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

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

Hi Tsjerk, What you said makes perfect sense. Since an atom could be considered as a point with uniform density, it's center of mass is indeed its position. Which, begs the question, what is the purpose of cmd.centerofmass() and how to calculate the center of mass of an entire structure (the

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

Hi Ahmad, The center of mass of an atom is its position. A function like cmd.centerofmass in the context of pymol only makes sense with a selection. E.g.: x,y,z = cmd.centerofmass('byres n. ca') print "COM of protein:", x, y, z Hope it helps, Tsjerk On Thu, Apr 6, 2017 at 6:30 AM, Ahmad

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

Well I'm assuming the selection goes in the argument of cmd.centerofmass(), however, does it have to be an atom? How should I calculate the center of mass for an entire protein? On Thu, Apr 6, 2017 at 4:48 AM, David Hall wrote: > It returns the x, y, and z coordinates of

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

It returns the x, y, and z coordinates of the center of mass as a list of 3 floats, presumably in that order? Is there another question? The page describes the arguments and their defaults so I am unsure what is lacking. -David > On Apr 5, 2017, at 10:29 PM, Ahmad Abdelzaher

[PyMOL] Calculating center of mass for the entire protein

I find the documentation about the python api here to be a bit lacking. https://pymolwiki.org/index.php/Centerofmass I would appreciate more info on how to use this: cmd.centerofmass() returns a list of 3 floats. --