not sure which version),
> 	> but typical ray-tracing jobs of simple cartoon-ribbons etc 
> 	> took mere seconds to a few minutes at most.  I just upgraded
> 	> to the new v0.98 and made some similar figures, but the
> 	> ray-tracing is taking 30 min to 1 hr or more.  This is pretty
> 	> much unusable if you need to ray-trace several times to get 
> 	> the figure to look how you want.  Am I the only one
> 	> experiencing slow ray-tracing with pymol?  I'm using the
> 	> windows build provided on the pymol website.  I tried 
> 2 PC computers:
> 	>
> 	> (1) 1.4 GHz athlon
> 	>     512 MB ram
> 	>     Geforce2 GTS (64MB) Graphics Card
> 	>     WinXP
> 	>
> 	> (2) Dell Inspiron XPS Gen 2 Desktop Replacement
> 	>     2 GHz cpu (pentium m 760)
> 	>     Geforce go 6800 ultra 
> 	>     1 GB ram
> 	>     WinXP media centre edition
> 	>
> 	> The Dell is more than powerful enough to render rapidly...but
> 	> both computers behaved similarly.  Anyone have any ideas?
> 	>
> 	> - Mark 
> 	>
> 	> Oh yeah, please make a clean way of aborting from a
> 	> ray-trace...please.
> 	>
> 	>
> 	>
> 	>
> 	>
> 	> -------------------------------------------------------
> 	> This SF.Net <http://SF.Net>  email is sponsored by Yahoo.
> 	> Introducing Yahoo! Search Developer Network - Create 
> apps using Yahoo!
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> 	> _______________________________________________
> 	> PyMOL-users mailing list
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> 	> https://lists.sourceforge.net/lists/listinfo/pymol-users 
> 	>
> 	
> 	
> 	
> 	
> 	-------------------------------------------------------
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> https://lists.sourceforge.net/lists/listinfo/pymol-users 
> <" rel="nofollow">https://lists.sourceforge.net/lists/listinfo/pymol-users> 
> 	
> 
> 
> 

> Is there a way to make the perspective effect more dramatic 
> than the default way?  I mean to make the far end smaller and 

set field_of_view to something large.

The default is 20 degrees.  50 to 70 degrees will give you a very strong
perspective effect.

(FYI: the field of view is in Y, not X as I would have otherwise
expected...its an "OpenGL thing")

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:wa...@de...      
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Jianghai Zhu
> Sent: Friday, May 27, 2005 6:11 PM
> To: 'pymol-users'
> Subject: [PyMOL] perspective rendering
> 
> Hi, all,
> 
> I am trying to render my picture in a perspective view in 
> pymol 0.98.  
> Is there a way to make the perspective effect more dramatic 
> than the default way?  I mean to make the far end smaller and 
> the close end bigger.
> 
> Thanks.
> 
> Jianghai
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by Yahoo.
> Introducing Yahoo! Search Developer Network - Create apps using Yahoo!
> Search APIs Find out how you can build Yahoo! directly into 
> your own Applications - visit 
> http://developer.yahoo.net/?fr=offad-ysdn-ostg-q22005
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

Hi, all,

I am trying to render my picture in a perspective view in pymol 0.98.  
Is there a way to make the perspective effect more dramatic than the 
default way?  I mean to make the far end smaller and the close end 
bigger.

Thanks.

Jianghai

Hi , I really like the slow transitions between scenes in Pymol 0.98. It is=
=20
a great benefit to structure presentation.

I had just one question is there a way to slow down the transitions by a=20
custom amount.=20

Any help/suggestions will be greatly appreciated
Hari Jayaram
Brandeis University

On 5/27/05, Warren DeLano <wa...@de...> wrote:
>=20
> Mark,
>=20
> 0.98 should rarely be more4X slower to ray-trace than 0.97 unless you are
> running out of RAM.
>=20
> To get the faster but orthoscopic 0.97 raytracing behavior, "set
> orthoscopic" before raytracing.
>=20
> > Oh yeah, please make a clean way of aborting from a
> > ray-trace...please.
>=20
> Actually, it exists...but it is not 100% general:
>=20
> To be able abort from ray tracing, it is necessary to run it asychronousl=
y
> (ray async=3D1). This is the default if you press the "ray" button in the
> Tcl/Tk GUI.
>=20
> Provide that a ray trace is running asychronously, then you can in abort=
=20
> it
> in 0.98 by clicking on the OpenGL window to get focus and then hitting th=
e
> backspace or delete keys.
>=20
> Cheers,
> Warren
>=20
>=20
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist
>=20
> . 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:wa...@de...
>=20
>=20
> > -----Original Message-----
> > From: pym...@li...
> > [mailto:pym...@li...] On Behalf Of
> > Mark Wilke
> > Sent: Friday, May 27, 2005 11:08 AM
> > To: pym...@li...
> > Subject: [PyMOL] v0.98 slow
> >
> > I last used pymol about a year ago (not sure which version),
> > but typical ray-tracing jobs of simple cartoon-ribbons etc
> > took mere seconds to a few minutes at most. I just upgraded
> > to the new v0.98 and made some similar figures, but the
> > ray-tracing is taking 30 min to 1 hr or more. This is pretty
> > much unusable if you need to ray-trace several times to get
> > the figure to look how you want. Am I the only one
> > experiencing slow ray-tracing with pymol? I'm using the
> > windows build provided on the pymol website. I tried 2 PC computers:
> >
> > (1) 1.4 GHz athlon
> > 512 MB ram
> > Geforce2 GTS (64MB) Graphics Card
> > WinXP
> >
> > (2) Dell Inspiron XPS Gen 2 Desktop Replacement
> > 2 GHz cpu (pentium m 760)
> > Geforce go 6800 ultra
> > 1 GB ram
> > WinXP media centre edition
> >
> > The Dell is more than powerful enough to render rapidly...but
> > both computers behaved similarly. Anyone have any ideas?
> >
> > - Mark
> >
> > Oh yeah, please make a clean way of aborting from a
> > ray-trace...please.
> >
> >
> >
> >
> >
> > -------------------------------------------------------
> > This SF.Net <http://SF.Net> email is sponsored by Yahoo.
> > Introducing Yahoo! Search Developer Network - Create apps using Yahoo!
> > Search APIs Find out how you can build Yahoo! directly into
> > your own Applications - visit
> > http://developer.yahoo.net/?fr=3Doffad-ysdn-ostg-q22005
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.Net <http://SF.Net> email is sponsored by Yahoo.
> Introducing Yahoo! Search Developer Network - Create apps using Yahoo!
> Search APIs Find out how you can build Yahoo! directly into your own
> Applications - visit http://developer.yahoo.net/?fr=3Doffad-ysdn-ostg-q22=
005
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

