Hello, I am trying to script distance measurements (distance monitor) between the Calpha of a residue and a few Hydrogens. I have pretty much everything working except that I am not able to figure out how to change the attributes (color, line style etc..) of the distances (pseudo-bonds). I know it can be changed using the GUI but I would rather script it. Any suggestions? Thank you Vamsee On Thu, Aug 2, 2012 at 1:00 PM, <chimera-users-request@cgl.ucsf.edu> wrote:
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Today's Topics:
1. combining mrc maps (Daniel Murin) 2. Re: combining mrc maps (Elaine Meng) 3. Re: combining mrc maps (Tom Goddard) 4. double bonds visualization ? (Marek Maly)
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Message: 1 Date: Wed, 1 Aug 2012 18:58:53 -0700 From: Daniel Murin <cmurin@scripps.edu> To: "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu> Subject: [Chimera-users] combining mrc maps Message-ID: < 83025BE3F3B8D644AA9F8CAA21F2640801A3D700C402@EXCH-CCR01.lj.ad.scripps.edu>
Content-Type: text/plain; charset="us-ascii"
Hi,
I was wondering if it is possible to combine two mrc volumes into a single volume and save that as a new mrc file? I haven't really been able to find anything and I suspect that this may not be possible with Chimera.
Thank you for your help,
Daniel
Charles Daniel Murin Graduate Student - Ward/Ollmann-Saphire Labs Department of Molecular Biology Kellogg School of Science and Technology The Scripps Research Institute 10550 North Torrey Pines Road, CB 227 La Jolla, CA 92037
Work: 858.784.9053 Fax: 858.784.8218 email: cmurin@scripps.edu
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Message: 2 Date: Thu, 2 Aug 2012 10:06:36 -0700 From: Elaine Meng <meng@cgl.ucsf.edu> To: Daniel Murin <cmurin@scripps.edu> Cc: "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] combining mrc maps Message-ID: <20D05B2F-142C-4433-B4A3-A8BAB0242919@cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii
Hi Daniel, You can add or subtract maps to make a new map using the "vop" command:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html>
That command has various other filtering and scaling options that may also be of interest. You can save the new map to a file using the Volume Viewer dialog (its File menu) or the "volume" command.
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 1, 2012, at 6:58 PM, Daniel Murin wrote:
Hi, I was wondering if it is possible to combine two mrc volumes into a single volume and save that as a new mrc file? I haven't really been able to find anything and I suspect that this may not be possible with Chimera. Thank you for your help, Daniel
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Message: 3 Date: Thu, 02 Aug 2012 10:07:18 -0700 From: Tom Goddard <goddard@sonic.net> To: Daniel Murin <cmurin@scripps.edu> Cc: "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] combining mrc maps Message-ID: <501AB3C6.2050900@sonic.net> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Daniel,
Yes, just add the two map with the volume operation command
vop add #1,2
This will extend the grid of map #1 to cover map #2 then interpolate map #2 on that grid and add it. You may also want to scale the values of one map so that the two maps have comparable density ranges using the "scaleFactors" option.
http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/vop.html#add
Tom
Hi,
I was wondering if it is possible to combine two mrc volumes into a single volume and save that as a new mrc file? I haven't really been able to find anything and I suspect that this may not be possible with Chimera.
Thank you for your help,
Daniel
Charles Daniel Murin Graduate Student - Ward/Ollmann-Saphire Labs Department of Molecular Biology Kellogg School of Science and Technology The Scripps Research Institute 10550 North Torrey Pines Road, CB 227 La Jolla, CA 92037
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Message: 4 Date: Thu, 02 Aug 2012 20:00:51 +0200 From: "Marek Maly" <marek.maly@ujep.cz> To: chimera-users@cgl.ucsf.edu Subject: [Chimera-users] double bonds visualization ? Message-ID: <op.wifdnpi4lc8gdf@pocitadlon.ujep.cz> Content-Type: text/plain; charset=iso-8859-2; format=flowed; delsp=yes
Hello,
I am just curious if it is possible to visualize double bonds as double bonds now similarly like in case of rings one can visualize them nicely (aromatic ring/disc).
Thanks for the info in advance,
Best wishes,
Marek
-- Tato zpr?va byla vytvo?ena p?evratn?m po?tovn?m klientem Opery: http://www.opera.com/mail/
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