## [PyMOL] Hydrogen Bond Parameters

 [PyMOL] Hydrogen Bond Parameters From: - 2009-02-16 19:29:07 ```Hello, Any help with the following would be greatly appreciated: The online PyMOL documentation (http://delsci.info/dsc/dokuwiki/doku.php?id=setting:h_bond&s=hydrogen%20bond) describes the h_bond parameters as follows: 1. h_bond_cone (float, default: 180.0) is a hydrogen-bond geometry parameter. 2. h_bond_cutoff_center (float, default: 3.6) is the maximum distance for ideal hydrogen bonds. 3. h_bond_cutoff_edge (float, default: 3.6) is the maximum distance for a marginal hydrogen bond. 4. h_bond_exclusion (integer, default: 3) controls suppression of hydrogen bonds around adjacent atoms. 5. h_bond_max_angle (float, default: 63.0) is the maximum angle for a marginal hydrogen bond. 6. h_bond_power_a (float, default: 1.6) is a hydrogen-bond geometry parameter. 7. h_bond_power_b (float, default: 5.0) is a hydrogen-bond geometry parameter. I was hoping someone (Warren?) might be able to elaborate on parameters 1-3 and 5-7 (or alternatively provide a reference and/or thread). Specifically, if a hydrogen bond consists of a donor (D), hydrogen (H), acceptor (A), and acceptor antecedent (B) illustrated as: D--H--A--B or alternatively: H--A / \ D B Then how are parameters 1-3, and 5-7 defined in terms of distances (HA, DA) and angles (DHA, DAB, HAB)? I would guess that "h_bond_cutoff_center" and "h_bond_cutoff_edge" both refer to the donor-acceptor (DA) distance, and I can make additional guesses about the other parameters, but I would prefer to proceed with a set of exact definitions if possible. Three additional questions: 1. Once the hydrogen bond parameters have been set, one uses the 'dist' command with mode=2 to find all hydrogen bonds, correct? For instance, if mc_H is the set generated by the command 'select mc_H, name h' and mc_O is the set generated by the command 'select mc_O, name o' then will the following command find all main-chain/main-chain hydrogen bonds for a given structure (using the previously-defined h_bond parameters as selection criteria): dist mcmc, mc_H, mc_O, mode=2 ? 2. Are hydrogen bonds considered a subset of "polar contacts" in PyMOL or are the two sets equivalent ({hydrogen bonds} = {polar contacts})? 3. At the risk of belaboring the point, what set of commands combined with the distance command would yield the same results as those generated by following menu selection: find > polar contacts > within selection assuming that the selection under consideration is an entire structure? Thanks in advance, Christopher ```

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 [PyMOL] Hydrogen Bond Parameters From: - 2009-02-16 19:29:07 ```Hello, Any help with the following would be greatly appreciated: The online PyMOL documentation (http://delsci.info/dsc/dokuwiki/doku.php?id=setting:h_bond&s=hydrogen%20bond) describes the h_bond parameters as follows: 1. h_bond_cone (float, default: 180.0) is a hydrogen-bond geometry parameter. 2. h_bond_cutoff_center (float, default: 3.6) is the maximum distance for ideal hydrogen bonds. 3. h_bond_cutoff_edge (float, default: 3.6) is the maximum distance for a marginal hydrogen bond. 4. h_bond_exclusion (integer, default: 3) controls suppression of hydrogen bonds around adjacent atoms. 5. h_bond_max_angle (float, default: 63.0) is the maximum angle for a marginal hydrogen bond. 6. h_bond_power_a (float, default: 1.6) is a hydrogen-bond geometry parameter. 7. h_bond_power_b (float, default: 5.0) is a hydrogen-bond geometry parameter. I was hoping someone (Warren?) might be able to elaborate on parameters 1-3 and 5-7 (or alternatively provide a reference and/or thread). Specifically, if a hydrogen bond consists of a donor (D), hydrogen (H), acceptor (A), and acceptor antecedent (B) illustrated as: D--H--A--B or alternatively: H--A / \ D B Then how are parameters 1-3, and 5-7 defined in terms of distances (HA, DA) and angles (DHA, DAB, HAB)? I would guess that "h_bond_cutoff_center" and "h_bond_cutoff_edge" both refer to the donor-acceptor (DA) distance, and I can make additional guesses about the other parameters, but I would prefer to proceed with a set of exact definitions if possible. Three additional questions: 1. Once the hydrogen bond parameters have been set, one uses the 'dist' command with mode=2 to find all hydrogen bonds, correct? For instance, if mc_H is the set generated by the command 'select mc_H, name h' and mc_O is the set generated by the command 'select mc_O, name o' then will the following command find all main-chain/main-chain hydrogen bonds for a given structure (using the previously-defined h_bond parameters as selection criteria): dist mcmc, mc_H, mc_O, mode=2 ? 2. Are hydrogen bonds considered a subset of "polar contacts" in PyMOL or are the two sets equivalent ({hydrogen bonds} = {polar contacts})? 3. At the risk of belaboring the point, what set of commands combined with the distance command would yield the same results as those generated by following menu selection: find > polar contacts > within selection assuming that the selection under consideration is an entire structure? Thanks in advance, Christopher ```