Mark,

0.98 should rarely be more4X slower to ray-trace than 0.97 unless you are
running out of RAM.

To get the faster but orthoscopic 0.97 raytracing behavior, "set
orthoscopic" before raytracing.

> Oh yeah, please make a clean way of aborting from a 
> ray-trace...please.

Actually, it exists...but it is not 100% general:

To be able abort from ray tracing, it is necessary to run it asychronously
(ray async=1).  This is the default if you press the "ray" button in the
Tcl/Tk GUI.  

Provide that a ray trace is running asychronously, then you can in abort it
in 0.98 by clicking on the OpenGL window to get focus and then hitting the
backspace or delete keys.

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:wa...@de...      
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Mark Wilke
> Sent: Friday, May 27, 2005 11:08 AM
> To: pym...@li...
> Subject: [PyMOL] v0.98 slow
> 
> I last used pymol about a year ago (not sure which version), 
> but typical ray-tracing jobs of simple cartoon-ribbons etc 
> took mere seconds to a few minutes at most.  I just upgraded 
> to the new v0.98 and made some similar figures, but the 
> ray-tracing is taking 30 min to 1 hr or more.  This is pretty 
> much unusable if you need to ray-trace several times to get 
> the figure to look how you want.  Am I the only one 
> experiencing slow ray-tracing with pymol?  I'm using the 
> windows build provided on the pymol website.  I tried 2 PC computers:
> 
> (1) 1.4 GHz athlon
>     512 MB ram
>     Geforce2 GTS (64MB) Graphics Card
>     WinXP
> 
> (2) Dell Inspiron XPS Gen 2 Desktop Replacement
>     2 GHz cpu (pentium m 760)
>     Geforce go 6800 ultra
>     1 GB ram
>     WinXP media centre edition
> 
> The Dell is more than powerful enough to render rapidly...but 
> both computers behaved similarly.  Anyone have any ideas?
> 
> - Mark
> 
> Oh yeah, please make a clean way of aborting from a 
> ray-trace...please.
> 
> 
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by Yahoo.
> Introducing Yahoo! Search Developer Network - Create apps using Yahoo!
> Search APIs Find out how you can build Yahoo! directly into 
> your own Applications - visit 
> http://developer.yahoo.net/?fr=offad-ysdn-ostg-q22005
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

I last used pymol about a year ago (not sure which version), but typical
ray-tracing jobs of simple cartoon-ribbons etc took mere seconds to a
few minutes at most.  I just upgraded to the new v0.98 and made some
similar figures, but the ray-tracing is taking 30 min to 1 hr or
more.  This is pretty much unusable if you need to ray-trace several times
to get the figure to look how you want.  Am I the only one experiencing
slow ray-tracing with pymol?  I'm using the windows build provided on the
pymol website.  I tried 2 PC computers:

(1) 1.4 GHz athlon
    512 MB ram
    Geforce2 GTS (64MB) Graphics Card
    WinXP

(2) Dell Inspiron XPS Gen 2 Desktop Replacement
    2 GHz cpu (pentium m 760)
    Geforce go 6800 ultra
    1 GB ram
    WinXP media centre edition

The Dell is more than powerful enough to render rapidly...but both
computers behaved similarly.  Anyone have any ideas?

- Mark

Oh yeah, please make a clean way of aborting from a ray-trace...please.

I want to get surface patches using expand like
select res, resi 14
select patch, res expand 6.0

But  I got some discontiguous surface patches which are not what I want.
How can I get rid of the discontiguous part of surface patches?
Thanks

Bingding


-- 
Bingding Huang
PhD student
Bioinformatics group
Biotec & Department of Computing
Tazberg 47, 01307
TU Dresden, Germany

Tel:    0049 351 46340064 (Office)
Tel:    0049 351 4403368  (Home)
Fax:    0049 351 46340061
Mobile: 01772981375
E-mail: bh...@bi...

