Re: [PyMOL] color by element

[Gerebtzoff, Gregori]

What I personally do is:

cmd.color(grey50,all)
util.cnc(all)

So that my carbons have the color I wish (grey50), and other atoms are colored 
by element.

Best,

Greg


-Original Message-
From: David Hall [mailto:li...@cowsandmilk.net] 
Sent: Wednesday, February 10, 2010 1:45 AM
To: Ariel Talavera
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] color by element

First of all, there is:
color atomic
which will do all the colors and for whatever reason does green for carbons

Additionally, there's a general class of util.cba? where question mark
is replaced by one letter representing the color of carbon.  I've been
told by people that these are supposed to be internal commands and I
shouldn't use them, but I do and they've been there as long as I've
used pymol.

Currently, these are:
util.cbab for slate
util.cbag for green
util.cbam for magenta
util.cbap for purple
util.cbaw for white
util.cbac for cyan
util.cbak for pink
util.cbao for orange
util.cbas for salmon
util.cbay for yellow

You can see how these are implemented in
http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol/modules/pymol/util.py?view=markup
if you want to make your own custom versions.

-David Hall

On Tue, Feb 9, 2010 at 5:46 PM, Ariel Talavera talav...@cim.sld.cu wrote:
 Hi Pymolers,

 How can I use the color by element (HNOS) function present in the GUI,
 in a script?

 Thanks in advanced,

 Best,
 Ariel

 --
 *
 Ariel Talavera Pérez, PhD
 Center of Molecular Immunology
 calle 216 esq. A 15, Atabey, Playa
 Havana 11600, CUBA
 tel: (53-7) 271 7933, ext. 221
 fax: (53-7) 272 0644
 email: talav...@cim.sld.cu
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[PyMOL] pml script execution speed

[Michael Zimmermann]

Dear PyMOL users,

I have noticed a few times now that when I run a .pml script from a
function (i.e. MATLAB generates a .pml file and then does a system
call for PyMOL to run it) or in batch mode (.bat file that just calls
PyMOL.exe -c -u file.pml) and if I am taking pictures with png
then it runs considerably slower than if I open the GUI and run the
script.  I'm doing this to automate frame generation for movie making.
 Any idea why this would be and how to make the system call at least
as fast as running the GUI?

I use:
Windows XP 64-bit SP2
PyMOL v. 1.2r1

-- 
Michael Zimmermann
Ph.D. student in Bioinformatics and Computational Biology
Department of Biochemistry, Biophysics and Molecular Biology
Iowa State University

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[PyMOL] Showing electric field lines

[Michael Lerner]

Hi all,

Someone recently asked me if there was a way to display field lines with
PyMOL or with an external plugin. Here's what I wrote:

It turns out that PyMOL recently grew the ability to display field lines.
After you've run APBS, you'll have a map object called pymol-generated. Try
this series of commands from the PyMOL prompt:

gradient my_grad, pymol-generated
ramp_new my_grad_ramp, pymol-generated
color my_grad_ramp, my_grad

I'm considering building this into the next version of the plugin.

Cheers,

-Michael

-- 
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IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
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