Reg: Hydrogen Bond Analysis
Dear Chimera Users,
I am new to chimera and I have some protein protein interaction results to be analysed. Most of the results are from HADDOCK server which gives a protein protein complex. So, is it possible to visualize the hydrogen bonds formed between the proteins using chimera? If yes, how? I am eagerly waiting for the answer.
Dear Amit, Yes, there is a FindHBond tool (in menu under Tools... Structure Analysis) and command "findhbond" with the same capabilities. Click the Help button on the tool to see its full instructions, or enter command "help findhbond" to see the command instructions.
There is an example of using FindHBond in the "Structure Analysis and Comparison" tutorial (see Chimera menu, Help... Tutorials).
You can also use Help... Search Documentation in the Chimera menu, for example to search for "hydrogen bonds" ... this will give several links into the user manual including the things I mentioned above. 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 Mar 23, 2013, at 11:02 AM, Amit Jaiswal wrote:
Dear Chimera Users, I am new to chimera and I have some protein protein interaction results to be analysed. Most of the results are from HADDOCK server which gives a protein protein complex. So, is it possible to visualize the hydrogen bonds formed between the proteins using chimera? If yes, how? I am eagerly waiting for the answer.
Dear Elaine, Many thanks for the suggestion and reply. I will do as said and will mail if any problem persists.
On Sat, Mar 23, 2013 at 11:41 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Dear Amit, Yes, there is a FindHBond tool (in menu under Tools... Structure Analysis) and command "findhbond" with the same capabilities. Click the Help button on the tool to see its full instructions, or enter command "help findhbond" to see the command instructions.
There is an example of using FindHBond in the "Structure Analysis and Comparison" tutorial (see Chimera menu, Help... Tutorials).
You can also use Help... Search Documentation in the Chimera menu, for example to search for "hydrogen bonds" ... this will give several links into the user manual including the things I mentioned above. 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 Mar 23, 2013, at 11:02 AM, Amit Jaiswal wrote:
Dear Chimera Users, I am new to chimera and I have some protein protein interaction results to be analysed. Most of the results are from HADDOCK server which gives a protein protein complex. So, is it possible to visualize the hydrogen bonds formed between the proteins using chimera? If yes, how? I am eagerly waiting for the answer.
Hi Elaine,
I addressed the question to CCP4BB but il did not seem to interest anyone . I state it again :
I wonder how much of an impact should there be on structure refinement, validation and, last but not least, molecular modeling, if we take into account the recent (2011) re-definition of the hydrogen bond made by the IUPAC. Ref: "Elangannan Arunan, Gautam R. Desiraju, Roger A. Klein, Joanna Sadlej, Steve Scheiner, Ibon Alkorta, David C. Clary, Robert H. Crabtree, Joseph J. Dannenberg, Pavel Hobza, Henrik G. Kjaergaard, Anthony C. Legon, Benedetta Mennucci, and David J. Nesbitt Pure Appl. Chem., Vol. 83, No. 8, pp. 1619–1636, 2011. doi:10.1351/PAC-REP-10-01-01 © 2011 IUPAC, Publication date (Web): 8 July 2011 Defining the hydrogen bond: An account (IUPAC Technical Report)*"
Tough job, isn't ?
My guess is that Chimera should be involved .
Nadir Mrabet
----- Mail original -----
Dear Elaine, Many thanks for the suggestion and reply. I will do as said and will mail if any problem persists.
On Sat, Mar 23, 2013 at 11:41 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Dear Amit, Yes, there is a FindHBond tool (in menu under Tools... Structure Analysis) and command "findhbond" with the same capabilities. Click the Help button on the tool to see its full instructions, or enter command "help findhbond" to see the command instructions.
There is an example of using FindHBond in the "Structure Analysis and Comparison" tutorial (see Chimera menu, Help... Tutorials).