This morning I upgraded from pymol 0.97 to pymol 0.98 and I've 
discovered some fairly substantial differences in behavior between the 
two versions.

I first noticed that some objects were being drawn much darker than 
before.  Specifically, protein surfaces and anything drawn using sticks 
(instead of lines) are very difficult to see.  This is illustrated in 
this screen capture:
http://www.mindspring.com/~greglandrum/pymol/normal-0.98.jpg
notice how bright the h-bond lines are compared to everything else; if I 
draw the molecule with lines instead of sticks, they come out this bright.

As a check, I then raytraced that scene and got something much more 
reasonable:
http://www.mindspring.com/~greglandrum/pymol/traced-0.98.jpg
(this scene took *way* too long to raytrace, I'll comment on that below).

Here's a similar scene as it appears in version 0.97:
http://www.mindspring.com/~greglandrum/pymol/normal-0.97.jpg

So I tried exporting a session file from 0.97 and loading it into 0.98. 
  The resulting rendering is, once again, way too dark:
http://www.mindspring.com/~greglandrum/pymol/normal-0.98-import.jpg
(notice that's it's also not exactly the same view, despite the fact I 
loaded a session file.  This is also a problem)

The raytracing results from 0.97 and 0.98 using the 0.97 session file 
are similar (aside from the view/perspective differences):
http://www.mindspring.com/~greglandrum/pymol/traced-0.97.jpg
and:
http://www.mindspring.com/~greglandrum/pymol/traced-0.98-import.jpg

Any clues as to what's going on here?

A note about raytracing time:
The initial raytrace with 0.98 took 227 seconds on this machine, the 
other raytraces took 2.3 seconds (using 0.97) and 9.9 seconds (using 
0.98 with the 0.97 session file). Why is 0.98 so much slower than 0.97? 
The scenes were generated programatically using the same sequences of 
commands (with the exception of details of the view, which I got close 
by hand), so any differences in the surfaces themselves must be due to 
changed default settings in the surface generation routines?


These results were obtained on a Windows 2K box, using Python 2.3.4

Thanks for any help,
-greg

FYI: Linux users who need to run with the nVidia driver versions 71.47 or
71.67...

The PyMOL 0.99beta01 version available at http://delsci.com/beta is able to
avoid the crash.  

However, performance is reduced by the workaround, so I wouldn't recommend
using this build unless you have to.

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:wa...@de...      
 

