- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Color Key
by YangMingjun 24 Apr '09

24 Apr '09

Dear Professor, Thanks so much. It works well now. Mingjun >Hi Mingjun, >your version is very, very old. For Color Key you need at least the >last production release, version 1.3 from 2008. If you go to the >Chimera home page, > >http://www.cgl.ucsf.edu/chimera/index.html > >there are download links on the left, "production release" for the >most recent production release, and "daily builds" for even newer >ones if you want the things that are described in the "what's new" >link right next to "daily builds." There are release notes for each >version that say what is new in that version. Color Key was a new >feature in the 1.3 release. > >Your version is so old it might not even have those color squares in >the Model Panel that I mentioned before! >Best, >Elaine > > >On Apr 23, 2009, at 6:45 PM, YangMingjun wrote: > >> Dear Professor, >> >> Thanks very much. >> I can't find the Color Key icon in my installed Chimera >> following the step in the link. Is it due to the version I am using? >> I am using Windows os and chimera-1[1].2422-win32.exe >.

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Re: [Chimera-users] Color Key
by YangMingjun 23 Apr '09

23 Apr '09

Dear Professor, Thanks very much. I can't find the Color Key icon in my installed Chimera following the step in the link. Is it due to the version I am using? I am using Windows os and chimera-1[1].2422-win32.exe Mingjun >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(a)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(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > >.

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Re: [Chimera-users] Chimera-users Digest, Vol 72, Issue 26
by YangMingjun 23 Apr '09

23 Apr '09

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(a)cgl.ucsf.edu Mingjun >Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > >To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > >You can reach the person managing the list at > chimera-users-owner(a)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. Color Key (Elaine Meng) > 2. Re: Color Key (Elaine Meng) > 3. Re. Volume squeeze (Priyaranjan.Bhakat(a)csiro.au) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Thu, 23 Apr 2009 09:32:05 -0700 >From: Elaine Meng <meng(a)cgl.ucsf.edu> >Subject: [Chimera-users] Color Key >To: YangMingjun <mjyang(a)dicp.ac.cn> >Cc: Chimera-users <Chimera-users(a)cgl.ucsf.edu> >Message-ID: <68DDED9E-E816-42B3-AEF3-6138C60F2BDA(a)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(a)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(a)cgl.ucsf.edu> >Subject: Re: [Chimera-users] Color Key >To: YangMingjun <mjyang(a)dicp.ac.cn> >Cc: Chimera-users BB <Chimera-users(a)cgl.ucsf.edu> >Message-ID: <02C7876C-10D1-4B2D-B6C4-0619D6EC2065(a)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(a)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(a)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(a)csiro.au> >Subject: [Chimera-users] Re. Volume squeeze >To: <chimera-users(a)cgl.ucsf.edu> >Message-ID: > <DB072BAE3B16E3488CEF9F65E6D35B3F2E3CF42A(a)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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Re. Volume squeeze
by Priyaranjan.Bhakat＠csiro.au 23 Apr '09

23 Apr '09

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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transition command
by Eaazhisai Kandiah 23 Apr '09

23 Apr '09

Hi, I found the answer for the transition command. Actually It has been discussed in the forum before. It is in the Experimental features site and under Animation commands. Will try that. Sorry about repeating the question. Eaazhisai Kandiah Laboratory of Structural Biology NIAMS, National Institutes of Health, Room 1511,Bldg 50 9000 Rockville Pike, Bethesda, MD-20892 kandiahe(a)mail.nih.gov Off: 301 451 2281 Fax: 301 480 7629

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transition command
by Eaazhisai Kandiah 23 Apr '09

23 Apr '09

Hello Developers, I would like to use the transition command to travel through the radius of an icosahedron surface. The builds and release I have, do not recognize the command 'transition'. Could you please tell me which version/build of chimera I should be using for this command? Thanks a lot, Eaazhisai Kandiah Laboratory of Structural Biology NIAMS, National Institutes of Health, Room 1511,Bldg 50 9000 Rockville Pike, Bethesda, MD-20892 kandiahe(a)mail.nih.gov Off: 301 451 2281 Fax: 301 480 7629

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Re: [Chimera-users] (no subject)
by YangMingjun 23 Apr '09

23 Apr '09

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 >Dear Mingjun, >After the rainbow-coloring, open the Model Panel (under Favorites in >the menu). There it will show the color for each model in a square. >If you click any of those squares, called "color wells," it will >bring up the color panel (Color Editor) set to that color. >I hope this helps, >Elaine >----- >Elaine C. Meng, Ph.D. meng(a)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 22, 2009, at 6:54 PM, YangMingjun wrote: > >> Dear Professor, >> Thanks very much for your detailed instruction. >> If I use rainbow models red,blue >> then can Chimera produce a color panel to denote the colors used? >> Thanks >> Mingjun >> >.