You can also use Help... Search Documentation in the Chimera menu, for example to search for "hydrogen bonds" ... this will give several links into the user manual including the things I mentioned above. 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 Mar 23, 2013, at 11:02 AM, Amit Jaiswal wrote:
Dear Chimera Users, I am new to chimera and I have some protein protein interaction results to be analysed. Most of the results are from HADDOCK server which gives a protein protein complex. So, is it possible to visualize the hydrogen bonds formed between the proteins using chimera? If yes, how? I am eagerly waiting for the answer.
--
Yours Sincerely,
Amit Jaiswal, Department of Bioinformatics, School of Life Sciences, Pondicherry Central University, Kalapet, Pondicherry, Puducherry - 605 014.
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Nadir,
Maybe it would help if you explained the change in definition, why you think this definition is an improvement over currently used measures, and whether the criteria are things that can be measured or calculated by molecular graphics & analysis programs. For example, if it requires quantum-mechanical calculations, that would be beyond the capabilities of several programs.
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 Mar 23, 2013, at 12:42 PM, Nadir Mrabet wrote:
Hi Elaine,
I addressed the question to CCP4BB but il did not seem to interest anyone. I state it again :
I wonder how much of an impact should there be on structure refinement, validation and, last but not least, molecular modeling, if we take into account the recent (2011) re-definition of the hydrogen bond made by the IUPAC. Ref: "Elangannan Arunan, Gautam R. Desiraju, Roger A. Klein, Joanna Sadlej, Steve Scheiner, Ibon Alkorta, David C. Clary, Robert H. Crabtree, Joseph J. Dannenberg, Pavel Hobza, Henrik G. Kjaergaard, Anthony C. Legon, Benedetta Mennucci, and David J. Nesbitt Pure Appl. Chem., Vol. 83, No. 8, pp. 1619–1636, 2011. doi:10.1351/PAC-REP-10-01-01 © 2011 IUPAC, Publication date (Web): 8 July 2011 Defining the hydrogen bond: An account (IUPAC Technical Report)*"
Tough job, isn't ?
My guess is that Chimera should be involved.
Nadir Mrabet
Dear Elaine, Many thanks for the suggestion and reply. I will do as said and will mail if any problem persists.
On Sat, Mar 23, 2013 at 11:41 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Dear Amit, Yes, there is a FindHBond tool (in menu under Tools... Structure Analysis) and command "findhbond" with the same capabilities. Click the Help button on the tool to see its full instructions, or enter command "help findhbond" to see the command instructions.
There is an example of using FindHBond in the "Structure Analysis and Comparison" tutorial (see Chimera menu, Help... Tutorials).
You can also use Help... Search Documentation in the Chimera menu, for example to search for "hydrogen bonds" ... this will give several links into the user manual including the things I mentioned above. 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 Mar 23, 2013, at 11:02 AM, Amit Jaiswal wrote:
Dear Chimera Users, I am new to chimera and I have some protein protein interaction results to be analysed. Most of the results are from HADDOCK server which gives a protein protein complex. So, is it possible to visualize the hydrogen bonds formed between the proteins using chimera? If yes, how? I am eagerly waiting for the answer.
--
Yours Sincerely,
Amit Jaiswal, Department of Bioinformatics, School of Life Sciences, Pondicherry Central University, Kalapet, Pondicherry, Puducherry - 605 014.
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Elaine,
I gave a reference that should be read before initiating a fruitful discussion. I give a second one, which is an (critical) essay and a synthetic summary : Desiraju G.R. (2011) "A Bond by Any Other Name", Angew. Chem. Int. Ed. 50: 52-59.
The hydrogen bond is designated X-H°°°Y-Z (4 atoms; there have been so many articles where only the 3 atoms of a H-bond, C-H°°°O (3) are considered). X must be more electronegative than H. The H-bond acceptor, Y, is electron rich (either lone electron pair, or pi-bonded pair in Y-Z). The evidence for H-bond may be experimental or theoretical, but better be both.
