Dear All
I'm trying to figure out for myself, what the two labels 'Label > Atom
Identifiers > ID' and 'Label > Atom Identifiers > index' mean, or what
the respective difference between the two is. For sure, the numerical
value is very different when I show the labels in a structure. ID seems
to
...
-- Forwarded message --
From: Tsjerk Wassenaar
Date: Mon, Oct 25, 2010 at 12:39 PM
Subject: Re: [PyMOL] Question about Iterate and Edit-Mode
To: Martin Hediger
Hi Martin,
Without diving into the source, I think it is more like:
for i in selection:
execute(command, atom=
Never get used to that only-reply-to-sender policy...
-- Forwarded message --
From: Tsjerk Wassenaar
Date: Mon, Oct 25, 2010 at 12:30 PM
Subject: Re: [PyMOL] What is the difference between Atom ID and Index
To: Martin Hediger
Hi Martin,
ID is indeed the atom id from the coord
Thanks Tsjerk (on both occasions).
As a matter of fact, I'm kind of making a living out of writing a Python
script once in a while, so thats no worry ;)
What I was trying to get at was that I was trying to understand how
certain PyMOL scripts work, and naturally from that become able to
improve
Hi Martin & Tsjerk,
There is a another difference between the two aside from the
off-by-one characteristic. PyMOL has to keep track of atoms, so a
simple 'index' could work. But, then when the user removes an atom
from the middle of a structure, do we shift indices above it down?
(This could mak
Hi Martin,
You could think of it as what Tsjerk purported:
# pseudocode for iterate
def iterate(sel,cmd):
for x in selection:
return cmd(x)
where each 'function' cmd would return a value per atom.
For example,
# pseucode for an instance of iterate
def iterate(organic, 'print b')
for
Hi all,
I'm using PyMOL version 1.3 installed via Fink on my MacBook Pro with Snow
Leopard 10.6.4. I've noticed a strange OS-specific bug when using the
Spaces feature of my Mac while running PyMOL. If I attempt to change Space,
my system appears to do some sort of restart, without actually rest
Hi Tom - I’ve also experienced this behavior, which led me to a) attempt to
learn not to switch Spaces while using Fink-installed X11 PyMOL (other X11
programs, e.g. CCP4i, appear not to have the same issue); b) make all of my
figures using .pml scripts so that if I’ve changed something it’s alr
