Re: [PyMOL] Help with alignments/ more general create and align question

I don't want to hijack the thread but I was curious if you can point to few pymol features for generating and rotating molecules and how they would play with other tools. For example, if I just go download pdb files or take output from DFT, it may be easier to do analysis with certain alignments

Re: [PyMOL] Help with alignments

Hi Jon, align prot1 and chain A, prot2 and chain X 'super' and 'cealign' should work similarly. Cheers, -- Jason On Tue, Dec 11, 2012 at 7:35 AM, Jonathan Grimes wrote: > > I am wanting to align proteins based on superposition of > particular chains. Is it possible to do the superposition

[PyMOL] Help with alignments

I am wanting to align proteins based on superposition of particular chains. Is it possible to do the superposition based on the chains, but to move, in this case the entire complex ??? Thanks Jon Sent from my iPad -

Re: [PyMOL] make bond between two atoms

Hena, > I created two objects as follows: > > pseudoatom A1, pos=[10.0, 10.0, 100.0] > pseudoatom A2, pos=[10.0, 10.0, -200.0] > > I want to create a bond between these two atoms. Could you please help me? I > need to display a 2 fold axis passing through these points. You can create a distance m

[PyMOL] make bond between two atoms

Hi, I created two objects as follows: pseudoatom A1, pos=[10.0, 10.0, 100.0] pseudoatom A2, pos=[10.0, 10.0, -200.0] I want to create a bond between these two atoms. Could you please help me? I need to display a 2 fold axis passing through these points. I tried to use make and fuse command. Migh

[PyMOL] alignto command

is there a way of getting the alignto command to print out RMS deviations over the aligned regions of the structures. thanks jon Dr. Jonathan M. Grimes, NDM Senior Reseach Fellow University Research Lecturer Division of Structural Biology Wellcome Trust Centre for Human Genetic

Re: [PyMOL] Delete empty objects

Hi Vitaly, Try for i in cmd.get_object_list(): cmd.get_model(i).get_coord_list() or cmd.delete(i) Ciao! Tsjerk On Tue, Dec 11, 2012 at 9:31 AM, V.V. wrote: > Hello, > Is there a quick way to delete the objects that do not contain any atoms? > > Thank you in advance, > Vitaly > > >

[PyMOL] Delete empty objects

Hello, Is there a quick way to delete the objects that do not contain any atoms? Thank you in advance, Vitaly -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices a

Re: [PyMOL] Viewing PyMol in 3D

Hi PyMOLers We recently bought Asus V278H monitors, which displays nice stereo under Linux (Ubuntu 12.04). The monitors were bundled with Nvidia 3D vision v2 glasses. We have Quadro FX5800 cards, but we do NOT use the 3-pin stereo port, but rather the built-in emitter in the monitors. I have