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
#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
chimera --nostatus --nogui pdb:1gcn dist.com printDist.py > dist.out
On Feb 22, 2008, at 11:40 AM, Elaine Meng wrote:
> 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:
> I hope this helps,
> 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
> 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>
>> 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.
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
More information about the Chimera-users