Now, the C atom can be recognized as an H-bond donor (if it fulfills the required criteria). Aromatic rings become H-bond acceptors.
For the purpose of optimizing energy, the angle, X-H°°°Y, must be as close as possible to 180 ° (not new!), but there is no constraint imposed on angle H°°°Y-Z (a point on which I disagree).
Quantum-mechanical calculation is not adamant, but should help (provided one uses an appropriate force field).
Therefore, even if force fields attribute partial atomic charges (Note that Amber does not agree "qualitatively" with others on some atoms) they usually mention only NH and OH (and sometimes S) as H-bond donors and N-Z or O-Z, as acceptors. C-H is not considered as an H-bond donor; the pi-electron cloud is not recognized as acceptor.
The tough job resides in the choice of an empirical force field that best correlates with experimental data. Redefining H-bond donors and acceptors and their partial charges is also to be done in the molecular modeling program(s).
I cannot be exhaustive in a matter of minutes. I just wish to start the discussion and see whether (or not) if it will impact on Chimera.
Best regards,
Nadir
Pr. Nadir T. Mrabet Structural & Molecular Biochemistry N-gere - INSERM U-954 University of Lorraine, Nancy School of Sciences and Technologies & School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: Nadir.Mrabet <at> univ-lorraine.fr Cell.: +33 (0)6.11.35.69.09
LEGAL NOTICE Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail, or any action taken (or not taken) in reliance on it, is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately.
On 25/03/2013 23:13, Elaine Meng wrote:
Hi Nadir,
Maybe it would help if you explained the change in definition, why you think this definition is an improvement over currently used measures, and whether the criteria are things that can be measured or calculated by molecular graphics & analysis programs. For example, if it requires quantum-mechanical calculations, that would be beyond the capabilities of several programs.
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 Mar 23, 2013, at 12:42 PM, Nadir Mrabet wrote:
Hi Elaine,
I addressed the question to CCP4BB but il did not seem to interest anyone. I state it again :
I wonder how much of an impact should there be on structure refinement, validation and, last but not least, molecular modeling, if we take into account the recent (2011) re-definition of the hydrogen bond made by the IUPAC. Ref: "Elangannan Arunan, Gautam R. Desiraju, Roger A. Klein, Joanna Sadlej, Steve Scheiner, Ibon Alkorta, David C. Clary, Robert H. Crabtree, Joseph J. Dannenberg, Pavel Hobza, Henrik G. Kjaergaard, Anthony C. Legon, Benedetta Mennucci, and David J. Nesbitt Pure Appl. Chem., Vol. 83, No. 8, pp. 1619–1636, 2011. doi:10.1351/PAC-REP-10-01-01 © 2011 IUPAC, Publication date (Web): 8 July 2011 Defining the hydrogen bond: An account (IUPAC Technical Report)*"
Tough job, isn't ?
My guess is that Chimera should be involved.
Nadir Mrabet
Dear Elaine, Many thanks for the suggestion and reply. I will do as said and will mail if any problem persists.
On Sat, Mar 23, 2013 at 11:41 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Dear Amit, Yes, there is a FindHBond tool (in menu under Tools... Structure Analysis) and command "findhbond" with the same capabilities. Click the Help button on the tool to see its full instructions, or enter command "help findhbond" to see the command instructions.
There is an example of using FindHBond in the "Structure Analysis and Comparison" tutorial (see Chimera menu, Help... Tutorials).
You can also use Help... Search Documentation in the Chimera menu, for example to search for "hydrogen bonds" ... this will give several links into the user manual including the things I mentioned above. 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 Mar 23, 2013, at 11:02 AM, Amit Jaiswal wrote:
Dear Chimera Users, I am new to chimera and I have some protein protein interaction results to be analysed. Most of the results are from HADDOCK server which gives a protein protein complex. So, is it possible to visualize the hydrogen bonds formed between the proteins using chimera? If yes, how? I am eagerly waiting for the answer.
