[Chimera-users] Chimera-users Digest, Vol 112, Issue 2

[vamsee]

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 at 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)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 1 Aug 2012 18:58:53 -0700
> From: Daniel Murin <cmurin at scripps.edu>
> To: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
> Subject: [Chimera-users] combining mrc maps
> Message-ID:
>         <
> 83025BE3F3B8D644AA9F8CAA21F2640801A3D700C402 at 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 at scripps.edu
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 2 Aug 2012 10:06:36 -0700
> From: Elaine Meng <meng at cgl.ucsf.edu>
> To: Daniel Murin <cmurin at scripps.edu>
> Cc: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] combining mrc maps
> Message-ID: <20D05B2F-142C-4433-B4A3-A8BAB0242919 at 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
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 02 Aug 2012 10:07:18 -0700
> From: Tom Goddard <goddard at sonic.net>
> To: Daniel Murin <cmurin at scripps.edu>
> Cc: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] combining mrc maps
> Message-ID: <501AB3C6.2050900 at 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
> >
>
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 02 Aug 2012 20:00:51 +0200
> From: "Marek Maly" <marek.maly at ujep.cz>
> To: chimera-users at cgl.ucsf.edu
> Subject: [Chimera-users] double bonds visualization ?
> Message-ID: <op.wifdnpi4lc8gdf at 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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> End of Chimera-users Digest, Vol 112, Issue 2
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