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(no subject)
by YangMingjun 22 Apr '09

22 Apr '09

Dear Professor, Thanks very much for your detailed instruction. If I use rainbow models red,blue then can Chimera produce a color panel to denote the colors used? Thanks Mingjun > Dear Professor, > I am going to use Chimera to plot 20 molecular frames (saved in > 10 files with the file name frame_$n.pdb) in one figure and have a > question about the color scheme. I'd like to check the > conformational changes from frame 1 to frame 20. Can you please tell > me how to color the frames, e.g. with gradual change of each frame > in color from red to blue ? > Does Chimera adopt a default method to color an ensemble of > structures when loaded? > Thanks so much. > Mingjun > Dear Mingjun, There isn't really a default just for ensembles. The default behavior is to use a different color for each "model" (generally each structure file makes one model). It is in the preferences, New Molecules category: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Mole… > You can use "rainbow" for coloring different models or chains or residues, gradually changing from one color to another. You can use either the "rainbow" command or the "Rainbow" graphical interface. For graphical interface, choose Tools... Depiction... Rainbow. In your case you would want to use the "model" option. You can change the colors by clicking the squares and using the Color Editor. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rainbow/rainbow.ht… > Similarly, you could just use the command "rainbow models" to use the default coloring, but there are additional keywords to use different colors. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rainbow.html> For example, if you really only want red->blue and not all the rainbow colors in between, the command would be rainbow models red,blue Here are the built-in color names: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/colortables.html#allcolors > For asking Chimera questions, please send mail to chimera-user at cgl.ucsf.edu and not to me directly, unless you are sending private data. 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

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[Chimera Help] Multiple Instances
by cdlau＠ucsd.edu 22 Apr '09

22 Apr '09

Dear Madam/Sir, I found this from a response 5 years ago in 2004 > As it works now, if you wish to send commands to an already running > Chimera, you cannot specify which instance of Chimera. So it is not > possible to communicate with multiple instances of Chimera as you might > want to support multiple web sessions. Dan Greenblatt may have ideas > for addressing this. > > Tom I was wondering if this is still the case. I am interested in running multiple instances of Chimera on a Tiled Wall Display and have global control over all the instances. Does anyone have any suggestions or resources for me to look into? Thanks in advance, Christoper

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Re: [Chimera-users] Straighten a helix
by Elaine Meng 22 Apr '09

22 Apr '09

Hi Francesco, You don't have to give the atom names for each residue, e.g. how about match #0:24-30 #1:24-30 (assuming these residues have equal numbers of atoms with the same names in the two structures) or match #0:24-30@n,ca,c,o #1:24-30@n,ca,c,o or match #0:24-30@ca #1:24-30@ca You may want to try the "iterate" option of the match command. You could use matchmaker instead of match, but that would use the whole chain rather than specific residues, so I doubt it fits your situation. Here is a discussion of the different ways to match things in Chimera: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html> Elaine ----- Elaine C. Meng, Ph.D. meng(a)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 22, 2009, at 10:32 AM, Francesco Pietra wrote: > Elaine: > I have found a way to get a nearly perfect alpha helix from what was a > bent alpha helix by imposing the phi and psi angles where they were > out of the norm. However, both the barycenter and the orientation of > the rectified helix have changed, so that it does no more fit its > partners. > > What I would like to do is using the Chimera "match" command to > superimpose the rectified helix to the bent helix, then remove the > bent helix and save pdb. Surely clashes will be there but perhaps not > so many to hinder MD. Is there a short command to tell to Chimera to > do the job without having to list atom per atom. The helix is long and > trial and errors will be many...it is not laziness alone. > > Or is anything better in Chimera than the match command? > thanks > francesco

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