Hope it helps... And thanks Elaine and Eric again! :) ---------- Forwarded message ---------- From: 吴超 <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, 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@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 PO.1055, NO.2 YuanMingYuan west road, Beingjing, 100094 P.R. China Tel: 86-10-62812484 E-mail: lynnwuchao@gmail.com -- 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 PO.1055, NO.2 YuanMingYuan west road, Beingjing, 100094 P.R. China Tel: 86-10-62812484 E-mail: lynnwuchao@gmail.com