[PyMOL] pymol crashes when try opening a file created by gromacs

Hi! I am running a simulation using Gromacs. I was able to visualise the .pdb file using pymol. But when I tried to visuals the files created by Gromacs, pymol crashed. Can you please help? Thank you in advance! -- Regards, Raag

Re: [PyMOL] loop through many pdb files and show their centre of masses

Hi Zakir, The following script computes the Center Of Mass (or alternative the geometric center) and then draws a pseudoatom . I think you could adapt the script to your needs if you find difficulties, don’t hesitate to contact the list again (your qu

[PyMOL] loop through many pdb files and show their centre of masses

Hi there, I have no experience in scripting what so ever thus this simple task drives me nuts. I was using ZDOCK to dock my protein on the complex. It spits me out 2000 pdb files that each contain a ligand and receptor. Receptor position is fixed, ligand is not. What I want to show is just cent

Re: [PyMOL] can we show ligand in 2D?

Hi Albert, Probably you should check Pose_View Cheers, Osvaldo. On Mon, Sep 14, 2015 at 11:52 AM, Albert wrote: Hello: > > I've got a 3D coordinate in 3D. I am just wondering is it possible to > show it in 2D diagram in Pymol for a ligand so that

[PyMOL] can we show ligand in 2D?

Hello: I've got a 3D coordinate in 3D. I am just wondering is it possible to show it in 2D diagram in Pymol for a ligand so that we can get more clear idea how exactly the ligand looks like? thanks a lot Albert -- __

[PyMOL] on surface function in the setting

Dear All， For my windows version of pymol, I cannot locate the surface function under the setting button. Will you please tell me how can I make my surface cavity pocket function workable? Best regards. Smith--