[Chimera-users] distance

Eric Pettersen pett at cgl.ucsf.edu
Fri Feb 22 12:00:11 PST 2008

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

dist :12 at c :17 at c
dist :14 at c :19 at c

Then you could run chimera like this:

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

to produce:

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


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 at 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, 吴超 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 at 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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