Send Chimera-users mailing list submissions to
        chimera-users@cgl.ucsf.edu

To subscribe or unsubscribe via the World Wide Web, visit
        http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
or, via email, send a message with subject or body 'help' to
        chimera-users-request@cgl.ucsf.edu

You can reach the person managing the list at
        chimera-users-owner@cgl.ucsf.edu

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Chimera-users digest..."


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@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



------------------------------

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




------------------------------

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
>



------------------------------

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/


------------------------------

_______________________________________________
Chimera-users mailing list
Chimera-users@cgl.ucsf.edu
http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users


End of Chimera-users Digest, Vol 112, Issue 2
*********************************************