[PyMOL] setting correct bond length

Dear all, I am trying to display a bound azetidine ring, but pymol is drawing also a bound between the C2 and C4 ring carbons. <<...OLE_Obj...>>bond length N-C 1.46Å, C-C 1.54Å and C2-C4 2.03Å !! See pymol picture attached. Is there a simple way of setting the bond length to be drawn corre

[PyMOL] (no subject)

dear all can we superimpose structures in pymolThanks & Regardssrilatha potlapellyMSc BiotechnologyDrug discovery, #450,4th D Main, 12th cross, Mahalakshmipuram - 560086 Bangalore Office: +9180-23495461-64  Extn.-1029

Re: [PyMOL] (no subject)

Hi try align or fit regards andrea 2006/3/3, srilath...@jubilantbiosys.com : > dear all > can we superimpose structures in pymol > Thanks & Regards > srilatha potlapelly > MSc Biotechnology > Drug discovery, > #450,4th D Main, 12th cross, > Mahalakshmipuram - 560086 > Bangalore > Office: +9180-2

Re: [PyMOL] setting correct bond length

try converting the coordinates into mol-format. On Friday 03 March 2006 13:05, Gerhardt, Stefan wrote: > Dear all, > > I am trying to display a bound azetidine ring, but pymol is drawing also a > bound between the C2 and C4 ring carbons. > > <<...OLE_Obj...>>bond length N-C 1.46Å, C-C 1.54Å a

RE: [PyMOL] setting correct bond length

Stefan, As recommended, I suggest loading the structure in using a file format that contains explicit connectivity information (MOL/SDF or MOL2). PyMOL generally does okay inferring protein connectivity from coordinates alone, but that is about it. another thing you can do is unbond the atoms

[PyMOL] CASTpyMOL Plugin

Greetings CASTpyMol Plugin Users: First, thank you to all the CASTpyMol users who have been using the plugin and have "encouraged" me to get a new version working. Like the PyMol project, I have been working to add improvements that to the plugin that hopefully will be of great value to the commu

[PyMOL] Arrows Too Short?

Hello all, I am using PyMOL V0.99pre06 (build from CVS repository) When viewing 1m6q.pdb (http://www.rcsb.org/pdb/files/1m6q.pdb) in cartoon mode, I think the arrows in beta sheet are rendered too short in comparison to other software (e.g. RasMOL). I posted this behavior already in the "bugs"-se

[PyMOL] Updated PyMOL v0.99 Release Candidate

Folks, These may be infamous last words, but I do believe that the latest PyMOL v0.99 release candidate has reached a level of stability, performance, and bug containment such that most everyone should feel comfortable downloading and updating to version 0.99. http://delsci.com/rel/099 Compared