> -----Original Message-----
> From: Michael Kutz [mailto:mk...@tt...] 
> Sent: Thursday, May 26, 2005 8:29 AM
> To: Fischmann, Thierry
> Cc: 'Warren DeLano'
> Subject: RE: [PyMOL] Linux FC3 upgrade causing pymol core dump
> 
> 
> Thierry,
> The machine i have is a 6221 also.  IBM's working on the 
> problem for us.  (there is at least one other person that has 
> called them with this problem) The solution IBM is proposing 
> - block out certein memory areas for kernel use.  i'll 
> forward the information when i get it. 
> 
> for us, not all 3rd party code works on RHEL 4, so we have to 
> use RHEL 3. 
> rhel 4 uses ONLY gcc 3.*, even "backward compatible" gcc is a 
> 3.* version.  the 3rd party software was compiled w/t 2.?? libraries. 
> 
> about your crash/bad sector/etc.... run "badblocks" before or 
> durring reinstall.  CAUTION: this will wipe a disk if not 
> done correctly. 
> Also, there should be a way, through "linux recover" to 
> re-build the boot sector if your /boot partition is fine.  
> (this is another reason why you ALWAYS make /boot a seperate 
> partition.)  if you have support, call redhat for help.  I'd 
> ask my guy how to do this but he's in Raleigh for RHCE training. 
> 
> other hints:  In your BIOS - turn HyperThreading OFF. 
>         turn your screen-saver off also. 
> 
> MK 
> 
> 
> "Fischmann, Thierry" <thi...@sp...> wrote on 
> 05/26/2005 10:42:28:
> 
> > Mike. 
> >   
> > I'd be most grateful if you could post the solution. 
> >   
> > My machine is an IBM Intellistation with Intel cpu and one of the 
> > latest NVIDIA quadro graphics cards). The OS is RHEL 4 WS. 
> I have the 
> > NVIDIA 7174 driver installed.
> >   
> > I have had pymol installed for a while, and it has worked 
> well so far 
> > ... then after reading your message I've started it again, just to 
> > make sure everything is fine and ...
> >   
> > Nasty crash ! The screen went blank, the keyboard would not 
> respond, 
> > and after ~ 1minute the computer rebooted itself on its own. The 
> > computer now claims that there is an error in the system 
> disk that is 
> > not recoverable, and refuses to boot from that disk.
> >   
> > I have been able to reboot from an installation CD in "linux rescue"
> > mode. I can see that the partition itself does not seem affected: 
> > the files are there and "look okay". So maybe only the boot 
> sector is 
> > corrupted. I am considering reinstalling everything from 
> scratch, as 
> > there may be more than just a boot sector that has become 
> corrupted (I 
> > keep my data on a separate system disk, and they are most 
> likely not 
> > affected).
> >   
> > No more NVIDIA drivers for me unless I have a solution to 
> the above ... 
> >   
> > Thierry
> > -----Original Message-----
> > From: Michael Kutz [mailto:mk...@tt...]
> > Sent: Thursday, May 26, 2005 10:00 AM
> > To: pym...@li...
> > Subject: Re: [PyMOL] Linux FC3 upgrade causing pymol core dump
> 
> > 
> > nvidia 7167 & 7174 drivers seem to have issues (see 
> previous e-mails 
> > in this list) VMD is also affected, but not many other openGL 
> > programs.  (i can run SPECperf just fine)
> > 
> > The issue you see here may be related to some other 
> non-pymol issues 
> > i've seen on my machine.
> > my vendor said my other issues may be caused by the nvidia driver 
> > overwriting some kernel space.
> > 
> > when/if i can, i'll e-mail the solution. 
> > 
> > MK
> > 
> > 
> > pym...@li... wrote on 05/26/2005 
> 05:16:56:
> > 
> > > Do you have nvidia drivers?
> > > If so, may be you came across the same problem I have:
> > > 
> > > I have installed the latest version of Mandriva Linux on a AMD
> > > Athlon(tm) MP 2400+ PC with
> > > a Quadro4 900 XGL graphich card and the NVIDIA-Linux-x86-1.0-7174 
> > > driver
> > > 
> > > When I run pymol and load a pdb file, the program crashes 
> with the 
> > > following message:
> > > 
> > >  CmdLoad: "GLGA/sup_models/pdb1rzu.ent" loaded as "pdb1rzu".
> > > *** glibc detected *** double free or corruption (!prev): 
> 0x08a76ba0 
> > > ***
> > > /usr/local/pymol-0.98-precompiled/pymol.com: line 14: 16877 
> > > Aborted                 (core dumped) $PYMOL_PATH/pymol.exe $*
> > > 
> > > However, if I set auto_show_lines=off and auto_show_nonbonded=off 
> > > BEFORE loading the molecule, the program loads the PDB 
> file without 
> > > crashing (and without showing any graphical object, of course). 
> > > Then, I can use the "show" command/button for any type of 
> > > representation (ribbons, nonbonded, sticks, ...) EXCEPT 
> the "lines" 
> > > representation, which causes a program crash.
> > > 
> > > This happens with both distributed binary and self compiled PyMol 
> > > versions. I have tried version 0.97 and 0.98 with the 
> same results.
> > > 
> > > Then, browsing the internet, I came across the following message 
> > > from
> > > Warren:
> > > 
> > > http://sourceforge.net/mailarchive/message.php?msg_id=11735911
> > > 
> > > and I decided to try the 0_99beta01 version 
> > > 
> (http://delsci.com/beta/pymol-0_99beta01-bin-linux-x86-nvidia-test.t
> > > gz), which seems to solve my problem for the moment.
> > > 
> > > 
> > > 
> > > gerwald jogl wrote:
> > > 
> > > > Hi everyone,
> > > >
> > > > Just wanted to send in a description of the following situation:
> > > > I was using pymol 0.98 precompiled on FC3 today and did an 
> > > > automatic update during the day (therefore, sorry but I 
> don't know 
> > > > which packages where upgraded :-( Afterwards, pymol would start 
> > > > up, but core dump immediately after loading a pdb file.
> > > > The same is happening with the 0.97 precompiled version 
> and with 
> > > > my own compile of the 0.98 source code.
> > > > This is what I get:
> > > > /xsoft/pymol-0.97precompiled/pymol.com: line 14: 19692 
> Segmentation 
> > > > fault      (core dumped) $PYMOL_PATH/pymol.exe $*
> > > >
> > > > or my compile:
> > > > /xsoft/pymol-0.98/pymol.com: line 2: 19785 Segmentation 
> fault      
> > > > (core dumped) /usr/bin/python
> > > > /usr/lib/python2.3/site-packages/pymol/__init__.py $*
> > > >
> > > >
> > > > Any comments on this would be greatly appreciated...
> > > > Gerwald
> > > >
> > > >
> > > > -------------------------------------------------------
> > > > SF.Net email is sponsored by: GoToMeeting - the easiest way to 
> > > > collaborate online with coworkers and clients while 
> avoiding the 
> > > > high cost of travel and communications. There is no 
> equipment to 
> > > > buy and you can meet as often as you want. Try it 
> > > > free.http://ads.osdn.com/?ad_id=7402&alloc_id=16135&op=click
> > > > _______________________________________________
> > > > PyMOL-users mailing list
> > > > PyM...@li...
> > > > https://lists.sourceforge.net/lists/listinfo/pymol-users
> > > >
> > > 
> > > --
> > > 
> > > --------------------------------------------------
> > > Stefano Trapani, PhD
> > > 
> > > Laboratoire de Virologie Moleculaire & Structurale UMR 2472  
> > > CNRS-GIF
> > > 1 Av. de la Terrasse, Bat. 14 B
> > > 91198 Gif-sur-Yvette FRANCE
> > > 
> > > phone: ++33 1 6982.3856
> > > FAX:   ++33 1 6982.4308
> > > --------------------------------------------------
> > > 
> > > 
> > > [attachment "trapani.vcf" deleted by Michael Kutz/TTP]
> > 
> > 
> > 
> *********************************************************************
> > This message and any attachments are solely for the intended 
> > recipient. If you are not the intended recipient, 
> disclosure, copying, 
> > use or distribution of the information included in this message is 
> > prohibited -- Please immediately and permanently delete.
> 

Hi everyone,

maybe I should have looked in the archive more carefully...
Yes, this is a nvidia quadro system, and yes, it's the 7174 drivers.
I have downloaded the 0.99beta01 version, and it seems to be stable in 
the first few tests I've done.