--
Yours Sincerely,
Amit Jaiswal, Department of Bioinformatics, School of Life Sciences, Pondicherry Central University, Kalapet, Pondicherry, Puducherry - 605 014.
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Nadir, I think it's fairly well known that hydrogen bonds are continuous phenomena and not discrete on/off entities as presented by Chimera (and most programs of its ilk). That's why Chimera allows you to loosen its H-bond criteria to explore interactions beyond the default cutoffs. Similarly, weak H-bond interactions can occur between chemical entities other than the ones examined by the Chimera H-bond code, e.g. carbon donors or pi-cloud acceptors. When Chimera's H-bond code was written, Chimera had no capability to assess the energetics of H-bond interactions and therefore simply uses the geometric criteria outlined in the Mills paper cited in Chimera's findhbond documentation to locate obvious H-bond interactions between well known donors and acceptors. C-H hydrogen bonds were excluded in the Mills paper due to their low occurrence and the fact that their geometry was frequently distorted to accommodate stronger H-bond interactions. Chimera isn't really trying to reinvent the wheel here. I think if one needs sophisticated analysis of all types of hydrogen bonding interactions then a dedicated QM or MM program should be used, not a visualization program. Nonetheless, if geometric criteria similar to those in the Mills paper were determined for some of these weaker interactions, I would consider adding them to the code.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Mar 26, 2013, at 7:25 AM, Nadir T. Mrabet wrote:
Hi Elaine,
I gave a reference that should be read before initiating a fruitful discussion. I give a second one, which is an (critical) essay and a synthetic summary : Desiraju G.R. (2011) "A Bond by Any Other Name", Angew. Chem. Int. Ed. 50: 52-59.
The hydrogen bond is designated X-H°°°Y-Z (4 atoms; there have been so many articles where only the 3 atoms of a H-bond, C-H°°°O (3) are considered). X must be more electronegative than H. The H-bond acceptor, Y, is electron rich (either lone electron pair, or pi-bonded pair in Y-Z). The evidence for H-bond may be experimental or theoretical, but better be both.
Now, the C atom can be recognized as an H-bond donor (if it fulfills the required criteria). Aromatic rings become H-bond acceptors.
For the purpose of optimizing energy, the angle, X-H°°°Y, must be as close as possible to 180 ° (not new!), but there is no constraint imposed on angle H°°°Y-Z (a point on which I disagree).
Quantum-mechanical calculation is not adamant, but should help (provided one uses an appropriate force field).
Therefore, even if force fields attribute partial atomic charges (Note that Amber does not agree "qualitatively" with others on some atoms) they usually mention only NH and OH (and sometimes S) as H-bond donors and N-Z or O-Z, as acceptors. C-H is not considered as an H-bond donor; the pi-electron cloud is not recognized as acceptor.
The tough job resides in the choice of an empirical force field that best correlates with experimental data. Redefining H-bond donors and acceptors and their partial charges is also to be done in the molecular modeling program(s).
I cannot be exhaustive in a matter of minutes. I just wish to start the discussion and see whether (or not) if it will impact on Chimera.
Best regards,
Nadir
Pr. Nadir T. Mrabet Structural & Molecular Biochemistry N-gere - INSERM U-954 University of Lorraine, Nancy School of Sciences and Technologies & School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: Nadir.Mrabet <at> univ-lorraine.fr Cell.: +33 (0)6.11.35.69.09
LEGAL NOTICE Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail, or any action taken (or not taken) in reliance on it, is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately.
On 25/03/2013 23:13, Elaine Meng wrote:
Hi Nadir,
Maybe it would help if you explained the change in definition, why you think this definition is an improvement over currently used measures, and whether the criteria are things that can be measured or calculated by molecular graphics & analysis programs. For example, if it requires quantum-mechanical calculations, that would be beyond the capabilities of several programs.
