[Chimera-users] distance in log

吴超 lynnwuchao at gmail.com
Thu Feb 28 00:10:09 PST 2008


Hope it helps...
And thanks Elaine and Eric again! :)

---------- Forwarded message ----------
From: 吴超 <lynnwuchao at gmail.com>
Date: 2008/2/23
Subject: [Chimera-users] distance
To: Eric Pettersen <pett at cgl.ucsf.edu>
Cc: Elaine Meng <meng at cgl.ucsf.edu>, Chimera BB <chimera-users at 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 at 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 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
>
> --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 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>
> >
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>


-- 
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 at 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 at gmail.com
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