Thanks!
Gerwald

Stefano Trapani wrote:

> Do you have nvidia drivers?
> If so, may be you came across the same problem I have:
>
> I have installed the latest version of Mandriva Linux on a AMD 
> Athlon(tm) MP 2400+ PC with
> a Quadro4 900 XGL graphich card and the NVIDIA-Linux-x86-1.0-7174 driver
>
> When I run pymol and load a pdb file, the program crashes with the 
> following message:
>
> CmdLoad: "GLGA/sup_models/pdb1rzu.ent" loaded as "pdb1rzu".
> *** glibc detected *** double free or corruption (!prev): 0x08a76ba0 ***
> /usr/local/pymol-0.98-precompiled/pymol.com: line 14: 16877 
> Aborted                 (core dumped) $PYMOL_PATH/pymol.exe $*
>
> However, if I set auto_show_lines=off and auto_show_nonbonded=off 
> BEFORE loading the molecule, the program loads the PDB file without 
> crashing (and without showing any graphical object, of course). Then, 
> I can use the "show" command/button for any type of representation 
> (ribbons, nonbonded, sticks, ...) EXCEPT the "lines" representation, 
> which causes a program crash.
>
> This happens with both distributed binary and self compiled PyMol 
> versions. I have tried version 0.97 and 0.98 with the same results.
>
> Then, browsing the internet, I came across the following message from 
> Warren:
>
> http://sourceforge.net/mailarchive/message.php?msg_id=11735911
>
> and I decided to try the 0_99beta01 version 
> (http://delsci.com/beta/pymol-0_99beta01-bin-linux-x86-nvidia-test.tgz), 
> which seems to solve my problem for the moment.
>
>
>
> gerwald jogl wrote:
>
>> Hi everyone,
>>
>> Just wanted to send in a description of the following situation:
>> I was using pymol 0.98 precompiled on FC3 today and did an automatic 
>> update during the day (therefore, sorry but I don't know which 
>> packages where upgraded :-(
>> Afterwards, pymol would start up, but core dump immediately after 
>> loading a pdb file.
>> The same is happening with the 0.97 precompiled version and with my 
>> own compile of the 0.98 source code.
>> This is what I get:
>> /xsoft/pymol-0.97precompiled/pymol.com: line 14: 19692 Segmentation 
>> fault      (core dumped) $PYMOL_PATH/pymol.exe $*
>>
>> or my compile:
>> /xsoft/pymol-0.98/pymol.com: line 2: 19785 Segmentation fault      
>> (core dumped) /usr/bin/python 
>> /usr/lib/python2.3/site-packages/pymol/__init__.py $*
>>
>>
>> Any comments on this would be greatly appreciated...
>> Gerwald
>>
>>
>> -------------------------------------------------------
>> SF.Net email is sponsored by: GoToMeeting - the easiest way to 
>> collaborate
>> online with coworkers and clients while avoiding the high cost of 
>> travel and
>> communications. There is no equipment to buy and you can meet as 
>> often as
>> you want. Try it 
>> free.http://ads.osdn.com/?ad_id=7402&alloc_id=16135&op=click
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>

nvidia 7167 & 7174 drivers seem to have issues (see previous e-mails in 
this list)
VMD is also affected, but not many other openGL programs.  (i can run 
SPECperf just fine)

The issue you see here may be related to some other non-pymol issues i've 
seen on my machine.
my vendor said my other issues may be caused by the nvidia driver 
overwriting some kernel space.

when/if i can, i'll e-mail the solution.

MK


pym...@li... wrote on 05/26/2005 05:16:56:

> Do you have nvidia drivers?
> If so, may be you came across the same problem I have:
> 
> I have installed the latest version of Mandriva Linux on a AMD 
> Athlon(tm) MP 2400+ PC with
> a Quadro4 900 XGL graphich card and the NVIDIA-Linux-x86-1.0-7174 driver
> 
> When I run pymol and load a pdb file, the program crashes with the 
> following message:
> 
>  CmdLoad: "GLGA/sup_models/pdb1rzu.ent" loaded as "pdb1rzu".
> *** glibc detected *** double free or corruption (!prev): 0x08a76ba0 ***
> /usr/local/pymol-0.98-precompiled/pymol.com: line 14: 16877 
> Aborted                 (core dumped) $PYMOL_PATH/pymol.exe $*
> 
> However, if I set auto_show_lines=off and auto_show_nonbonded=off BEFORE 

> loading the molecule, the program loads the PDB file without crashing 
> (and without showing any graphical object, of course). Then, I can use 
> the "show" command/button for any type of representation (ribbons, 
> nonbonded, sticks, ...) EXCEPT the "lines" representation, which causes 
> a program crash.
> 
> This happens with both distributed binary and self compiled PyMol 
> versions. I have tried version 0.97 and 0.98 with the same results.
> 
> Then, browsing the internet, I came across the following message from 
> Warren:
> 
> http://sourceforge.net/mailarchive/message.php?msg_id=11735911
> 
> and I decided to try the 0_99beta01 version 
> (http://delsci.com/beta/pymol-0_99beta01-bin-linux-x86-nvidia-test.tgz), 

