Re: [PyMOL] Messed up structures in movie

2012-05-23 Thread Thomas Holder
regarding CONECT records and whether to use them, try: set connect_mode, 1 load youfile.pdb See also: http://www.pymolwiki.org/index.php/Connect_mode http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg10413.html Cheers, Thomas Nat Echols wrote, On 05/23/12 20:01: > On Wed, May

Re: [PyMOL] Messed up structures in movie

2012-05-23 Thread Schubert, Carsten [JRDUS]
Carsten From: Folmer Fredslund [mailto:folm...@gmail.com] Sent: Wednesday, May 23, 2012 1:53 PM To: Rituparna Sengupta Cc: PyMol Users Mailing List Subject: Re: [PyMOL] Messed up structures in movie Hi again Ritu, This does seem odd. I have no idea what might be wrong, but could you

Re: [PyMOL] Messed up structures in movie

2012-05-23 Thread Nat Echols
On Wed, May 23, 2012 at 10:20 AM, Rituparna Sengupta wrote: > Sorry about the lack of description in the previous post. > The chemicals show incorrect bond connections. Some of the rings go missing. > In all, the structure changes and just by looking at it, its possible to tell > that the struct

Re: [PyMOL] Messed up structures in movie

2012-05-23 Thread Folmer Fredslund
Hi again Ritu, This does seem odd. I have no idea what might be wrong, but could you provide an example pdb, or a png of the output you see? I would personally try to strip all extra information from the ligand pdb (so only ATOM and HETATM records is included) and then try loading that pdb. Best

Re: [PyMOL] Messed up structures in movie

2012-05-23 Thread Rituparna Sengupta
Hi, Sorry about the lack of description in the previous post. The chemicals show incorrect bond connections. Some of the rings go missing. In all, the structure changes and just by looking at it, its possible to tell that the structure is not right. I didn't see much details though, except that

Re: [PyMOL] Messed up structures in movie

2012-05-23 Thread Folmer Fredslund
Hi Ritu, Could you elaborate on "some of the ligand structures get completely messed up when viewed as sticks or lines"? To get the best possible answer a few more details would help. Best regards, Folmer 2012/5/23 Rituparna Sengupta > Hi, > > Just observed something weird. When I try loading

[PyMOL] Messed up structures in movie

2012-05-23 Thread Rituparna Sengupta
Hi, Just observed something weird. When I try loading protein -ligand complexes as frames of a movie (same protein but different ligands for different frames), some of the ligand structures get completely messed up when viewed as sticks or lines. Right now I'm using spheres instead, but wonderi