Re: [Chimera-users] [chimera-dev] Hello~ how to make a 3D structure for a number of family genes
Hi Tao Zhao, Chimera does not do homology modeling directly, but it can connect to a web server running the Modeller program. To use this feature, you would first need to go to the Modeller web site and sign up for a license key <http://www.salilab.org/modeller/registration.html> -- it is free for noncommercial use. A full explanation of homology modeling is not feasible for this mailing list (there are probably several books and thousands of papers on this topic), but for a description of the Modeller interface in Chimera, see: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#comparative> ... and for more about how to get the input ready... it sounds like you are "Starting with a structure already known to be a suitable template": <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#approaches> There is also a tutorial, but be aware that it is only one example, and the process may be different depending on your protein of interest and what is known about it. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html> 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 P.S. better to send questions about using Chimera to chimera-users@cgl.ucsf.edu (CC'd on this message), not chimera-dev@cgl.ucsf.edu which is meant for programmers On Dec 2, 2012, at 10:21 PM, tao zhao wrote:
Hello, I am new to chinmera, this tool seems really powerful. Here is my question, I want to build a structure for a number of peptide sequences, all belongs to the AP2 family. It has one homology NMR model, PDB ID: 1gcc. And I don't know what to do next.
Could you please give me some instruction? Thank you very much.
Tao Zhao Northwest A&F University,Yangling, China
I forgot to say: you should use Chimera version 1.7 for these calculations. The Modeller interface has been improved since version 1.6, and the manual and tutorial links below describe version 1.7. Chimera 1.7 is available as snapshot and daily builds: <http://www.cgl.ucsf.edu/chimera/download.html#snapshots> <http://www.cgl.ucsf.edu/chimera/download.html#daily> Best, Elaine On Dec 3, 2012, at 3:56 PM, Elaine Meng wrote:
Hi Tao Zhao, Chimera does not do homology modeling directly, but it can connect to a web server running the Modeller program. To use this feature, you would first need to go to the Modeller web site and sign up for a license key <http://www.salilab.org/modeller/registration.html> -- it is free for noncommercial use.
A full explanation of homology modeling is not feasible for this mailing list (there are probably several books and thousands of papers on this topic), but for a description of the Modeller interface in Chimera, see:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#comparative>
... and for more about how to get the input ready... it sounds like you are "Starting with a structure already known to be a suitable template": <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#approaches>
There is also a tutorial, but be aware that it is only one example, and the process may be different depending on your protein of interest and what is known about it. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html>
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
P.S. better to send questions about using Chimera to chimera-users@cgl.ucsf.edu (CC'd on this message), not chimera-dev@cgl.ucsf.edu which is meant for programmers
On Dec 2, 2012, at 10:21 PM, tao zhao wrote:
Hello, I am new to chinmera, this tool seems really powerful. Here is my question, I want to build a structure for a number of peptide sequences, all belongs to the AP2 family. It has one homology NMR model, PDB ID: 1gcc. And I don't know what to do next.
Could you please give me some instruction? Thank you very much.
Tao Zhao Northwest A&F University,Yangling, China
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
That's very kind of you, thank you very much!I read the websites you gave me and can get a model from one sequence based on the templete now.and what I really want to do is to construct a conserved model of all 35 sequences in this gene family.The final picuture can have different colors in the different regions, showing various conservation.I can't manage this right now. Best regardsTao
Subject: Re: [Chimera-users] [chimera-dev] Hello~ how to make a 3D structure for a number of family genes From: meng@cgl.ucsf.edu Date: Mon, 3 Dec 2012 16:00:11 -0800 CC: chimera-users@cgl.ucsf.edu To: zhaotaoshine@hotmail.com
I forgot to say: you should use Chimera version 1.7 for these calculations. The Modeller interface has been improved since version 1.6, and the manual and tutorial links below describe version 1.7.
Chimera 1.7 is available as snapshot and daily builds: <http://www.cgl.ucsf.edu/chimera/download.html#snapshots> <http://www.cgl.ucsf.edu/chimera/download.html#daily>
Best, Elaine
On Dec 3, 2012, at 3:56 PM, Elaine Meng wrote:
Hi Tao Zhao, Chimera does not do homology modeling directly, but it can connect to a web server running the Modeller program. To use this feature, you would first need to go to the Modeller web site and sign up for a license key <http://www.salilab.org/modeller/registration.html> -- it is free for noncommercial use.
A full explanation of homology modeling is not feasible for this mailing list (there are probably several books and thousands of papers on this topic), but for a description of the Modeller interface in Chimera, see:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#comparative>
... and for more about how to get the input ready... it sounds like you are "Starting with a structure already known to be a suitable template": <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#approaches>
There is also a tutorial, but be aware that it is only one example, and the process may be different depending on your protein of interest and what is known about it. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html>
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
P.S. better to send questions about using Chimera to chimera-users@cgl.ucsf.edu (CC'd on this message), not chimera-dev@cgl.ucsf.edu which is meant for programmers
On Dec 2, 2012, at 10:21 PM, tao zhao wrote:
Hello, I am new to chinmera, this tool seems really powerful. Here is my question, I want to build a structure for a number of peptide sequences, all belongs to the AP2 family. It has one homology NMR model, PDB ID: 1gcc. And I don't know what to do next.
Could you please give me some instruction? Thank you very much.
Tao Zhao Northwest A&F University,Yangling, China
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Tao, If you wanted a 3D model of each different protein you would just repeat the Modeller process 35 times. However, it sounds like maybe instead you want to color one structure to show sequence conservation in the family. In that case you would need: (1) one 3D structure, which you already made (or maybe even just the template structure would work) (2) a sequence alignment containing the 35 sequences Although you can add sequences one by one to make a sequence alignment in Chimera, I would not recommend it for your 35 sequences -- instead use some sequence alignment program to align them, or get a sequence alignment for the proteins in that family from a database (if possible). Some ways to get sequence alignments are listed here: <http://www.cgl.ucsf.edu/home/meng/sources.html> ... some sequence alignment webservers are listed at the bottom: <http://www.cgl.ucsf.edu/home/meng/sources.html#d> Chimera understands many sequence alignment formats, and sequence alignments are automatically shown in the Multalign Viewer tool. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#alignment> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html> You can open both files in Chimera (the 3D structure and the sequence alignment). The structure should automatically associate with the alignment, <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#association> but if it doesn't happen automatically, you can associate it manually using "Structure...Associations" in the sequence window menu. Then you can color the structure to show the conservation in the alignment, see "Structure.... Render by Conservation" in the sequence window menu. There is also an example of conservation coloring at the bottom of this tutorial: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/super.html> 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 Dec 3, 2012, at 10:18 PM, tao zhao wrote:
That's very kind of you, thank you very much! I read the websites you gave me and can get a model from one sequence based on the templete now. and what I really want to do is to construct a conserved model of all 35 sequences in this gene family. The final picuture can have different colors in the different regions, showing various conservation. I can't manage this right now. Best regards Tao
I can do it now.Thank you so much for your help! You really save me a lot of time. Thank you and Merry Christmas. Best regards,Tao.
Subject: Re: [Chimera-users] Hello~ how to make a 3D structure for a number of family genes From: meng@cgl.ucsf.edu Date: Tue, 4 Dec 2012 15:58:53 -0800 CC: chimera-users@cgl.ucsf.edu To: zhaotaoshine@hotmail.com
Hi Tao, If you wanted a 3D model of each different protein you would just repeat the Modeller process 35 times.
However, it sounds like maybe instead you want to color one structure to show sequence conservation in the family. In that case you would need:
(1) one 3D structure, which you already made (or maybe even just the template structure would work) (2) a sequence alignment containing the 35 sequences
Although you can add sequences one by one to make a sequence alignment in Chimera, I would not recommend it for your 35 sequences -- instead use some sequence alignment program to align them, or get a sequence alignment for the proteins in that family from a database (if possible). Some ways to get sequence alignments are listed here: <http://www.cgl.ucsf.edu/home/meng/sources.html> ... some sequence alignment webservers are listed at the bottom: <http://www.cgl.ucsf.edu/home/meng/sources.html#d>
Chimera understands many sequence alignment formats, and sequence alignments are automatically shown in the Multalign Viewer tool. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#alignment> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html>
You can open both files in Chimera (the 3D structure and the sequence alignment). The structure should automatically associate with the alignment, <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#association> but if it doesn't happen automatically, you can associate it manually using "Structure...Associations" in the sequence window menu.
Then you can color the structure to show the conservation in the alignment, see "Structure.... Render by Conservation" in the sequence window menu. There is also an example of conservation coloring at the bottom of this tutorial: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/super.html>
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 Dec 3, 2012, at 10:18 PM, tao zhao wrote:
That's very kind of you, thank you very much! I read the websites you gave me and can get a model from one sequence based on the templete now. and what I really want to do is to construct a conserved model of all 35 sequences in this gene family. The final picuture can have different colors in the different regions, showing various conservation. I can't manage this right now. Best regards Tao
That's great! I'm glad you understood it so quickly! Merry Christmas to you too, Elaine On Dec 4, 2012, at 11:55 PM, tao zhao wrote:
I can do it now. Thank you so much for your help! You really save me a lot of time. Thank you and Merry Christmas.
Best regards, Tao.
Subject: Re: [Chimera-users] Hello~ how to make a 3D structure for a number of family genes From: meng@cgl.ucsf.edu Date: Tue, 4 Dec 2012 15:58:53 -0800 CC: chimera-users@cgl.ucsf.edu To: zhaotaoshine@hotmail.com
Hi Tao, If you wanted a 3D model of each different protein you would just repeat the Modeller process 35 times.
However, it sounds like maybe instead you want to color one structure to show sequence conservation in the family. In that case you would need: ! > (1) one 3D structure, which you already made (or maybe even just the template structure would work) (2) a sequence alignment containing the 35 sequences
Although you can add sequences one by one to make a sequence alignment in Chimera, I would not recommend it for your 35 sequences -- instead use some sequence alignment program to align them, or get a sequence alignment for the proteins in that family from a database (if possible). Some ways to get sequence alignments are listed here: <http://www.cgl.ucsf.edu/home/meng/sources.html> ... some sequence alignment webservers are listed at the bottom: <http://www.cgl.ucsf.edu/home/meng/sources.html#d>
Chimera understands many sequence alignment formats, and sequence alignments are automatically shown in the Multalign Viewer tool. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#alignment> <http://! www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html>
You can open both files in Chimera (the 3D structure and the sequence alignment). The structure should automatically associate with the alignment, <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#association> but if it doesn't happen automatically, you can associate it manually using "Structure...Associations" in the sequence window menu.
Then you can color the structure to show the conservation in the alignment, see "Structure.... Render by Conservation" in the sequence window menu. There is also an example of conservation coloring at the bottom of this tutorial: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/super.html>
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 Dec 3, 2012, at 10:18 PM, tao zhao wrote:
That's very kind of you, thank you very much! I read the websites you gave me and can get a model from one sequence based on the templete now. and what I really want to do is to construct a conserved model of all 35 sequences in this gene family. The final picuture can have different colors in the different regions, showing various conservation. I can't manage this right now. Best regards Tao
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Chimera developers, I wanted to thank you for all the work that is being done on Chimera. It's a great software and now with the new display of the pdbs it's amazing. I was curious whether there is a way to display the saved views and user-defined colors in a session ? I inherited a number session files from a colleague and it poses a nuisance to search through the .py file for the names of views,selections and colors + definitions. Would it be possible to display it on the startup (thunderbolt icon) screen ? Best regards, Jean-Paul
Hi Jean-Paul, Any named selections should already be listed in the middle bottom area of the Rapid Access interface (the startup screen), as well as in the menu: Select... Named Selections [...]. However, there is no compact way to show their definitions. Although saved positions are not on this interface, if you restore a position and then save a scene, the scene will be shown with a thumbnail in the middle top area of Rapid Access. Clicking the thumbnail is one way to restore that scene. Positions only include positions, whereas scenes include colors, representations etc. and are thus more accurately represented by a thumbnail image. One caveat is that saved scenes will increase session size more than saved positions, because they include much more information. More details on Rapid Access and scenes: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/rapid.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/animation/animation.html#scenes> I don't know of a way to retrieve a list of custom colors other than by looking in the session file, however. If you already know the name of the custom color, "colordef name" will report its color components (not the same as seeing the color, I know). Maybe there should be a colordef option to list the names. The problem might be in distinguishing the 169 color names that are automatically defined by Chimera from any additional ones defined by the user. Personally I never use named selections. Instead I use the "alias" command to create aliases and to list any previously created aliases. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html> 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 Dec 4, 2012, at 3:46 AM, Jean-Paul Armache wrote:
Dear Chimera developers,
I wanted to thank you for all the work that is being done on Chimera. It's a great software and now with the new display of the pdbs it's amazing. I was curious whether there is a way to display the saved views and user-defined colors in a session ? I inherited a number session files from a colleague and it poses a nuisance to search through the .py file for the names of views,selections and colors + definitions. Would it be possible to display it on the startup (thunderbolt icon) screen ? Best regards,
Jean-Paul
To supplement Elaine's response: You can get a list of saved positions with "savepos list". Adding saved positions to the Rapid Access interface is an interesting idea. I'll think about it. Also, being able to get a list of the user-defined color names seems like a good idea. Perhaps "colordef" with no args could report that. I'll definitely add that to my to-do list. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Dec 4, 2012, at 3:46 AM, Jean-Paul Armache wrote:
Dear Chimera developers,
I wanted to thank you for all the work that is being done on Chimera. It's a great software and now with the new display of the pdbs it's amazing. I was curious whether there is a way to display the saved views and user-defined colors in a session ? I inherited a number session files from a colleague and it poses a nuisance to search through the .py file for the names of views,selections and colors + definitions. Would it be possible to display it on the startup (thunderbolt icon) screen ? Best regards,
Jean-Paul
Thank you for your answers, already it was very helpful. Best regards, Jean-Paul
participants (4)
-
Elaine Meng -
Eric Pettersen -
Jean-Paul Armache -
tao zhao