> which seems to solve my problem for the moment.
> 
> 
> 
> gerwald jogl wrote:
> 
> > Hi everyone,
> >
> > Just wanted to send in a description of the following situation:
> > I was using pymol 0.98 precompiled on FC3 today and did an automatic 
> > update during the day (therefore, sorry but I don't know which 
> > packages where upgraded :-(
> > Afterwards, pymol would start up, but core dump immediately after 
> > loading a pdb file.
> > The same is happening with the 0.97 precompiled version and with my 
> > own compile of the 0.98 source code.
> > This is what I get:
> > /xsoft/pymol-0.97precompiled/pymol.com: line 14: 19692 Segmentation 
> > fault      (core dumped) $PYMOL_PATH/pymol.exe $*
> >
> > or my compile:
> > /xsoft/pymol-0.98/pymol.com: line 2: 19785 Segmentation fault 
> > (core dumped) /usr/bin/python 
> > /usr/lib/python2.3/site-packages/pymol/__init__.py $*
> >
> >
> > Any comments on this would be greatly appreciated...
> > Gerwald
> >
> >
> > -------------------------------------------------------
> > SF.Net email is sponsored by: GoToMeeting - the easiest way to 
> > collaborate
> > online with coworkers and clients while avoiding the high cost of 
> > travel and
> > communications. There is no equipment to buy and you can meet as often 
as
> > you want. Try it 
> > free.http://ads.osdn.com/?ad_id=7402&alloc_id=16135&op=click
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> 
> -- 
> 
> --------------------------------------------------
> Stefano Trapani, PhD
> 
> Laboratoire de Virologie Moleculaire & Structurale
> UMR 2472  CNRS-GIF
> 1 Av. de la Terrasse, Bat. 14 B
> 91198 Gif-sur-Yvette FRANCE
> 
> phone: ++33 1 6982.3856
> FAX:   ++33 1 6982.4308
> --------------------------------------------------
> 
> 
> [attachment "trapani.vcf" deleted by Michael Kutz/TTP] 

The auto-stop feature would definitely be useful. With only one state, I 
never even noticed that I had accidentally pressed "play".

Jacob

Warren DeLano wrote:
> Jacob,
> 
> Thanks for the sending me the session file -- this is a common problem that
> results having the movie "play" button active when trying to ray trace.  
> 
> Hit the stop button or type "mstop" before raytracing and then your image
> will render fine.  
> 
> Perhaps we should probably have the ray command automatically stop the movie
> if it is playing...so that others don't suffer the same fate!
> 
> 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:wa...@de...      
>  
> 
> 
>>-----Original Message-----
>>From: pym...@li... 
>>[mailto:pym...@li...] On Behalf Of 
>>Jacob Corn
>>Sent: Wednesday, May 25, 2005 3:52 PM
>>To: pymol-users
>>Subject: [PyMOL] Raytracing "lies" in v0.98
>>
>>Hi all,
>>I have a session that I am completely unable to render. If I 
>>just issue a "ray" command, the view window shows a progress 
>>bar and the command window eventually reports that raytracing 
>>has finished normally, but the view window isn't updated with 
>>the raytraced image. If I try to png the output, all I get is 
>>the OpenGL image. If I specify a size larger than the view 
>>windows (eg - "ray 1600,800") I don't even get the 
>>white-screen "image too big for window" message.
>>
>>The only thing I can think of that might be funky about the 
>>scene is two objects with different cartoon transparencies. 
>>But if I set them to both have the same transparency, no dice.
>>This behavior occurs with this session across computers and 
>>across OSes (WinXP and OSX). Has anyone else seen this? 
>>Warren, if this is a bug, shall I send you the scene file?
>>
>>Jacob
>>
>>--
>>Jacob Corn
>>The Berger Lab
>>UC Berkeley - Molecular and Cell Biology jc...@uc...
>>phone: 510-643-8893
>>fax: 510-643-9290
>>
>>
>>-------------------------------------------------------
>>SF.Net email is sponsored by: GoToMeeting - the easiest way 
>>to collaborate
>>online with coworkers and clients while avoiding the high 
>>cost of travel and
>>communications. There is no equipment to buy and you can meet 
>>as often as
>>you want. Try it 
>>free.http://ads.osdn.com/?ad_id=7402&alloc_id=16135&op=click
>>_______________________________________________
>>PyMOL-users mailing list
>>PyM...@li...
>>https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
> 
> 
> 
> 
> 
> -------------------------------------------------------
> SF.Net email is sponsored by: GoToMeeting - the easiest way to collaborate
> online with coworkers and clients while avoiding the high cost of travel and
> communications. There is no equipment to buy and you can meet as often as
> you want. Try it free.http://ads.osdn.com/?ad_id=7402&alloc_id=16135&op=click
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Do you have nvidia drivers?
If so, may be you came across the same problem I have:

I have installed the latest version of Mandriva Linux on a AMD 
Athlon(tm) MP 2400+ PC with
a Quadro4 900 XGL graphich card and the NVIDIA-Linux-x86-1.0-7174 driver

When I run pymol and load a pdb file, the program crashes with the 
following message:

 CmdLoad: "GLGA/sup_models/pdb1rzu.ent" loaded as "pdb1rzu".
*** glibc detected *** double free or corruption (!prev): 0x08a76ba0 ***
/usr/local/pymol-0.98-precompiled/pymol.com: line 14: 16877 
Aborted                 (core dumped) $PYMOL_PATH/pymol.exe $*

However, if I set auto_show_lines=off and auto_show_nonbonded=off BEFORE 
loading the molecule, the program loads the PDB file without crashing 
(and without showing any graphical object, of course). Then, I can use 
the "show" command/button for any type of representation (ribbons, 
nonbonded, sticks, ...) EXCEPT the "lines" representation, which causes 
a program crash.

