Hope it helps...<br>And thanks Elaine and Eric again! :)<br><br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">Îⳬ</b> <<a href="mailto:lynnwuchao@gmail.com" target="_blank">lynnwuchao@gmail.com</a>><br>
Date: 2008/2/23<br>Subject: [Chimera-users] distance<br>
To: Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" target="_blank">pett@cgl.ucsf.edu</a>><br>Cc: Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>>, Chimera BB <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a>><br>
<br><br>Thanks very much, Elaine and Eric!<br>Both of methods worked very well...<div><div></div><div><br><br><div class="gmail_quote">On Sat, Feb 23, 2008 at 4:00 AM, Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" target="_blank">pett@cgl.ucsf.edu</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">In particular, if you have a script (name "<a href="http://dist.com" target="_blank">dist.com</a>" for instance)<br>
that sets up your distance measurements, something like:<br>
<br>
dist :12@c :17@c<br>
dist :14@c :19@c<br>
<br>
Then you could run chimera like this:<br>
<br>
chimera --nostatus --nogui pdb:1gcn <a href="http://dist.com" target="_blank">dist.com</a> printDist.py<br>
<br>
to produce:<br>
<br>
#0:12.A@C <-> #0:17.A@C 8.74043923381<br>
#0:14.A@C <-> #0:19.A@C 8.19707020831<br>
<br>
on standard output. You could redirect the output into a file named<br>
"dist.out" with:<br>
<br>
chimera --nostatus --nogui pdb:1gcn <a href="http://dist.com" target="_blank">dist.com</a> printDist.py > dist.out<br>
<br>
--Eric<br>
<div><div></div><div><br>
On Feb 22, 2008, at 11:40 AM, Elaine Meng wrote:<br>
<br>
> Hi!<br>
> Eric has kindly provided a python script (attached at the bottom)<br>
> that will write all the current distance measurements to the Reply<br>
> Log. Just open the python file with Chimera and it will happen.<br>
><br>
> Alternatively, depending on your situation, you could use<br>
> "findclash," as discussed in these chimera-users messages a few<br>
> months ago:<br>
><br>
> <a href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-November/" target="_blank">http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-November/</a><br>
> 002061.html<br>
> <a href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-November/" target="_blank">http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-November/</a><br>
> 002069.html<br>
> <a href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-November/" target="_blank">http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-November/</a><br>
> 002070.html<br>
><br>
> I hope this helps,<br>
> Elaine<br>
> -----<br>
> Elaine C. Meng, Ph.D. <a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a><br>
> UCSF Computer Graphics Lab and Babbitt Lab<br>
> Department of Pharmaceutical Chemistry<br>
> University of California, San Francisco<br>
> <a href="http://www.cgl.ucsf.edu/home/meng/index.html" target="_blank">http://www.cgl.ucsf.edu/home/meng/index.html</a><br>
><br>
> On Feb 21, 2008, at 5:24 PM, Îⳬ wrote:<br>
><br>
>> Thanks, Elaine!<br>
>> The problem is that I want to automatically calculate a number of<br>
>> distances in non-gui interface, and sent the date to a file, just<br>
>> like the logfile.<br>
>> So is there a chance that I can achieve it using chimera?<br>
>><br>
>> On Fri, Feb 22, 2008 at 1:00 AM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>><br>
>> wrote:<br>
>><br>
>> The distances are listed in a separate dialog - choose "Tools...<br>
>> Structure Analysis... Distances" from the menu to open that dialog.<br>
>> You can adjust the number of decimal places in the measurement, and<br>
>> there is a "Save" button if you want to save distances or other<br>
>> measurements to a text file.<br>
><br>
</div></div>> <printDist.py><br>
<div>><br>
> _______________________________________________<br>
> Chimera-users mailing list<br>
> <a href="mailto:Chimera-users@cgl.ucsf.edu" target="_blank">Chimera-users@cgl.ucsf.edu</a><br>
</div>> <a href="http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users" target="_blank">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br>
<br>
</blockquote></div><br><br clear="all"><br></div></div><div><div></div><div>-- <br>Chao Wu<br><br>Currently:<br>National Institute of Biological Sciences, Beijing<br>Huang Niu's Lab<br><a href="http://www.nibs.ac.cn/" target="_blank">http://www.nibs.ac.cn/</a><br>
Tel: 80726688-8572<br>
Address: Beijing ZhongGuanCun Life Science Park, NO.7 Science Park East Road, NIBS B427<br>Postcode: 102206<br><br><br><br>Life Science Honors Program, China Agricultural University<br>PO.1055, NO.2 YuanMingYuan west road, Beingjing, 100094<br>
P.R. China<br>Tel: 86-10-62812484<br>E-mail: <a href="mailto:lynnwuchao@gmail.com" target="_blank">lynnwuchao@gmail.com</a>
</div></div></div><br><br clear="all"><br>-- <br>Chao Wu<br><br>Currently:<br>National Institute of Biological Sciences, Beijing<br>Huang Niu's Lab<br><a href="http://www.nibs.ac.cn/" target="_blank">http://www.nibs.ac.cn/</a><br>
Tel: 80726688-8572<br>
Address: Beijing ZhongGuanCun Life Science Park, NO.7 Science Park East Road, NIBS B427<br>Postcode: 102206<br><br><br><br>Life Science Honors Program, China Agricultural University<br>PO.1055, NO.2 YuanMingYuan west road, Beingjing, 100094<br>
P.R. China<br>Tel: 86-10-62812484<br>E-mail: <a href="mailto:lynnwuchao@gmail.com" target="_blank">lynnwuchao@gmail.com</a>