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 Mar 23, 2013, at 12:42 PM, Nadir Mrabet wrote:
Hi Elaine,
I addressed the question to CCP4BB but il did not seem to interest anyone. I state it again :
I wonder how much of an impact should there be on structure refinement, validation and, last but not least, molecular modeling, if we take into account the recent (2011) re-definition of the hydrogen bond made by the IUPAC. Ref: "Elangannan Arunan, Gautam R. Desiraju, Roger A. Klein, Joanna Sadlej, Steve Scheiner, Ibon Alkorta, David C. Clary, Robert H. Crabtree, Joseph J. Dannenberg, Pavel Hobza, Henrik G. Kjaergaard, Anthony C. Legon, Benedetta Mennucci, and David J. Nesbitt Pure Appl. Chem., Vol. 83, No. 8, pp. 1619–1636, 2011. doi:10.1351/PAC-REP-10-01-01 © 2011 IUPAC, Publication date (Web): 8 July 2011 Defining the hydrogen bond: An account (IUPAC Technical Report)*"
Tough job, isn't ?
My guess is that Chimera should be involved.
Nadir Mrabet
Dear Elaine, Many thanks for the suggestion and reply. I will do as said and will mail if any problem persists.
On Sat, Mar 23, 2013 at 11:41 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Dear Amit, Yes, there is a FindHBond tool (in menu under Tools... Structure Analysis) and command "findhbond" with the same capabilities. Click the Help button on the tool to see its full instructions, or enter command "help findhbond" to see the command instructions.
There is an example of using FindHBond in the "Structure Analysis and Comparison" tutorial (see Chimera menu, Help... Tutorials).
You can also use Help... Search Documentation in the Chimera menu, for example to search for "hydrogen bonds" ... this will give several links into the user manual including the things I mentioned above. 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 Mar 23, 2013, at 11:02 AM, Amit Jaiswal wrote:
Dear Chimera Users, I am new to chimera and I have some protein protein interaction results to be analysed. Most of the results are from HADDOCK server which gives a protein protein complex. So, is it possible to visualize the hydrogen bonds formed between the proteins using chimera? If yes, how? I am eagerly waiting for the answer.
--
Yours Sincerely,
Amit Jaiswal, Department of Bioinformatics, School of Life Sciences, Pondicherry Central University, Kalapet, Pondicherry, Puducherry - 605 014.
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
In case you don't get enough from Chimera, I think pisa from CCP4mg is specialized in analyzing protein interfaces.
http://www.ccp4.ac.uk/MG/ccp4mg_help/pisa.html
On 03/24/2013 03:32 AM, Amit Jaiswal wrote:
Dear Elaine, Many thanks for the suggestion and reply. I will do as said and will mail if any problem persists.
On Sat, Mar 23, 2013 at 11:41 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Dear Amit, Yes, there is a FindHBond tool (in menu under Tools... Structure Analysis) and command "findhbond" with the same capabilities. Click the Help button on the tool to see its full instructions, or enter command "help findhbond" to see the command instructions.
There is an example of using FindHBond in the "Structure Analysis and Comparison" tutorial (see Chimera menu, Help... Tutorials).
You can also use Help... Search Documentation in the Chimera menu, for example to search for "hydrogen bonds" ... this will give several links into the user manual including the things I mentioned above. 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 Mar 23, 2013, at 11:02 AM, Amit Jaiswal wrote:
Dear Chimera Users, I am new to chimera and I have some protein protein interaction results to be analysed. Most of the results are from HADDOCK server which gives a protein protein complex. So, is it possible to visualize the hydrogen bonds formed between the proteins using chimera? If yes, how? I am eagerly waiting for the answer.
participants (6)
-
Amit Jaiswal -
Elaine Meng -
Eric Pettersen -
Francois Berenger -
Nadir Mrabet -
Nadir T. Mrabet