[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) o

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 versio

[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 "", line 1 formal_charge=0;flags=flags&

Re: [PyMOL] eMovie question

2009-05-11 Thread Jianghai Zhu
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:

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 rep

[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

[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 foll