I am working with a protein in explicit water. Using AMBER tools, I have selected the 100 closest water molecules in and around the protein. Is there a way in Chimera to identify which amino acid residues that the waters are hydrogen bonded to? Or, is there a way to visualize which amino acids the water molecules are closest to? Thanks! John M. Beale, Jr., Ph.D. Professor of Medicinal Chemistry and Pharmacognosy Saint Louis College of Pharmacy 4588 Parkview Place Saint Louis, Missouri 63110 314-446-8461 Cell: 314-315-0409 FAX: 314-446-8460 jbeale@stlcop.edu<mailto:jbeale@stlcop.edu>
Hi John, Please see the previous reply to a similar question: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-August/005459.html> To summarize, the "Find Clashes/Contacts" tool identifies contacts of all types and "FindHBond" identifies hydrogen bonds. There are various choices of what to do with the identified contacts, such as selecting them or writing out all the information to a file. Selections can be further acted upon (for example, their residue labels shown) using the Actions menu. See the previous reply for links to the relevant manual pages. Examples of use are included in the "Structure Analysis and Comparison" tutorial: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html> Best, 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 Nov 29, 2010, at 12:10 PM, Beale, John wrote:
I am working with a protein in explicit water. Using AMBER tools, I have selected the 100 closest water molecules in and around the protein. Is there a way in Chimera to identify which amino acid residues that the waters are hydrogen bonded to? Or, is there a way to visualize which amino acids the water molecules are closest to?
Hi Elaine, Thanks. Your suggestions were indeed very helpful. I have another question that maybe you can answer. Is there a way in Chimera to select only internal amino acids of a protein (I would like to select hydrophobic amino acids away under the surface of my protein to try and identify hydrophobic core groups)? Thanks! John John M. Beale, Jr., Ph.D. Professor of Medicinal Chemistry and Pharmacognosy Saint Louis College of Pharmacy 4588 Parkview Place Saint Louis, Missouri 63110 314-446-8461 Cell: 314-315-0409 FAX: 314-446-8460 jbeale@stlcop.edu<mailto:jbeale@stlcop.edu> From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Monday, November 29, 2010 6:19 PM To: Beale, John Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Closest Waters Hi John, Please see the previous reply to a similar question: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-August/005459.html> To summarize, the "Find Clashes/Contacts" tool identifies contacts of all types and "FindHBond" identifies hydrogen bonds. There are various choices of what to do with the identified contacts, such as selecting them or writing out all the information to a file. Selections can be further acted upon (for example, their residue labels shown) using the Actions menu. See the previous reply for links to the relevant manual pages. Examples of use are included in the "Structure Analysis and Comparison" tutorial: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html> Best, 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 Nov 29, 2010, at 12:10 PM, Beale, John wrote: I am working with a protein in explicit water. Using AMBER tools, I have selected the 100 closest water molecules in and around the protein. Is there a way in Chimera to identify which amino acid residues that the waters are hydrogen bonded to? Or, is there a way to visualize which amino acids the water molecules are closest to?
On Nov 30, 2010, at 4:55 AM, Beale, John wrote:
I have another question that maybe you can answer. Is there a way in Chimera to select only internal amino acids of a protein (I would like to select hydrophobic amino acids away under the surface of my protein to try and identify hydrophobic core groups)?
Hi John, After you have displayed a surface, then (even if you hide the surface), the atoms and residues will have surface area values assigned as an attribute. Amino acid hydrophobicity is another attribute. You can select by attribute values or combinations of attribute values, for example, residues with little exposed surface area but high hydrophobicity values. Example: open 2gbp surface ~surf select :/areaSES<10 and kdHydrophobicity>1 ... you wouldn't necessarily use those cutoffs, may want to experiment and see what works best in your case. Then you could choose "Actions... Write List" from the menu to save a list of the selected residues to a text file. More details: The surface area attributes are named areaSES (solvent-excluded, where the probe surface goes; this is the type of surface Chimera displays) and areaSAS (solvent-accessible, where the probe sphere center goes), as described here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces> The hydrophobicity attribute is named kdHydrophobicity and is described here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html> The names of the attributes are relevant because you would choose them in the "Select by Attribute" dialog (menu Select... By Attribute Value), or enter the names in the Command Line to select residues by their values. To use a combination of multiple attributes, I would use the Command Line approach. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#descriptors> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#resprops> However, the "Select by Attribute" dialog can still be useful for showing you histograms of the values in your structure; you would need to change to attributes of "residues" and then choose the particular attribute by name to see its histogram. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#select> 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
Hi Elaine, This question has come up several times and requires some steps to answer. It strikes me as a good question to base a screen-capture video demo on. Tom
On Nov 30, 2010, at 4:55 AM, Beale, John wrote:
** *I have another question that maybe you can answer. Is there a way in Chimera to select only internal amino acids of a protein (I would like to select hydrophobic amino acids away under the surface of my protein to try and identify hydrophobic core groups)?*
Hi John, After you have displayed a surface, then (even if you hide the surface), the atoms and residues will have surface area values assigned as an attribute. Amino acid hydrophobicity is another attribute. You can select by attribute values or combinations of attribute values, for example, residues with little exposed surface area but high hydrophobicity values.
Example:
open 2gbp surface ~surf select :/areaSES<10 and kdHydrophobicity>1
... you wouldn't necessarily use those cutoffs, may want to experiment and see what works best in your case. Then you could choose "Actions... Write List" from the menu to save a list of the selected residues to a text file.
More details:
The surface area attributes are named areaSES (solvent-excluded, where the probe surface goes; this is the type of surface Chimera displays) and areaSAS (solvent-accessible, where the probe sphere center goes), as described here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces>
The hydrophobicity attribute is named kdHydrophobicity and is described here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html>
The names of the attributes are relevant because you would choose them in the "Select by Attribute" dialog (menu Select... By Attribute Value), or enter the names in the Command Line to select residues by their values. To use a combination of multiple attributes, I would use the Command Line approach. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#descriptors>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#resprops>
However, the "Select by Attribute" dialog can still be useful for showing you histograms of the values in your structure; you would need to change to attributes of "residues" and then choose the particular attribute by name to see its histogram. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#select>
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
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participants (3)
-
Beale, John -
Elaine Meng -
Tom Goddard