[Chimera-users] Chimera-users Digest, Vol 72, Issue 26
YangMingjun
mjyang at dicp.ac.cn
Thu Apr 23 18:47:10 PDT 2009
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 at 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 at csiro.au)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Thu, 23 Apr 2009 09:32:05 -0700
>From: Elaine Meng <meng at cgl.ucsf.edu>
>Subject: [Chimera-users] Color Key
>To: YangMingjun <mjyang at dicp.ac.cn>
>Cc: Chimera-users <Chimera-users at cgl.ucsf.edu>
>Message-ID: <68DDED9E-E816-42B3-AEF3-6138C60F2BDA at 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 at 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
>
>
>------------------------------
>
>Message: 2
>Date: Thu, 23 Apr 2009 10:34:06 -0700
>From: Elaine Meng <meng at cgl.ucsf.edu>
>Subject: Re: [Chimera-users] Color Key
>To: YangMingjun <mjyang at dicp.ac.cn>
>Cc: Chimera-users BB <Chimera-users at cgl.ucsf.edu>
>Message-ID: <02C7876C-10D1-4B2D-B6C4-0619D6EC2065 at 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 at 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 at cgl.ucsf.edu
>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
>
>------------------------------
>
>Message: 3
>Date: Thu, 23 Apr 2009 12:07:33 +1000
>From: <Priyaranjan.Bhakat at csiro.au>
>Subject: [Chimera-users] Re. Volume squeeze
>To: <chimera-users at cgl.ucsf.edu>
>Message-ID:
> <DB072BAE3B16E3488CEF9F65E6D35B3F2E3CF42A at 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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