Re: [Chimera-users] Chimera-users Digest, Vol 72, Issue 26
Sorry that I send my question to you directly by replying your last response in the mailing list. I have sent one to the chimera-users@cgl.ucsf.edu Mingjun
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Today's Topics:
1. Color Key (Elaine Meng) 2. Re: Color Key (Elaine Meng) 3. Re. Volume squeeze (Priyaranjan.Bhakat@csiro.au)
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Message: 1 Date: Thu, 23 Apr 2009 09:32:05 -0700 From: Elaine Meng <meng@cgl.ucsf.edu> Subject: [Chimera-users] Color Key To: YangMingjun <mjyang@dicp.ac.cn> Cc: Chimera-users <Chimera-users@cgl.ucsf.edu> Message-ID: <68DDED9E-E816-42B3-AEF3-6138C60F2BDA@cgl.ucsf.edu> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
Dear Mingjun, Oh, now I see -- you want a color key! Yes, you can do that in Chimera: choose Tools... Utilities... Color Key. In that dialog you can set the colors and the value labels. You can click and drag with the mouse to draw the key in the Chimera window. If you need more text, you can add it with 2D Labels, which is another tab on the same dialog as Color Key.
Here is the full description: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/ 2dlabels.html#colorkey>
and here is an example image with both Color Key and 2D Labels: <http://www.cgl.ucsf.edu/chimera/feature_highlights/2gbp-bfactor.png>
You would add that stuff while you are still in Chimera, and then when you save the image, it will be included. You might also be interested in this page on "tips" for making images: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/print.html#tips>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Apr 23, 2009, at 12:18 AM, YangMingjun wrote:
Dear Professor, Thanks so much. I am the first time to use Chimera so I am sorry that if my questions seem to be too simple... Sorry that I didn't describe my question clearly in last post. I had got the figure of 20 frames which are colored by using the command "rainbow models red, blue". Then I saved the figure with the file name a.png. Now I'd like to use the color range to denote each frame in the paper, e.g. color range from red to blue gradual changes corresponds to colors used by model 1 to 20 in the saved figure. Since I don't know what is the name it is should be called in English language, I send you an example in the attachment. Many thanks. Mingjun
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Message: 2 Date: Thu, 23 Apr 2009 10:34:06 -0700 From: Elaine Meng <meng@cgl.ucsf.edu> Subject: Re: [Chimera-users] Color Key To: YangMingjun <mjyang@dicp.ac.cn> Cc: Chimera-users BB <Chimera-users@cgl.ucsf.edu> Message-ID: <02C7876C-10D1-4B2D-B6C4-0619D6EC2065@cgl.ucsf.edu> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
I forgot to mention that you can drag colors from the squares in the Model Panel to the squares in the Color Key dialog. That is probably the easiest way to make the intermediate colors match. Best, Elaine
On Apr 23, 2009, at 9:32 AM, Elaine Meng wrote:
Dear Mingjun, Oh, now I see -- you want a color key! Yes, you can do that in Chimera: choose Tools... Utilities... Color Key. In that dialog you can set the colors and the value labels. You can click and drag with the mouse to draw the key in the Chimera window. If you need more text, you can add it with 2D Labels, which is another tab on the same dialog as Color Key.
Here is the full description: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/ 2dlabels.html#colorkey>
and here is an example image with both Color Key and 2D Labels: <http://www.cgl.ucsf.edu/chimera/feature_highlights/2gbp-bfactor.png>
You would add that stuff while you are still in Chimera, and then when you save the image, it will be included. You might also be interested in this page on "tips" for making images: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/print.html#tips>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Apr 23, 2009, at 12:18 AM, YangMingjun wrote:
Dear Professor, Thanks so much. I am the first time to use Chimera so I am sorry that if my questions seem to be too simple... Sorry that I didn't describe my question clearly in last post. I had got the figure of 20 frames which are colored by using the command "rainbow models red, blue". Then I saved the figure with the file name a.png. Now I'd like to use the color range to denote each frame in the paper, e.g. color range from red to blue gradual changes corresponds to colors used by model 1 to 20 in the saved figure. Since I don't know what is the name it is should be called in English language, I send you an example in the attachment. Many thanks. Mingjun
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Message: 3 Date: Thu, 23 Apr 2009 12:07:33 +1000 From: <Priyaranjan.Bhakat@csiro.au> Subject: [Chimera-users] Re. Volume squeeze To: <chimera-users@cgl.ucsf.edu> Message-ID: <DB072BAE3B16E3488CEF9F65E6D35B3F2E3CF42A@exvic-mbx01.nexus.csiro.au> Content-Type: text/plain; charset="us-ascii"
Hi, I was trying to overlay two volumes one from PDB and other from single particle reconstruction software EMAN (*.mrc). When I open EMAN generated 3D volume and then PDB file, EMAN 3D volume got reduce. However, when EMAN generated 3D volume is only in the 'volume viewer' screen, there is no change. Furthermore, if I press 'center' tab of 'volume viewer' volume became squeeze again. Alternatively, what the best way to overlay and compare two volumes. Thanks in advance for any clue, Priya
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YangMingjun