This happens with both distributed binary and self compiled PyMol 
versions. I have tried version 0.97 and 0.98 with the same results.

Then, browsing the internet, I came across the following message from 
Warren:

http://sourceforge.net/mailarchive/message.php?msg_id=11735911

and I decided to try the 0_99beta01 version 
(http://delsci.com/beta/pymol-0_99beta01-bin-linux-x86-nvidia-test.tgz), 
which seems to solve my problem for the moment.



gerwald jogl wrote:

> Hi everyone,
>
> Just wanted to send in a description of the following situation:
> I was using pymol 0.98 precompiled on FC3 today and did an automatic 
> update during the day (therefore, sorry but I don't know which 
> packages where upgraded :-(
> Afterwards, pymol would start up, but core dump immediately after 
> loading a pdb file.
> The same is happening with the 0.97 precompiled version and with my 
> own compile of the 0.98 source code.
> This is what I get:
> /xsoft/pymol-0.97precompiled/pymol.com: line 14: 19692 Segmentation 
> fault      (core dumped) $PYMOL_PATH/pymol.exe $*
>
> or my compile:
> /xsoft/pymol-0.98/pymol.com: line 2: 19785 Segmentation fault      
> (core dumped) /usr/bin/python 
> /usr/lib/python2.3/site-packages/pymol/__init__.py $*
>
>
> Any comments on this would be greatly appreciated...
> Gerwald
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by: GoToMeeting - the easiest way to 
> collaborate
> online with coworkers and clients while avoiding the high cost of 
> travel and
> communications. There is no equipment to buy and you can meet as often as
> you want. Try it 
> free.http://ads.osdn.com/?ad_id=7402&alloc_id=16135&op=click
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

-- 

--------------------------------------------------
Stefano Trapani, PhD

Laboratoire de Virologie Moleculaire & Structurale
UMR 2472  CNRS-GIF
1 Av. de la Terrasse, Bat. 14 B
91198 Gif-sur-Yvette FRANCE

phone: ++33 1 6982.3856
FAX:   ++33 1 6982.4308
--------------------------------------------------

gerwald jogl writes:
 > Hi everyone,
 > 
 > Just wanted to send in a description of the following situation:
 > I was using pymol 0.98 precompiled on FC3 today and did an automatic 
 > update during the day (therefore, sorry but I don't know which packages 
 > where upgraded :-(

You can get a list of RPMs on the system in the order of installation
date by doing e.g.

   rpm -qa --last | less


Mikko

Jacob,

Thanks for the sending me the session file -- this is a common problem that
results having the movie "play" button active when trying to ray trace.  

Hit the stop button or type "mstop" before raytracing and then your image
will render fine.  

Perhaps we should probably have the ray command automatically stop the movie
if it is playing...so that others don't suffer the same fate!

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:wa...@de...      
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Jacob Corn
> Sent: Wednesday, May 25, 2005 3:52 PM
> To: pymol-users
> Subject: [PyMOL] Raytracing "lies" in v0.98
> 
> Hi all,
> I have a session that I am completely unable to render. If I 
> just issue a "ray" command, the view window shows a progress 
> bar and the command window eventually reports that raytracing 
> has finished normally, but the view window isn't updated with 
> the raytraced image. If I try to png the output, all I get is 
> the OpenGL image. If I specify a size larger than the view 
> windows (eg - "ray 1600,800") I don't even get the 
> white-screen "image too big for window" message.
> 
> The only thing I can think of that might be funky about the 
> scene is two objects with different cartoon transparencies. 
> But if I set them to both have the same transparency, no dice.
> This behavior occurs with this session across computers and 
> across OSes (WinXP and OSX). Has anyone else seen this? 
> Warren, if this is a bug, shall I send you the scene file?
> 
> Jacob
> 
> --
> Jacob Corn
> The Berger Lab
> UC Berkeley - Molecular and Cell Biology jc...@uc...
> phone: 510-643-8893
> fax: 510-643-9290
> 
> 
> -------------------------------------------------------
> SF.Net email is sponsored by: GoToMeeting - the easiest way 
> to collaborate
> online with coworkers and clients while avoiding the high 
> cost of travel and
> communications. There is no equipment to buy and you can meet 
> as often as
> you want. Try it 
> free.http://ads.osdn.com/?ad_id=7402&alloc_id=16135&op=click
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

