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.
-- Yours Sincerely, ~~~~~~~~~~~~~~~~~~~~~~~~ Amit Jaiswal, Department of Bioinformatics, School of Life Sciences, Pondicherry Central University, Kalapet, Pondicherry, Puducherry - 605 014. Phone No.: +91 8124954834. ~~~~~~~~~~~~~~~~~~~~~~~~~
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.
~~~~~~~~~~~~~~~~~~~~~~~~~
-- 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.
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Elaine Meng