electrostatic interactions
Hi Elaine I do see "Find out clashes and contacts" feature in Chimera. I am wondering if there is any feature which can check on electrostatic interactions as well. Please let me know. Thanks !! Regards Ruchika
Hi Ruchika, There is a FindHBond tool, and also coloring the surface by electrostatic potential. Of course you can just look at the help pages for all the tools or commands you are interested in. The list of all tools has links to their individual help pages: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecontrib.html> ... but I recommend going through these tutorials for examples of using them: (1) Structure Analysis and Comparison (includes Find Contacts, FindHBond, surface coloring by hydrophobicity) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html> (2) Image Tutorial: Surface Properties (surface coloring by hydrophobicity and electrostatic potential) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 18, 2020, at 5:57 PM, Ruchika <Ruchika@ucsf.edu> wrote:
Hi Elaine I do see "Find out clashes and contacts" feature in Chimera. I am wondering if there is any feature which can check on electrostatic interactions as well. Please let me know. Thanks !! Regards Ruchika
Hi Elaine, thanks for your response !! I am just wondering if this Find H-bond tool can also find any other polar interactions than Hydrogen bonds, like salt bridges. Please let me know. Thanks !! Regards Ruchika ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Saturday, September 19, 2020 9:18 AM To: Ruchika <Ruchika@ucsf.edu> Cc: Chimera <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] electrostatic interactions Hi Ruchika, There is a FindHBond tool, and also coloring the surface by electrostatic potential. Of course you can just look at the help pages for all the tools or commands you are interested in. The list of all tools has links to their individual help pages: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecontrib.html> ... but I recommend going through these tutorials for examples of using them: (1) Structure Analysis and Comparison (includes Find Contacts, FindHBond, surface coloring by hydrophobicity) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html> (2) Image Tutorial: Surface Properties (surface coloring by hydrophobicity and electrostatic potential) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 18, 2020, at 5:57 PM, Ruchika <Ruchika@ucsf.edu> wrote:
Hi Elaine I do see "Find out clashes and contacts" feature in Chimera. I am wondering if there is any feature which can check on electrostatic interactions as well. Please let me know. Thanks !! Regards Ruchika
Hi Ruchika, H-bonds include salt bridge interactions. That is, many H-bonds are salt bridges, and biomolecular (e.g. protein-protein) salt bridges are generally H-bonds. See the FindHBonds page for a description of what atom types it considers: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html#criteria> Regards Elaine
On Sep 21, 2020, at 9:27 PM, Ruchika <Ruchika@ucsf.edu> wrote:
Hi Elaine, thanks for your response !! I am just wondering if this Find H-bond tool can also find any other polar interactions than Hydrogen bonds, like salt bridges. Please let me know. Thanks !! Regards Ruchika From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Saturday, September 19, 2020 9:18 AM To: Ruchika <Ruchika@ucsf.edu> Cc: Chimera <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] electrostatic interactions
Hi Ruchika, There is a FindHBond tool, and also coloring the surface by electrostatic potential.
Of course you can just look at the help pages for all the tools or commands you are interested in. The list of all tools has links to their individual help pages: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecontrib.html>
... but I recommend going through these tutorials for examples of using them:
(1) Structure Analysis and Comparison (includes Find Contacts, FindHBond, surface coloring by hydrophobicity) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
(2) Image Tutorial: Surface Properties (surface coloring by hydrophobicity and electrostatic potential) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 18, 2020, at 5:57 PM, Ruchika <Ruchika@ucsf.edu> wrote:
Hi Elaine I do see "Find out clashes and contacts" feature in Chimera. I am wondering if there is any feature which can check on electrostatic interactions as well. Please let me know. Thanks !! Regards Ruchika
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Elaine Thanks for the confirmation !! I tried looking into these details, however, I still wanted to confirm with you. Thanks again !! I have another question. I do understand that I can mutate a residue to the different one using the rotamer tool. I am just wondering if I would like to make an insertion or deletion mutation in the protein, are there any available tools in the chimera. Please let me know. Thanks !! Regards Ruchika ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, September 22, 2020 8:57 AM To: Ruchika <Ruchika@ucsf.edu> Cc: Chimera <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] electrostatic interactions Hi Ruchika, H-bonds include salt bridge interactions. That is, many H-bonds are salt bridges, and biomolecular (e.g. protein-protein) salt bridges are generally H-bonds. See the FindHBonds page for a description of what atom types it considers: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html#criteria> Regards Elaine
On Sep 21, 2020, at 9:27 PM, Ruchika <Ruchika@ucsf.edu> wrote:
Hi Elaine, thanks for your response !! I am just wondering if this Find H-bond tool can also find any other polar interactions than Hydrogen bonds, like salt bridges. Please let me know. Thanks !! Regards Ruchika From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Saturday, September 19, 2020 9:18 AM To: Ruchika <Ruchika@ucsf.edu> Cc: Chimera <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] electrostatic interactions
Hi Ruchika, There is a FindHBond tool, and also coloring the surface by electrostatic potential.
Of course you can just look at the help pages for all the tools or commands you are interested in. The list of all tools has links to their individual help pages: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecontrib.html>
... but I recommend going through these tutorials for examples of using them:
(1) Structure Analysis and Comparison (includes Find Contacts, FindHBond, surface coloring by hydrophobicity) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
(2) Image Tutorial: Surface Properties (surface coloring by hydrophobicity and electrostatic potential) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 18, 2020, at 5:57 PM, Ruchika <Ruchika@ucsf.edu> wrote:
Hi Elaine I do see "Find out clashes and contacts" feature in Chimera. I am wondering if there is any feature which can check on electrostatic interactions as well. Please let me know. Thanks !! Regards Ruchika
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Ruchika I changed the Subject line to describe your current question. This helps other people decide whether they want to read the answer. There is no simple tool in Chimera for modeling insertions or deletions, but I can think of two possibilities. Neither is necessarily a good approach for your project, so you may need to investigate other programs instead. I only mention them since you're asking what is available in Chimera. (A) If you have a template structure and target-template sequence alignment, you could use Chimera to run Modeller to build the target protein using a web service. Help page for this feature: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html> Tutorial example: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html> (B) Another possibility is to manually delete or add residues, delete and form new bonds as needed (see Build Structure tool), and minimize the result. However, minimization only has a very limited ability to "fix" a structure and it is most definitely not a prediction of how the structure would really change, or whether it could even form a stable fold. Here are the help pages for these tools: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 23, 2020, at 2:32 PM, Ruchika <Ruchika@ucsf.edu> wrote:
Hi Elaine Thanks for the confirmation !! I tried looking into these details, however, I still wanted to confirm with you. Thanks again !! I have another question. I do understand that I can mutate a residue to the different one using the rotamer tool. I am just wondering if I would like to make an insertion or deletion mutation in the protein, are there any available tools in the chimera. Please let me know. Thanks !! Regards Ruchika
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Elaine Meng -
Ruchika