Re: [PyMOL] Calculating center of mass for the entire protein

@Dr. Abdelzaher, Please don't feel terrible! Sorry to jump in to the thread. You have some of the nicest people around in this forum, especially, Dr. Holder and Dr.Wassenaar. Just remember to likewise offer to help newcomers and you will have played your part well. Regards, Rajib A Layperson On

Re: [PyMOL] Calculating center of mass for the entire protein

Oh, pymol.finish_launching() was missing, I feel so terrible now. Thanks a lot for your help. Regards. On Thu, Apr 6, 2017 at 4:36 PM, Thomas Holder wrote: > Hi Ahmad, > > I assume you don't launch PyMOL properly, please read >

Re: [PyMOL] Calculating center of mass for the entire protein

Hi Ahmad, I assume you don't launch PyMOL properly, please read https://pymolwiki.org/index.php/Launching_From_a_Script Cheers, Thomas On 06 Apr 2017, at 16:01, Ahmad Abdelzaher wrote: > I did remove it. I get the same error. > > Regards. > > On Thu, Apr 6, 2017

Re: [PyMOL] Calculating center of mass for the entire protein

I did remove it. I get the same error. Regards. On Thu, Apr 6, 2017 at 3:59 PM, Jed Goldstone wrote: > centerofmass 1a5m > works just fine for me from the console. > Try removing the ".pdb" from the command > "com = cmd.centerofmass('1a5m.pdb')" > > Jed > > On 4/6/2017 9:36

Re: [PyMOL] Calculating center of mass for the entire protein

I don't fully get what you mean, however, with or without the .pdb, I get the same error. On Thu, Apr 6, 2017 at 3:28 PM, João M. Damas wrote: > When you do the load, the .pdb is stripped off. The selection is 1a5m and > not 1a5m.pdb > > On Thu, Apr 6, 2017 at 3:18 PM,

Re: [PyMOL] Calculating center of mass for the entire protein

When you do the load, the .pdb is stripped off. The selection is 1a5m and not 1a5m.pdb On Thu, Apr 6, 2017 at 3:18 PM, Ahmad Abdelzaher wrote: > In the documentation, it said "atom selection. However i tried the > following as you suggested: > > import __main__ >

Re: [PyMOL] Calculating center of mass for the entire protein

In the documentation, it said "atom selection. However i tried the following as you suggested: import __main__ __main__.pymol_argv = ['pymol','-qc'] import pymol from pymol import cmd cmd.delete('all') cmd.load('1a5m.pdb') com = cmd.centerofmass('1a5m.pdb') print(com) I received the following:

Re: [PyMOL] Calculating center of mass for the entire protein

> how to calculate the center of mass of an entire structure Let's say I want the center of mas of the structure from the PDB 1vdd cmd.fetch('1vdd', async=0) cmd.centerofmass('1vdd') Now, I see 1vdd has a bunch of water molecules that I don't want in in my calculation cmd.centerofmass('1vdd