[PyMOL] Using povray with pymol

2009-05-11 Thread Abhinav Verma
I am trying to use povray tracer with pymol. I got povray and installed it
and tried to follow the instructions for the patch.. The patch seems too old
written in 1999 and the current povray code is cpp and not c. so I skipped
that part.. and now when I set smooth_color_triangle = 1, I get the
following parse error..

pigment{color rgb1.1,0.0904,0.}}
mesh {
smooth_color_triangle
Parse Error: No triangles in triangle mesh.

If I donot swich it on, I get really ugly colored picture from the
tmp_povray.pov file generated by pymol.
Any Ideas to get  similars colors that comes with pymol inbuild ray tracer
and use povray ( I want to use povray as pymol is crashing because of size )

Thanks in advance,
Abhi
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[PyMOL] Dashed loops in cartoon?

2009-05-11 Thread Dirk Kostrewa
Dear PyMolers,

I want to show a tentative trace through very weak electron density in  
a cartoon representation with dashed loops, along with the usual  
helices, sheets and solid loops for the reliable part of the  
structure. I could not find a description for this task - is this  
possible? If not, I will just show dashed bonds between the C-alphas  
of the tentative trace.

Best regards,

Dirk.

***
Dirk Kostrewa
Gene Center, A 5.07
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76999
E-mail: kostr...@lmb.uni-muenchen.de
***





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Re: [PyMOL] Using povray with pymol

2009-05-11 Thread Tsjerk Wassenaar
Hi Abhi,

I got and read the e-mail through the list, but would have to test
with pymol 1.0 before being able to give a sensible reply. As I'm now
underway that's a bit too much for me :) I'll come back on this one
later.
By the way, you only sent this mail this afternoon. Don't expect
instant replies or assume something didn't come through just because
you didn't get an answer within a few hours :)

Cheers,

Tsjerk

On Mon, May 11, 2009 at 5:05 PM, Abhinav Verma abhinav1...@gmail.com wrote:
 Hi Tsjerk,

  I am sending this email personally to you (sorry for that).  I am sorry,
 but I posted it to pymol mailing list but it seems to have been stuck
 somewhere.
  Any idea would be helpful,

 thanks,
 Abhi

 -- Forwarded message --
 From: Abhinav Verma abhinav1...@gmail.com
 Date: Mon, May 11, 2009 at 3:06 PM
 Subject: Using povray with pymol
 To: pymol-users pymol-users@lists.sourceforge.net


 I am trying to use povray tracer with pymol. I got povray and installed it
 and tried to follow the instructions for the patch.. The patch seems too old
 written in 1999 and the current povray code is cpp and not c. so I skipped
 that part.. and now when I set smooth_color_triangle = 1, I get the
 following parse error..

 pigment{color rgb1.1,0.0904,0.}}
 mesh {
 smooth_color_triangle
 Parse Error: No triangles in triangle mesh.

 If I donot swich it on, I get really ugly colored picture from the
 tmp_povray.pov file generated by pymol.
 Any Ideas to get  similars colors that comes with pymol inbuild ray tracer
 and use povray ( I want to use povray as pymol is crashing because of size )

 Thanks in advance,
 Abhi





-- 
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

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processing features enabled. http://p.sf.net/sfu/kodak-com
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[PyMOL] Vacuum electrostatics

2009-05-11 Thread Mark Wehner
Hi everyone,

in the newer version of pymol I realized it is not possible to generate vacuum 
electrostatics, there's an error while assigning the formal charges. The error 
message is:

Alter-Error: Aborting on error. Assignment may be incomplete.
  File string, line 1
formal_charge=0;flags=flags0x-8388609

I build the source code (rev 3719) using Python 2.6.2. Is anyone experiencing 
similar problems at the moment?

Mark

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Re: [PyMOL] Vacuum electrostatics

2009-05-11 Thread Warren DeLano
Mark,

Should be fixed now (in rev 3720).

Cheers,
Wawrren


 -Original Message-
 From: Mark Wehner [mailto:mark.weh...@rub.de]
 Sent: Monday, May 11, 2009 12:11 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Vacuum electrostatics
 
 Hi everyone,
 
 in the newer version of pymol I realized it is not possible to
generate
 vacuum
 electrostatics, there's an error while assigning the formal charges.
The
 error
 message is:
 
 Alter-Error: Aborting on error. Assignment may be incomplete.
   File string, line 1
 formal_charge=0;flags=flags0x-8388609
 
 I build the source code (rev 3719) using Python 2.6.2. Is anyone
 experiencing
 similar problems at the moment?
 
 Mark
 


--
 
 The NEW KODAK i700 Series Scanners deliver under ANY circumstances!
Your
 production scanning environment may not be a perfect world - but
thanks to
 Kodak, there's a perfect scanner to get the job done! With the NEW
KODAK
 i700
 Series Scanner you'll get full speed at 300 dpi even with all image
 processing features enabled. http://p.sf.net/sfu/kodak-com
 ___
 PyMOL-users mailing list
 PyMOL-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/pymol-users
 
 
 



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production scanning environment may not be a perfect world - but thanks to
Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700
Series Scanner you'll get full speed at 300 dpi even with all image 
processing features enabled. http://p.sf.net/sfu/kodak-com
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[PyMOL] Error: unknown type

2009-05-11 Thread Shiven Shandilya
Hello List,

Any ideas on why this script keeps failing in the newer PyMOL builds...

http://pymolwiki.org/index.php/Zero_residues

I keep getting the error message:


Error: unknown type: '1hpv'


where 1hpv is an actual pdb file/object

I am running pymol 1.2b5 rev. 3706 (compiled from svn) on Ubuntu 8.10


Anyone else face a similar issue, or is it just me


Thanks!

--Shiven

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production scanning environment may not be a perfect world - but thanks to
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