[PyMOL] discontiguous surface patches

[Bingding Huang]

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: bhu...@biotec.tu-dresden.de

[PyMOL] v0.98 slow

[Mark Wilke]

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.

RE: [PyMOL] v0.98 slow (includes: ray abort info...)

[Warren DeLano]

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:war...@delsci.com  
 

> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net 
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
> Mark Wilke
> Sent: Friday, May 27, 2005 11:08 AM
> To: pymol-users@lists.sourceforge.net
> 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.
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> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

Re: [PyMOL] v0.98 slow (includes: ray abort info...)

[hari jayaram]

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  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:war...@delsci.com
> 
> 
> > -Original Message-
> > From: pymol-users-ad...@lists.sourceforge.net
> > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> > Mark Wilke
> > Sent: Friday, May 27, 2005 11:08 AM
> > To: pymol-users@lists.sourceforge.net
> > 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
> > PyMOL-users@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> 
> 
> 
> 
> ---
> 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
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>

[PyMOL] perspective rendering

[Jianghai Zhu]

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

RE: [PyMOL] perspective rendering

[Warren DeLano]

> 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:war...@delsci.com  
 

> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net 
> [mailto:pymol-users-ad...@lists.sourceforge.net] 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
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>