[PyMOL] Capping the ends of peptides

Dear All, I made a tripeptide of the form gly-X-gly using the Build function. The amino end has a single hydrogen on the nitrogen, and the carboxyl end has only one oxygen so that additional amino acids could be added to it.  How do I make the amino end into an -NH3with a plus charge and the

[PyMOL] Installing in Linux

Greetings, I've downloaded the Pymol package of executable files and had no trouble installing in Windows but don't know how to proceed in Linux? Can anyone point me in the right direction? Thanks, Peter -- Peter C. Kahn, Ph.D. Professor of Biochemistry Department of Biochemistry & Microbiol

Re: [PyMOL] How to show that one docking is better than another with Pymol visually

Hello, Try calculating the solvent accessible surface areas of the docked and undocked molecules, including the ligand. Color atoms whose water accessible surfaces are reduced or eliminated by the docking differently from the rest of the structures. As an added feature, you might color occlu

[PyMOL] Embedding a pymol window within a Powerpoint slide

Dear All, How can I embed a Pymol window within a Powerpoint slide that has other material in the slide? Thanks, -- Peter C. Kahn, Ph.D. Professor of Biochemistry Department of Biochemistry & Microbiology Rutgers University 76 Lipman Drive New Brunswick, NJ 08901 Telephone: 848-932-5618 Tele

Re: [PyMOL] Backbone RMSD

until it finds no further statistical reason to remove any more.If you want only an alignment that uses all CA atoms, you can restrict the calculation to one iteration as follows: PyMOL>super PDBfile1CA, PDBfile2CA, cycles=0 Then save the aligned files as above. Peter Kahn On 9/1

[PyMOL] Installation problem

Dear All: Help! Re-installing Pymol 1.7.0.5 after uninstalling failed with the following error: "Pymol 64 bit setup:Object already exists." When I pressed OK, the following message appeared: "Setup wizard ended prematurely because of an error. To install at a later time run setup wizard aga