Hi,
            In general, coloring of a molecule is mapped onto the atoms.
For example carbon =3D green, hydrogen =3D gray. The bond between the =
carbon
and the hydrogen would then be two-tone; half of the bond nearest the
carbon would be green, the other half of the bond nearest the hydrogen
would be gray.=20
            Is it possible to color the bonds in a molecule independent
of the atoms they are incident with? We have some software that computes
which bonds in a molecular structure can rotate (flexible) and which can
not rotate (rigid). I'd like to be able to distinguish these bonds
(flexible versus rigid) with different colors.=20
The problem is that atoms can be incident with both flexible bonds and
rigid bonds, so we can't simply color an atom appropriately.=20
Something like "atom_1   atom_2     color" would be nice.
Any thoughts?
=20
Brandon Hespenheide

Hi all,
I have a session that I am completely unable to render. If I just issue 
a "ray" command, the view window shows a progress bar and the command 
window eventually reports that raytracing has finished normally, but the 
view window isn't updated with the raytraced image. If I try to png the 
output, all I get is the OpenGL image. If I specify a size larger than 
the view windows (eg - "ray 1600,800") I don't even get the white-screen 
"image too big for window" message.

The only thing I can think of that might be funky about the scene is two 
objects with different cartoon transparencies. But if I set them to both 
have the same transparency, no dice.
This behavior occurs with this session across computers and across OSes 
(WinXP and OSX). Has anyone else seen this? Warren, if this is a bug, 
shall I send you the scene file?

Jacob

-- 
Jacob Corn
The Berger Lab
UC Berkeley - Molecular and Cell Biology
jc...@uc...
phone: 510-643-8893
fax: 510-643-9290

Hi everyone,

Just wanted to send in a description of the following situation:
I was using pymol 0.98 precompiled on FC3 today and did an automatic 
update during the day (therefore, sorry but I don't know which packages 
where upgraded :-(
Afterwards, pymol would start up, but core dump immediately after 
loading a pdb file.
The same is happening with the 0.97 precompiled version and with my own 
compile of the 0.98 source code.
This is what I get:
/xsoft/pymol-0.97precompiled/pymol.com: line 14: 19692 Segmentation 
fault      (core dumped) $PYMOL_PATH/pymol.exe $*

or my compile:
/xsoft/pymol-0.98/pymol.com: line 2: 19785 Segmentation fault      (core 
dumped) /usr/bin/python 
/usr/lib/python2.3/site-packages/pymol/__init__.py $*


Any comments on this would be greatly appreciated...
Gerwald

hide cartoon, not ss H+S


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> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Neil Ranson
> Sent: Wednesday, May 25, 2005 7:15 AM
> To: pym...@li...
> Subject: [PyMOL] removing loops
> 
> Dear All,
> 
> I'm sure this is a really stupid question, but can you turn 
> off the loops in a "cartoon auto" representation, to leave 
> (visually) disconnected helices and strands?
> 
> I've tried "set cartoon_loop_radius, 0" which kind-of works 
> but leaves unfortunate ghosting artefacts in the image.
> 
> Any help would be much appreciated.
> 
> Cheers,
> 
> Neil.
> 
>  
> 
> *************************************
> 
> Neil Ranson PhD
> 
> University Research Fellow,
> 
> Astbury Centre for Structural Molecular Biology,
> 
> School of Biochemistry & Microbiology,
> 
> University of Leeds,
> 
> Leeds, LS2 9JT. UK.
> 
>  
> 
> Tel: +44 (0) 113 343 7065
> 
> Fax: +44 (0) 113 343 3167
> 
> n.a...@le...
> 
>  
> 
> *************************************
> 
>  
> 
> 

You could just specify a selection of residues for which you want to=20
display the cartoon if that's not
too much trouble.

e.g. 'show cartoon, i. 1:20' displays the cartoon for residues 1-20

I hope that's what you meant.

Uwe

Neil Ranson wrote:

> Dear All,
>
> I=92m sure this is a really stupid question, but can you turn off the=20
> loops in a =93cartoon auto=94 representation, to leave (visually)=20
> disconnected helices and strands?
>
> I=92ve tried =93set cartoon=5Floop=5Fradius, 0=94 which kind-of works but=
 leaves=20
> unfortunate ghosting artefacts in the image.
>
> Any help would be much appreciated.
>
> Cheers,
>
> Neil.
>
> *************************************
>
> Neil Ranson PhD
>
> University Research Fellow,
>
> Astbury Centre for Structural Molecular Biology,
>
> School of Biochemistry & Microbiology,
>
> University of Leeds,
>
> Leeds, LS2 9JT. UK.
>
> Tel: +44 (0) 113 343 7065
>
> Fax: +44 (0) 113 343 3167
>
> n.a...@le...
>
> *************************************
>

Dear All,

I'm sure this is a really stupid question, but can you turn off the =
loops in
a "cartoon auto" representation, to leave (visually) disconnected =
helices
and strands?

I've tried "set cartoon_loop_radius, 0" which kind-of works but leaves
unfortunate ghosting artefacts in the image.

Any help would be much appreciated.

Cheers,

Neil.

=20

*************************************

Neil Ranson PhD

University Research Fellow,

Astbury Centre for Structural Molecular Biology,

School of Biochemistry & Microbiology,

University of Leeds,

Leeds, LS2 9JT. UK.

=20

Tel: +44 (0) 113 343 7065

Fax: +44 (0) 113 343 3167

n.a...@le...

=20

*************************************

=20