From: Rituparna S. <rse...@wi...> - 2012-05-23 16:40:10
|
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 wondering if there's a way to work around the problem and still view the ligands as sticks/lines. Thanks, Ritu |
From: Folmer F. <fo...@gm...> - 2012-05-23 16:52:25
|
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 <rse...@wi...> > 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 > wondering if there's a way to work around the problem and still view the > ligands as sticks/lines. > > > Thanks, > Ritu > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Folmer Fredslund |
From: Rituparna S. <rse...@wi...> - 2012-05-23 17:20:27
|
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 the atom connections seem to be wrong. Thanks, Ritu On 05/23/12, Folmer Fredslund wrote: > 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 <PyM...@li... <rse...@wi...')" target="1">rse...@wi...> > > > 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 wondering if there's a way to work around the problem and still view the ligands as sticks/lines. > > > > > > Thanks, > > Ritu > > > > ------------------------------------------------------------------------------ > > Live Security Virtual Conference > > Exclusive live event will cover all the ways today's security and > > threat landscape has changed and how IT managers can respond. Discussions > > will include endpoint security, mobile security and the latest in malware > > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > > _______________________________________________ > > PyMOL-users mailing list (https://lists.sourceforge.net/lists/listinfo/pymol-users(javascript:main.compose('new', 't=PyM...@li...>) > > Info Page: <a href=) > > Archives: http://www.mail-archive.com/pym...@li... > > > > > > > -- > Folmer Fredslund |
From: Folmer F. <fo...@gm...> - 2012-05-23 17:53:27
|
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 regards, Folmer 2012/5/23 Rituparna Sengupta <rse...@wi...> > 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 the atom connections seem to be wrong. > > > Thanks, > Ritu > > On 05/23/12, Folmer Fredslund > wrote: > > 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 <PyM...@li... < > rse...@wi...')" target="1">rse...@wi...> > > > > > 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 wondering if there's a way to work around the problem and still > view the ligands as sticks/lines. > > > > > > > > > Thanks, > > > Ritu > > > > > > > ------------------------------------------------------------------------------ > > > Live Security Virtual Conference > > > Exclusive live event will cover all the ways today's security and > > > threat landscape has changed and how IT managers can respond. > Discussions > > > will include endpoint security, mobile security and the latest in > malware > > > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > > > _______________________________________________ > > > PyMOL-users mailing list ( > https://lists.sourceforge.net/lists/listinfo/pymol-users(javascript:main.compose('new', > 't=PyM...@li...>) > > > Info Page: <a href=) > > > Archives: > http://www.mail-archive.com/pym...@li... > > > > > > > > > > > > > -- > > Folmer Fredslund > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Folmer Fredslund |
From: Schubert, C. [JRDUS] <CSC...@it...> - 2012-05-23 18:02:33
|
Ritu, just an idea. It could be that your PDB files contains CONECT records for your ligands. Those bonds are defined by atom number or atom index I believe. There could be a conflict between the different files you are loading. Try stripping the CONECT records and see if that helps. HTH Carsten From: Folmer Fredslund [mailto:fo...@gm...] 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 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 regards, Folmer 2012/5/23 Rituparna Sengupta <rse...@wi...> 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 the atom connections seem to be wrong. Thanks, Ritu On 05/23/12, Folmer Fredslund wrote: > 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 <PyM...@li... <rse...@wi...')" target="1">rse...@wi...> > > > 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 wondering if there's a way to work around the problem and still view the ligands as sticks/lines. > > > > > > Thanks, > > Ritu > > > > ------------------------------------------------------------------------ ------ > > Live Security Virtual Conference > > Exclusive live event will cover all the ways today's security and > > threat landscape has changed and how IT managers can respond. Discussions > > will include endpoint security, mobile security and the latest in malware > > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > > _______________________________________________ > > PyMOL-users mailing list (https://lists.sourceforge.net/lists/listinfo/pymol-users(javascript:mai n.compose('new <https://lists.sourceforge.net/lists/listinfo/pymol-users%28javascript:m ain.compose%28%27new> ', 't=PyM...@li...>) > > Info Page: <a href=) > > Archives: http://www.mail-archive.com/pym...@li... > > > > > > > -- > Folmer Fredslund ------------------------------------------------------------------------ ------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ PyMOL-users mailing list (PyM...@li...) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... -- Folmer Fredslund |
From: Nat E. <nat...@gm...> - 2012-05-23 18:01:41
|
On Wed, May 23, 2012 at 10:20 AM, Rituparna Sengupta <rse...@wi...> 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 structure is not right. I didn't see much details though, except that the atom connections seem to be wrong. A screenshot would be helpful here, but my guess is that PyMOL's automatic detection of bond's didn't work for your input structure. This can happen for non-standard chemistries or distorted geometries; the most frequent artifact is more bonds than are appropriate. The reason it happens is that instead of applying some chemically sensible rules and/or prior knowledge to determine bonding (which would be relatively slow), PyMOL simply bonds every atom pair within some radius (probably excluding certain obvious cases, although I'm not sure). This is very fast, simple, and easily confused. I thought perhaps PyMOL can understand CONECT records in the PDB file - adding these might fix your problem, although I'm not sure how to generate them. Alternately, you can use the 'bond' and 'unbond' commands, but this can be non-trivial to do on a large scale. -Nat |
From: Thomas H. <sp...@us...> - 2012-05-24 05:55:53
|
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/pym...@li.../msg10413.html Cheers, Thomas Nat Echols wrote, On 05/23/12 20:01: > On Wed, May 23, 2012 at 10:20 AM, Rituparna Sengupta <rse...@wi...> 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 structure is not right. I didn't see much details though, except that the atom connections seem to be wrong. > > A screenshot would be helpful here, but my guess is that PyMOL's > automatic detection of bond's didn't work for your input structure. > This can happen for non-standard chemistries or distorted geometries; > the most frequent artifact is more bonds than are appropriate. The > reason it happens is that instead of applying some chemically sensible > rules and/or prior knowledge to determine bonding (which would be > relatively slow), PyMOL simply bonds every atom pair within some > radius (probably excluding certain obvious cases, although I'm not > sure). This is very fast, simple, and easily confused. > > I thought perhaps PyMOL can understand CONECT records in the PDB file > - adding these might fix your problem, although I'm not sure how to > generate them. Alternately, you can use the 'bond' and 'unbond' > commands, but this can be non-trivial to do on a large scale. > > -Nat -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |