Dear Chimera, Thanks for giving such a wonderful software for molecular modelling. I am a PhD student in Germany and using the CHIMERA programme for my molecule. I want to increase the font and the font size of the highlighted amino acid in my protein and thats why I was trying in the Command: Tools - Utilities - Colour key where there is a option for font size but so far remain unsuccessful. Can you kindly advise me how I should proceed. Waiting eagerly for your kind reply, Soumya Ghosh, TUM, Freising, Germany
Dear Soumya, The font size settings in "2D Labels" and "Color Key" (these are two tabs on the same dialog) affect only 2D labels and color key labels. If you are just showing the regular 3D labels that rotate along with your structure, the font size is controlled in the Preferences (in menu, Favorites... Preferences): change to category "Background" and adjust "Label font" settings. Then remember to click Save if you want this change to apply to later uses of Chimera. 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 May 8, 2009, at 9:07 AM, Soumya Ghosh (Systembiologie) wrote:
Dear Chimera, Thanks for giving such a wonderful software for molecular modelling. I am a PhD student in Germany and using the CHIMERA programme for my molecule. I want to increase the font and the font size of the highlighted amino acid in my protein and thats why I was trying in the Command: Tools - Utilities - Colour key where there is a option for font size but so far remain unsuccessful. Can you kindly advise me how I should proceed.
Waiting eagerly for your kind reply, Soumya Ghosh, TUM, Freising, Germany
Dear Dr. Elaine C. Meng, Thanks a lot for your kind help. It really worked nicely.Can I afford to have some more questions. When I put my protein in the CHIMERA, I get the 3D module of it and it exhibits the α-helices and the ß-sheets very nicely. Now if I want to highlight the aminoacids that are specifically on the surface of the N -terminal or the amino acids that specifically embedded in the core, is there any provision to that. I tried with the Action; surface; show. With these commands it is visible that a structure appears that cover sometime the loops/helices/sheets fully or partially. Now my problem is, that is the sructure which is visible is it the surface? The amino acids which are highlighted are also from the surface? Can you kindly help me in this regard. Thanks with regards, Soumya Elaine Meng wrote ..
Dear Soumya,
The font size settings in "2D Labels" and "Color Key" (these are two tabs on the same dialog) affect only 2D labels and color key labels. If you are just showing the regular 3D labels that rotate along with your structure, the font size is controlled in the Preferences (in menu, Favorites... Preferences): change to category "Background" and adjust "Label font" settings. Then remember to click Save if you want this change to apply to later uses of Chimera.
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 May 8, 2009, at 9:07 AM, Soumya Ghosh (Systembiologie) wrote:
Dear Chimera, Thanks for giving such a wonderful software for molecular modelling. I am a PhD student in Germany and using the CHIMERA programme for my molecule. I want to increase the font and the font size of the highlighted amino acid in my protein and thats why I was trying in the Command: Tools - Utilities - Colour key where there is a option for font size but so far remain unsuccessful. Can you kindly advise me how I should proceed.
Waiting eagerly for your kind reply, Soumya Ghosh, TUM, Freising, Germany
Dear Soumya, When you show a surface, the surface area values are automatically assigned to atoms and residues. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces
You can select resides with surface area greater than some value, which will be the residues at the surface. The residues with small or zero surface area will be the ones buried on the inside. For example, open a structure (I opened PDB 2gbp as an example) use menu "Actions... Surface... show" then you can hide the surface, "Actions... Surface... hide" then to select by surface area value, choose "Select... by Attribute Value" in that dialog: change from attributes of "atoms" to "residues" if you want to select whole residues choose Attribute: "areaSAS" (if you want solvent-accessible surface area) or "areaSES" (if you want solvent-excluded surface area) move the vertical green bars to enclose the values of interest, click Apply It is the solvent-excluded surface that is displayed in Chimera. For example, I chose residues with areaSES values >30 (one green bar near 30, the other near the maximum value). You could use a different cutoff, but probably it should be bigger than zero. That generally selects the residues on the surface, and now you can use the Actions menu to do something else to those residues (color them, label them, write list of residues to a file, etc.) Instead of a dialog you could also select them with a command, e.g. select :/areaSES>30 One thing to think about is that usually there are surface bubbles on the inside, and some of the residues may have surface area from these bubbles and not the real outer surface of the protein. You can change the surface to not include these inside bubbles: open Model Panel (menu "Favorites... Model Panel") in that dialog: choose the MSMS surface model in the left side click "attributes" button on the right side in that, change "show disjoint surfaces" to "false" Close dialog now choose "Select... by Attribute Value" again in that dialog: Refresh... Values and proceed as above to choose residues by surface area value (or again, you could use the command instead) Here is a previous answer to a similar question: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003291.html
I hope this helps, Elaine On May 14, 2009, at 5:46 AM, Soumya Ghosh (Systembiologie) wrote:
Dear Dr. Elaine C. Meng, Thanks a lot for your kind help. It really worked nicely.Can I afford to have some more questions. When I put my protein in the CHIMERA, I get the 3D module of it and it exhibits the α- helices and the ß-sheets very nicely. Now if I want to highlight the aminoacids that are specifically on the surface of the N -terminal or the amino acids that specifically embedded in the core, is there any provision to that. I tried with the Action; surface; show. With these commands it is visible that a structure appears that cover sometime the loops/helices/sheets fully or partially. Now my problem is, that is the sructure which is visible is it the surface? The amino acids which are highlighted are also from the surface? Can you kindly help me in this regard.
Thanks with regards,
Soumya
Dear Dr.Elaine Meng, Thanks a lot for your kind advise. It really helped me a lot. Regards, Soumya Elaine Meng wrote ..
Dear Soumya, When you show a surface, the surface area values are automatically assigned to atoms and residues. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces
You can select resides with surface area greater than some value, which will be the residues at the surface. The residues with small or zero surface area will be the ones buried on the inside.
For example,
open a structure (I opened PDB 2gbp as an example) use menu "Actions... Surface... show" then you can hide the surface, "Actions... Surface... hide" then to select by surface area value, choose "Select... by Attribute Value" in that dialog: change from attributes of "atoms" to "residues" if you want to select whole residues choose Attribute: "areaSAS" (if you want solvent-accessible surface area) or "areaSES" (if you want solvent-excluded surface area) move the vertical green bars to enclose the values of interest, click Apply It is the solvent-excluded surface that is displayed in Chimera. For example, I chose residues with areaSES values >30 (one green bar near 30, the other near the maximum value). You could use a different cutoff, but probably it should be bigger than zero. That generally selects the residues on the surface, and now you can use the Actions menu to do something else to those residues (color them, label them, write list of residues to a file, etc.)
Instead of a dialog you could also select them with a command, e.g.
select :/areaSES>30
One thing to think about is that usually there are surface bubbles on the inside, and some of the residues may have surface area from these bubbles and not the real outer surface of the protein. You can change the surface to not include these inside bubbles:
open Model Panel (menu "Favorites... Model Panel") in that dialog: choose the MSMS surface model in the left side click "attributes" button on the right side in that, change "show disjoint surfaces" to "false" Close dialog now choose "Select... by Attribute Value" again in that dialog: Refresh... Values and proceed as above to choose residues by surface area value (or again, you could use the command instead)
Here is a previous answer to a similar question: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003291.html
I hope this helps, Elaine
On May 14, 2009, at 5:46 AM, Soumya Ghosh (Systembiologie) wrote:
Dear Dr. Elaine C. Meng, Thanks a lot for your kind help. It really worked nicely.Can I afford to have some more questions. When I put my protein in the CHIMERA, I get the 3D module of it and it exhibits the α- helices and the ß-sheets very nicely. Now if I want to highlight the aminoacids that are specifically on the surface of the N -terminal or the amino acids that specifically embedded in the core, is there any provision to that. I tried with the Action; surface; show. With these commands it is visible that a structure appears that cover sometime the loops/helices/sheets fully or partially. Now my problem is, that is the sructure which is visible is it the surface? The amino acids which are highlighted are also from the surface? Can you kindly help me in this regard.
Thanks with regards,
Soumya
Dear Dr. Elaine Meng, sorry to bother you once again. Actually after you explain me the things it become very much easier , otherwise the user's guide is too hard for me to decipher the solution of the specific problem.I am asking you a small problem. I have protein called GID1a whose 3D model I retrieved from the SWISS MODEL.I know that this particular protein interacts via alpha helices and ß sheets with the interacting protein GAI. I also retrieved the 3D model of GAI. Now in simple words I want to see at what points these two proteins interact.What are the interacting domains involved in the interaction with bonds and every thing. When I took these two proteins on the CHIMERA and using the command Tools-Structural comparison- Match maker, these two proteins does not show the points of interaction. Can I do this here? Eagerly waiting for your kind reply. Thanks with regards, Soumya Elaine Meng wrote ..
