Hi,
I might be wrong, but might it be that you need the axis through the
structure that minimises the distance of all the points to it. Or, to
put it another way, the least-square-plane through the structure, the
normal to that plane, and a thir axis perpendicular to both.
If this is the case, yo
Sean,
orient selection
followed by a 90 degree rotation about the camera's ]X-axis should give you a
couple of views with the desired characteristics.
turn x, 90
Cheers,
Warren
From: gilleain torrance [mailto:gilleain.torra...@gmail.com]
Sent: Wed 6/3/2
Hi
Is there a way I can get the color of a given atom?
eg if I do
cmd.color( color, sele )
is there a function like
gotten_color = cmd.get_color_of_selection( sele )
so that something like
assert( gotten_color == color )
or atleast a function to get the color a given atom?
Many
Hello Warren,
Thank you very much for your advice.
I guess I was not being very clear. what i meant was that i would also
like to save the coordinates of this reoriented polymer. Let me be
clear:
I have a polymer aligned along y-axis. I change some of the dihedral
angles. As a result, the chain
The way I use (which I'm sure could be improved), is to get the color
index with "iterate sele, print color", followed by "print
cmd.get_color_index( idx )". This gives you the rgb tuple for the color
on 0-1 scale.
I'd be curious to know if there's a way to avoid the iterate step, or
get the col
Warren,
After a deja vu moment, I realized that I had posed a similar question to you
before about this (although, we didn't really have a resolution then). I had
already tried your suggestion before I had posted to the mailing list but
perhaps an example would be more appropriate in terms of
Matt,
Unfortunately, as a somewhat experienced PyMOL user, I already have
"orthoscopic view" turned off (along with depth cue turned off). Thanks for
your suggestion though.
Sean
> Subject: Re: [PyMOL] Principal Axes of Rotation
> To: magic...@hotmail.com
> CC: pymol-users@lists.sourceforge.
Sean Law wrote on 06/03/2009 12:52:45 PM:
> Warren,
>
> After a deja vu moment, I realized that I had posed a similar
> question to you before about this (although, we didn't really have a
> resolution then). I had already tried your suggestion before I had
> posted to the mailing list but per
Sean,
Apologies for not understanding...
You definitely need orthoscopic, but there's more to it.
set orthoscopic
fetch 1bna, async=0
orient 1bna
cmd.matrix_copy(None,"1bna")
reset
from chempy.cpv import average
cmd.origin(position=average(*cmd.get_extent()))
center origin
#
Great! I'll give that a try.
Sean
Subject: RE: [PyMOL] Principal Axes of Rotation
Date: Wed, 3 Jun 2009 12:55:51 -0700
From: war...@delsci.com
To: magic...@hotmail.com; matthew.frank...@imclone.com
CC: pymol-users@lists.sourceforge.net
Sean,
Apologies for not
understanding...
You
I would like to have distinct labels for hydrogen bond lengths on a
ball-and-stick image
with white background (as required for publication in a particular
journal). No matter
what I do, the labels come out washed out and usually light grey. This
includes
experimenting with label color, size and
Vivek,
Please see the example I posted today for Sean Law -- the cmd.matrix_copy
command embedded therein (followed by "reset") performs exactly the action
you're looking for.
Cheers,
Warren
From: Vivek Ranjan [mailto:vran...@gmail.com]
Sent: Wed 6/3/2009 9:
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