---------- Forwarded message ----------
From: Ові¬ <lynnwuchao@gmail.com>
Date: 2008/2/23
Subject: [Chimera-users] distance
To: Eric Pettersen <pett@cgl.ucsf.edu>
Cc: Elaine Meng <meng@cgl.ucsf.edu>, Chimera BB <chimera-users@cgl.ucsf.edu>

Thanks very much, Elaine and Eric!
Both of methods worked very well...

On Sat, Feb 23, 2008 at 4:00 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:

In particular, if you have a script (name "dist.com" for instance)
that sets up your distance measurements, something like:

dist :12@c :17@c
dist :14@c :19@c

Then you could run chimera like this:

chimera --nostatus --nogui pdb:1gcn dist.com printDist.py

to produce:

#0:12.A@C <-> #0:17.A@C 8.74043923381
#0:14.A@C <-> #0:19.A@C 8.19707020831

on standard output. You could redirect the output into a file named
"dist.out" with:

chimera --nostatus --nogui pdb:1gcn dist.com printDist.py > dist.out

--Eric

On Feb 22, 2008, at 11:40 AM, Elaine Meng wrote:

> Hi!
> Eric has kindly provided a python script (attached at the bottom)
> that will write all the current distance measurements to the Reply
> Log. Just open the python file with Chimera and it will happen.
>
> Alternatively, depending on your situation, you could use
> "findclash," as discussed in these chimera-users messages a few
> months ago:
>
> http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-November/
> 002061.html
> http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-November/
> 002069.html
> http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-November/
> 002070.html
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> http://www.cgl.ucsf.edu/home/meng/index.html
>
> On Feb 21, 2008, at 5:24 PM, Ові¬ wrote:
>
>> Thanks, Elaine!
>> The problem is that I want to automatically calculate a number of
>> distances in non-gui interface, and sent the date to a file, just
>> like the logfile.
>> So is there a chance that I can achieve it using chimera?
>>
>> On Fri, Feb 22, 2008 at 1:00 AM, Elaine Meng <meng@cgl.ucsf.edu>
>> wrote:
>>
>> The distances are listed in a separate dialog - choose "Tools...
>> Structure Analysis... Distances" from the menu to open that dialog.
>> You can adjust the number of decimal places in the measurement, and
>> there is a "Save" button if you want to save distances or other
>> measurements to a text file.
>

> <printDist.py>

>
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--
Chao Wu

Currently:
National Institute of Biological Sciences, Beijing
Huang Niu's Lab
http://www.nibs.ac.cn/
Tel: 80726688-8572
Address: Beijing ZhongGuanCun Life Science Park, NO.7 Science Park East Road, NIBS B427
Postcode: 102206

Life Science Honors Program, China Agricultural University
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E-mail: lynnwuchao@gmail.com