[PyMOL] Error: unknown type
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 -- 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
Re: [PyMOL] Vacuum electrostatics
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 "", line 1 > formal_charge=0;flags=flags&0x-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 > > > -- 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
[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 "", line 1 formal_charge=0;flags=flags&0x-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
Re: [PyMOL] eMovie question
Simon, Thanks for the suggestion. That is exactly my workaround. But I found out that I don't have to render the first 70 frames. I used "mpng xxx, 70, 300" and it worked fine. So this should save some rendering time. -- Jianghai On May 10, 2009, at 7:59 AM, Simon Kolstoe wrote: > Hi Jianghai, > > I've had a similar problem. I think it is to do with a mismatch > between the mpng command and moving the movie to the next frame. It > looks to me as if the mpng command saves what's in the pymol viewer > regardless of whether the next frame has actually played. The main > solution I've found is to use a computer with more RAM as this seems > to minimise the problem. The alternative is to put a pause at the > beginning of the move before getting into the animation. In your > case I would put a 70 frame pause at the beginning of the movie and > then edit it out at a later date. > > Simon > > > On 10 May 2009, at 02:01, Jianghai Zhu wrote: > >> Thanks for the suggestion. I have brought the movie back to frame 1 >> before I save the movie or images. So I still have no fix for this >> yet. >> >> -- Jianghai >> >> >> >> >> >> >> On May 9, 2009, at 8:13 PM, Carlos Huerta wrote: >> >>> Jianghai, >>> >>> I hope I am not over-simplifying your problem, as I had a similar >>> situation as you in saving the sequential images. If you play a >>> movie you made in PyMol using eMovie, it is best to go back to your >>> first Scene by clicking on your Scene button before saving the >>> images. Also, you can use the rewind button on the PyMol tool bar >>> menu. Hope this solves your problem. >>> >>> Sincerely, >>> >>> Carlos >>> >>> >> Jianghai Zhu 05/08/09 10:51 PM >>> >>> Hi all, >>> >>> I am trying to make a simple movie using eMovie. I rotate the >>> molecule >>> 360 degrees and then move to another region. The movie is fine >>> when I >>> play it in pymol. However, when I tried to save the movie as >>> sequential images or as a movie, the movie won't play until 70ish >>> frames and it won't finish the 360 degree rotation but just move to >>> the other region. So my first 70 or so images are just repeating >>> frame 1. Has anybody know a fix for this? Thanks. >>> >>> -- Jianghai >>> >>> >>> >>> >>> >>> >>> >>> -- >>> 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 >>> >>> >>> -- >>> 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 >>> >> >> >> -- >> 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 > -- 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
Re: [PyMOL] Using povray with pymol
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 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
> Date: Mon, May 11, 2009 at 3:06 PM
> Subject: Using povray with pymol
> To: pymol-users
>
>
> 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 rgb<1.1,0.0904,0.>}}
> 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
--
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
___
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[PyMOL] Dashed loops in cartoon?
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 *** -- 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
[PyMOL] Using povray with pymol
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 rgb<1.1,0.0904,0.>}}
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
--
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
