Re: [Chimera-users] Chimera-users Digest, Vol 112, Issue 2
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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End of Chimera-users Digest, Vol 112, Issue 2 *********************************************
Hi Vamsee, You can use the "setattr" command (general command to set attribute values). It works on lots of things, including pseudobonds and pseudobond groups. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html> The command requires knowing the name of the attribute, its possible values, and whether it is an attribute of an individual pseudobond ("p" in the command) or the whole pseudobond group ("g). You can figure out all this stuff by looking in the GUI: Pseudobond attributes panel or the Selection Inspector, and using its balloon help (pop-up text when you put the mouse cursor over some option): <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/pbattrib.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/inspection.html> A few example commands: setattr g lineWidth 3 setattr g lineType 1 setattr p color hot pink setattr p label " " Those would change all pseudobonds, but you can limit the scope by specifying atoms at the end (meaning all pseudobonds with both endpoint atoms specified). 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 3, 2012, at 12:15 PM, vamsee wrote:
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
Hi Elaine, That helped immensely. Thank you -Vamsee On Fri, Aug 3, 2012 at 1:36 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Vamsee, You can use the "setattr" command (general command to set attribute values). It works on lots of things, including pseudobonds and pseudobond groups. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>
The command requires knowing the name of the attribute, its possible values, and whether it is an attribute of an individual pseudobond ("p" in the command) or the whole pseudobond group ("g).
You can figure out all this stuff by looking in the GUI: Pseudobond attributes panel or the Selection Inspector, and using its balloon help (pop-up text when you put the mouse cursor over some option): <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/pbattrib.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/inspection.html>
A few example commands:
setattr g lineWidth 3 setattr g lineType 1 setattr p color hot pink setattr p label " "
Those would change all pseudobonds, but you can limit the scope by specifying atoms at the end (meaning all pseudobonds with both endpoint atoms specified).
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 3, 2012, at 12:15 PM, vamsee wrote:
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
participants (2)
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Elaine Meng -
vamsee