Re: [Chimera-users] Regarding Hydrogen Bond
Dear Amit, You can identify hydrogen bonds with FindHBond (in menu under Tools... Structure Analysis). Click the Help button on that tool or see here for instructions: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html
If you want to analyze the environment around the metal and then add metal coordination bonds, you could use Metal Geometry (in menu under Tools... Structure Analysis): http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/metalgeom/metalgeom.html
If you don't care about analysis and just want to draw a line between two atoms, you could do that using either of the following: (A) distance measurements, for example using the Distances tool (change label to "none" if you don't want to see the distance value) http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances (B) PseudoBond Reader http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.html
Please send Chimera questions to the chimera-users@cgl.ucsf.edu address so that everybody can benefit.
You can search the manual using Help... Search Documentation in the Chimera menu, and you can search the chimera-users messages here: http://www.cgl.ucsf.edu/chimera/docs/feedback.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 Oct 24, 2012, at 8:54 AM, Amit Jaiswal wrote:
Dear Dr.Meng, Many thanks for your mail and suggestion for Metal fixation. I have done what you have advised. So, now my metal is near the catalytic site. So the next step is to form bond between Mg and Aspartic Acid residues. Now, I am confused. So I want to ask weather hydrogen bond and co-ordinate bond can be formed in Chimera? Please do let me know.
Dear Elaine,
Thanks for your mail and suggestions. I will post questions on chimera-users@cgl.ucsf.edu from next time on wards. I will try the tips and thus report you if problem persists.
With kind regards, Amit Jaiswal, Pondicherry University, Pondicherry, India.
On Wed, Oct 24, 2012 at 10:03 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Dear Amit, You can identify hydrogen bonds with FindHBond (in menu under Tools... Structure Analysis). Click the Help button on that tool or see here for instructions: < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond...
If you want to analyze the environment around the metal and then add metal coordination bonds, you could use Metal Geometry (in menu under Tools... Structure Analysis): < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/metalgeom/metalgeom...
If you don't care about analysis and just want to draw a line between two atoms, you could do that using either of the following: (A) distance measurements, for example using the Distances tool (change label to "none" if you don't want to see the distance value) < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/struc...
(B) PseudoBond Reader < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.h...
Please send Chimera questions to the chimera-users@cgl.ucsf.edu address so that everybody can benefit.
You can search the manual using Help... Search Documentation in the Chimera menu, and you can search the chimera-users messages here: http://www.cgl.ucsf.edu/chimera/docs/feedback.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 Oct 24, 2012, at 8:54 AM, Amit Jaiswal wrote:
Dear Dr.Meng, Many thanks for your mail and suggestion for Metal fixation. I have
done what you have advised. So, now my metal is near the catalytic site. So the next step is to form bond between Mg and Aspartic Acid residues. Now, I am confused. So I want to ask weather hydrogen bond and co-ordinate bond can be formed in Chimera?
Please do let me know.
Dear Elaine, I am stuck with a new problem and that is can I select multiple residues from different chains and check their interaction. There are some results from Haddock and I want to study the interaction residues from different chains. Is it also possible to know their bonding pattern? Please help me out.
On Thu, Oct 25, 2012 at 9:53 AM, Amit Jaiswal amitjai20@gmail.com wrote:
Dear Elaine,
Thanks for your mail and suggestions. I will post
questions on chimera-users@cgl.ucsf.edu from next time on wards. I will try the tips and thus report you if problem persists.
With kind regards, Amit Jaiswal, Pondicherry University, Pondicherry, India.
On Wed, Oct 24, 2012 at 10:03 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Dear Amit, You can identify hydrogen bonds with FindHBond (in menu under Tools... Structure Analysis). Click the Help button on that tool or see here for instructions: < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond...
If you want to analyze the environment around the metal and then add metal coordination bonds, you could use Metal Geometry (in menu under Tools... Structure Analysis): < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/metalgeom/metalgeom...
If you don't care about analysis and just want to draw a line between two atoms, you could do that using either of the following: (A) distance measurements, for example using the Distances tool (change label to "none" if you don't want to see the distance value) < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/struc...
(B) PseudoBond Reader < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.h...
Please send Chimera questions to the chimera-users@cgl.ucsf.edu address so that everybody can benefit.
You can search the manual using Help... Search Documentation in the Chimera menu, and you can search the chimera-users messages here: http://www.cgl.ucsf.edu/chimera/docs/feedback.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 Oct 24, 2012, at 8:54 AM, Amit Jaiswal wrote:
Dear Dr.Meng, Many thanks for your mail and suggestion for Metal fixation. I have
done what you have advised. So, now my metal is near the catalytic site. So the next step is to form bond between Mg and Aspartic Acid residues. Now, I am confused. So I want to ask weather hydrogen bond and co-ordinate bond can be formed in Chimera?
Please do let me know.
--
Yours Sincerely,
Amit Jaiswal, Department of Bioinformatics, School of Life Sciences, Pondicherry Central University, Kalapet, Pondicherry, Puducherry - 605 014. Phone No.: +91 8124954834.
Hi Amit, You can check between any residues you want.
With FindHBond, you can select one set of atoms and then choose the option "Only find H-bonds" with at least one end, exactly one end, or both ends selected, or between the selection and a second set of specified atoms. See the manual: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html
With Find Clashes/Contacts, you can select one set of atoms, "designate" it, then look for contacts among those atoms, or between those atoms and all other atoms, or between those atoms and a second set of designated atoms. See the manual: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html
Both those tools are in the menu under Tools... Structure Analysis. The commands findhbond and findclash have the same capabilities.
Here is information on how to "select" atoms in Chimera: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html ...and how to specify atoms in the command line: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html
For example, the following command would select residues 12 and 14-16 in chain A of model 0:
select #0:12.a,14-16.a
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 Oct 31, 2012, at 11:13 PM, Amit Jaiswal wrote:
Dear Elaine, I am stuck with a new problem and that is can I select multiple residues from different chains and check their interaction. There are some results from Haddock and I want to study the interaction residues from different chains. Is it also possible to know their bonding pattern? Please help me out.
participants (2)
-
Amit Jaiswal
-
Elaine Meng