@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 06
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
> https://pymolwiki.org/index.php/Launching_From_a_Script
>
> Cheers,
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 at 3:59 PM, Jed Goldstone
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 AM, Ahmad Abdelzaher
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, Ahmad Abdelzaher
> 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, Ahmad Abdelzaher
wrote:
> In the documentation, it said "atom selection. However i tried the
> following as you suggested:
>
> import __main__
> __main__.pymol_argv = ['pymol','
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:
> 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 an
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 only
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 Abdelz
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 the center of mass as a
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 wrote:
>
> I fin
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.
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