[Chimera-users] sequence viewer
Gatsogiannis, Christos
gatsogia at uni-mainz.de
Wed Dec 17 17:05:49 PST 2008
Hi all,
i ve just installed the latest daily build version and i´ve noticed that the sequence viewer has a new "look".
However, i have difficulties to get used to it...
Some examples:
-when i want to view the sequence of a pdb file containing seven chains, i get seven different pop-up windows (...) showing the sequences corresponding to the seven different chain ID´s....
-Moreover, it isn´t so "easy" anymore to select aminoacids directly in the sequence viewer (e.g. too many colors) and therefore now i´m selecting residues using only the command line..
My colleagues also prefer the older version..
is there a simple way to install the latest chimera version but keep the old version of the sequence viewer?
Thanks!
-Christos
-------------------------------
Christos Gatsogiannis
Insitute of Zoology, Dpt. II
cryoEM Lab, AG Markl
Joh. v. Müllerweg 6
Johannes Gutenberg University
Mainz, Germany
+49-6131-3923091
-------------------------------
________________________________________
Von: chimera-users-bounces at cgl.ucsf.edu [chimera-users-bounces at cgl.ucsf.edu] im Auftrag von chimera-users-request at cgl.ucsf.edu [chimera-users-request at cgl.ucsf.edu]
Gesendet: Mittwoch, 17. Dezember 2008 21:00
An: chimera-users at cgl.ucsf.edu
Betreff: Chimera-users Digest, Vol 68, Issue 22
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Today's Topics:
1. Re: (Thermal ellipsoids) anisotropic temperature factor
ellipsoids (Eric Pettersen)
2. Re: (Thermal ellipsoids) anisotropic temperature factor
ellipsoids (Eric Pettersen)
3. possibilities to save parts of models (selection)?
(Sebastian Kruggel)
4. Re: possibilities to save parts of models (selection)?
(Elaine Meng)
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Message: 1
Date: Tue, 16 Dec 2008 14:59:34 -0800
From: Eric Pettersen <pett at cgl.ucsf.edu>
Subject: Re: [Chimera-users] (Thermal ellipsoids) anisotropic
temperature factor ellipsoids
To: Tom Goddard <goddard at cgl.ucsf.edu>
Cc: 'Chimera BB' <chimera-users at cgl.ucsf.edu>
Message-ID: <9A34751B-6356-4AF4-A8C7-31757E5FFBF1 at cgl.ucsf.edu>
Content-Type: text/plain; charset="us-ascii"
On Dec 12, 2008, at 10:40 AM, Tom Goddard wrote:
> Hi David,
>
> Ok I see now, it's a matter of choosing the size of each ellipsoid to
> have a 50% chance of finding the atom in that volume. This
> shouldn't be
> too hard but I'll let Eric tackle it if he has time.
Hi David,
This is one of those things that I'll endeavor to get into Chimera's
production version of thermal ellipsoids, but that I can't spare the
time for until then. My guess is that the eigenvectors/values of the
U matrix are at the 50% probability level, but verifying that would
require some research. If you do look into and find that that's not
the case, just change the setting of the 'scale' variable of the start
of the script to change the ellipsoid sizes to whatever size encloses
50%.
--Eric
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Message: 2
Date: Tue, 16 Dec 2008 15:29:15 -0800
From: Eric Pettersen <pett at cgl.ucsf.edu>
Subject: Re: [Chimera-users] (Thermal ellipsoids) anisotropic
temperature factor ellipsoids
To: David Chenoweth <dchen at caltech.edu>
Cc: Chimera BB <chimera-users at cgl.ucsf.edu>
Message-ID: <A5D8EC26-B4C9-4FA4-9D96-9E327D4FA16A at cgl.ucsf.edu>
Content-Type: text/plain; charset="us-ascii"
On Dec 11, 2008, at 3:43 PM, David Chenoweth wrote:
> Hi Eric,
> Thank you very much for the ellipsoid script! I really appreciate
> your help and I think this will do the trick for now. I have been
> learning some python on my own and I was wondering if you have some
> good beginner examples of scripts for making geometrical shapes,
> changing size and color, orientation, etc. that work in chimera.
Hi David,
You can show cones, arrows, boxes, and a variety of simple geometric
shapes by opening a BILD format file in Chimera: BILD format. It may
be a little awkward having a script write a temporary file, so instead
you can use a StringIO object, as described here: [Chimera-users] BILD
object question
You can also use the 'shape' command to draw spheres, cylinders, and
icosahedrons. You can run any Chimera command from Python by using
Chimera's 'runCommand' function, e.g.:
from chimera import runCommand
runCommand("shape sphere center ligand color dodger blue radius 25")
Feel free to ask more questions!
--Eric
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Message: 3
Date: Wed, 17 Dec 2008 10:14:54 +0100
From: Sebastian Kruggel <kruggel at chemie.uni-hamburg.de>
Subject: [Chimera-users] possibilities to save parts of models
(selection)?
To: chimera-users at cgl.ucsf.edu
Message-ID: <4948C30E.6090706 at chemie.uni-hamburg.de>
Content-Type: text/plain; charset=ISO-8859-15; format=flowed
Hi all,
is there a simple way to save incomplete models (eg the
current selection)? The write command seems to work only
with complete models and not with atomic specifications and
the split command does only give me the possibility to split
complete chains.
Probabaly I just don't see something *very* easy...
Thanks for help!
Sebastian
--
Sebastian Kruggel
Institut f?r Pharmazie
Bundesstr. 45 | Raum 112
D 20146 Hamburg
Tel +49(0) 40 42838 3626
------------------------------
Message: 4
Date: Wed, 17 Dec 2008 09:17:15 -0800
From: Elaine Meng <meng at cgl.ucsf.edu>
Subject: Re: [Chimera-users] possibilities to save parts of models
(selection)?
To: Sebastian Kruggel <kruggel at chemie.uni-hamburg.de>
Cc: chimera-users at cgl.ucsf.edu
Message-ID: <D4D992B7-BC06-4BB0-80D6-AE698FE01213 at cgl.ucsf.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
Hi Sebastian,
The write command has a "selected" option to write only the selected
atoms, and a "displayed" option to write only the displayed atoms:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html>
There are analogous options on the GUI (File... Save PDB).
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
http://www.cgl.ucsf.edu/home/meng/index.html
On Dec 17, 2008, at 1:14 AM, Sebastian Kruggel wrote:
> Hi all,
> is there a simple way to save incomplete models (eg the
> current selection)? The write command seems to work only
> with complete models and not with atomic specifications and
> the split command does only give me the possibility to split
> complete chains.
> Probabaly I just don't see something *very* easy...
> Thanks for help!
> Sebastian
------------------------------
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