Dear Soumya, When you show a surface, the surface area values are automatically assigned to atoms and residues. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces
You can select resides with surface area greater than some value, which will be the residues at the surface. The residues with small or zero surface area will be the ones buried on the inside.
For example,
open a structure (I opened PDB 2gbp as an example) use menu "Actions... Surface... show" then you can hide the surface, "Actions... Surface... hide" then to select by surface area value, choose "Select... by Attribute Value" in that dialog: change from attributes of "atoms" to "residues" if you want to select whole residues choose Attribute: "areaSAS" (if you want solvent-accessible surface area) or "areaSES" (if you want solvent-excluded surface area) move the vertical green bars to enclose the values of interest, click Apply It is the solvent-excluded surface that is displayed in Chimera. For example, I chose residues with areaSES values >30 (one green bar near 30, the other near the maximum value). You could use a different cutoff, but probably it should be bigger than zero. That generally selects the residues on the surface, and now you can use the Actions menu to do something else to those residues (color them, label them, write list of residues to a file, etc.)
Instead of a dialog you could also select them with a command, e.g.
select :/areaSES>30
One thing to think about is that usually there are surface bubbles on the inside, and some of the residues may have surface area from these bubbles and not the real outer surface of the protein. You can change the surface to not include these inside bubbles:
open Model Panel (menu "Favorites... Model Panel") in that dialog: choose the MSMS surface model in the left side click "attributes" button on the right side in that, change "show disjoint surfaces" to "false" Close dialog now choose "Select... by Attribute Value" again in that dialog: Refresh... Values and proceed as above to choose residues by surface area value (or again, you could use the command instead)
Here is a previous answer to a similar question: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003291.html
I hope this helps, Elaine
On May 14, 2009, at 5:46 AM, Soumya Ghosh (Systembiologie) wrote:
Dear Dr. Elaine C. Meng, Thanks a lot for your kind help. It really worked nicely.Can I afford to have some more questions. When I put my protein in the CHIMERA, I get the 3D module of it and it exhibits the α- helices and the ß-sheets very nicely. Now if I want to highlight the aminoacids that are specifically on the surface of the N -terminal or the amino acids that specifically embedded in the core, is there any provision to that. I tried with the Action; surface; show. With these commands it is visible that a structure appears that cover sometime the loops/helices/sheets fully or partially. Now my problem is, that is the sructure which is visible is it the surface? The amino acids which are highlighted are also from the surface? Can you kindly help me in this regard.
Thanks with regards,
Soumya
Dear Soumya, Matchmaker is for superimposing related structures, not for finding interactions. To find interactions in Chimera, the two proteins would already need to be in the correct positions. Chimera will not predict how one protein should be positioned to interact with the other; for that you would need to use some other program or web server. However, if the proteins are already in their correct interacting position, you can use the following tools in Chimera: (a) FindHBond (or command "findhbond") (b) Find Contacts/Clashes (or command "findclash") Both are under Tools... Structure Analysis. They are also used in the "Structure Analysis and Comparison" tutorial. Please see: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond...
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash...
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ squalene.html> "Help... Search Documentation" in the Chimera menu can be used to search for topics, for example "find interactions". It will give you a list of links to the relevant manual pages. 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 May 16, 2009, at 1:16 PM, Soumya Ghosh (Systembiologie) wrote:
Dear Dr. Elaine Meng, sorry to bother you once again. Actually after you explain me the things it become very much easier , otherwise the user's guide is too hard for me to decipher the solution of the specific problem.I am asking you a small problem. I have protein called GID1a whose 3D model I retrieved from the SWISS MODEL.I know that this particular protein interacts via alpha helices and ß sheets with the interacting protein GAI. I also retrieved the 3D model of GAI. Now in simple words I want to see at what points these two proteins interact.What are the interacting domains involved in the interaction with bonds and every thing. When I took these two proteins on the CHIMERA and using the command Tools-Structural comparison- Match maker, these two proteins does not show the points of interaction. Can I do this here? Eagerly waiting for your kind reply.
Thanks with regards, Soumya
participants (2)
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Elaine Meng -
Soumya Ghosh (Systembiologie)