Proteopedia - User contributions [en]

Hydrogen bonds

2008-11-10T17:21:07Z

Warren DeLano: /* Finding and Visualizing Hbonds */

==Donor and Acceptor Atoms==
<table align='right' border='0' width='184' cellpadding='10' bgcolor='#d0d0d0' hspace='8'><tr><td rowspan='2'> </td><td bgcolor='#e8e8e8'>
[[Image:Hbond.gif]]</td></tr><tr><td bgcolor='#e8e8e8'><div style='color: white; background-color: black;'>   Elements: {{Template:ColorKey_Element_C}}, {{Template:ColorKey_Element_H}}, {{Template:ColorKey_Element_N}}, {{Template:ColorKey_Element_O}}.</div>A hydrogen bond (dotted white line) between a <font color='#6565b4'><b>nitrogen donor</b></font> and an <font color='red'><b>oxygen acceptor</b></font>. Distances shown in Å are typical for those found in proteins.</td></tr></table>

Hydrogen bonds ("hbonds") are non-covalent bonds that occur when a ''donor'' atom donates its covalently bonded hydrogen atom to an electronegative ''acceptor'' atom. Typical donor atoms are the oxygens in -OH (e.g. the sidechains of Ser, Thr, Tyr), HOH, and the nitrogen in -NH3+ (as in the sidechains of Lys, Arg) or -NH- (as in the main chain peptide bond, and the sidechains of Trp, His, Arg, and nucleotide bases). The lone electron pairs on these same donors can serve as hbond acceptor sites. So can those on carbonyl oxygens =O (as in the protein main chain) or nitrogens with three covalent bonds =N- (as in the sidechains of His, Trp, or in nucleotide bases). Lacking hydrogens, these latter cannot serve as donors.

==Distances and Energies==
The mean donor-acceptor distances in protein secondary structure elements are close to 3.0 Å, as are those between bases in Watson-Crick pairing (Jeffrey<ref name='jeffrey' />, pp. 191, 200). Jeffrey<ref name='jeffrey'>Jeffrey, George A., An introduction to hydrogen bonding, Oxford University Press, 1997.</ref> (page 12) categorizes hbonds with donor-acceptor distances of 2.2-2.5 Å as "strong, mostly covalent", 2.5-3.2 Å as "moderate, mostly electrostatic", and 3.2-4.0 Å as "weak, electrostatic". Energies are given as 40-14, 15-4, and <4 kcal/mol respectively. Most hbonds in proteins are in the moderate category. Strong hbonds require moieties or conditions that are rare within proteins. The hydrogen atoms in moderate hbonds often do not lie on the straight line connecting the donor to acceptor, so donor-acceptor distance slightly underestimates the length of the hbond (Jeffrey<ref name='jeffrey' />, p. 14).

==Finding and Visualizing Hbonds==
Few, if any, free molecular visualization programs show hbonds as rods or sticks between atoms. This is because determining the positions of hbonds with high confidence requires expert and detailed examination of the donor-acceptor chemistry and geometry. Instead, some molecular visualization programs display potential donor-acceptor pairs, deeming them "putatively" hbonded. [[Protein Explorer]] and [[FirstGlance in Jmol]] have ''Contacts'' dialogs that show putatively hbonded donors and acceptors based simply on the chemical elements and interatomic distances. [[PyMOL]] likewise displays "polar contacts" using dashed bonds between the involved atoms, leaving further assessment of hydrogen bonding to the user.

Since many [[PDB file|PDB files]] lack [[Hydrogen in macromolecular models|hydrogen atoms]], the possibility of an energetically significant hydrogen bond exists when donor and acceptor atoms are within about 3.5 Å of each other. However, before rigorously concluding that a hydrogen bond is present in a macromolecular crystal structure, viewers should first:

* Consider the overall coordinate error implied by the resolution of the structure.
* Survey local temperature factor values to see if the involved model coordinates are well-determined.
* Factor in corroborating evidence such as involvement in surrounding elements of secondary structure.
* Inspect the electron density, if available, to confirm that the model coordinates are actually in density.
* Assess whether or not nearby side chain conformations make sense (ASN, GLN, and HIS must often be flipped).
* Evaluate the local electrostatic potential to confirm that it is consistent with the assumed ionization states.
* If the putative hydrogen bond involves a small-molecule ligand, check that the ligand donors and acceptors have been correctly assigned (hydroxyl vs. ketone, amine vs. imine, etc.).

[[FirstGlance in Jmol]] has a ''Contacts'' dialog, where you can select any moiety by clicking on it. (The moiety can be a chain, a segment of a chain, a single residue or ligand, or a single atom.) All the likely non-covalent bonds to the designated target moiety are then shown automatically. The putatively non-covalently bonded atoms can be hidden or shown in any combination of seven subsets: hydrogen bonds not involving water, hydrogen bonds involving water, water bridges, hydrophobic interactions, salt bridges, cation-pi orbital interactions, metal and miscellaneous interactions. This display defines "likely hydrogen bonded bonded" oxygens and nitrogens (shown as balls) as those within 3.5 Å of other oxygens or nitrogens.

''An interactive example in Jmol is needed here.''

==Content Attribution==

The text initially provided on this page was adapted by [[User:Eric Martz|Eric Martz]] from the ''hydrogen bonds'' entry that he wrote several years earlier for the glossary in [http://proteinexplorer.org ProteinExplorer.Org].

==References==
<references />

Hydrogen bonds

2008-11-10T17:20:19Z

Warren DeLano: /* Finding and Visualizing Hbonds */

==Donor and Acceptor Atoms==
<table align='right' border='0' width='184' cellpadding='10' bgcolor='#d0d0d0' hspace='8'><tr><td rowspan='2'> </td><td bgcolor='#e8e8e8'>
[[Image:Hbond.gif]]</td></tr><tr><td bgcolor='#e8e8e8'><div style='color: white; background-color: black;'>   Elements: {{Template:ColorKey_Element_C}}, {{Template:ColorKey_Element_H}}, {{Template:ColorKey_Element_N}}, {{Template:ColorKey_Element_O}}.</div>A hydrogen bond (dotted white line) between a <font color='#6565b4'><b>nitrogen donor</b></font> and an <font color='red'><b>oxygen acceptor</b></font>. Distances shown in Å are typical for those found in proteins.</td></tr></table>

Hydrogen bonds ("hbonds") are non-covalent bonds that occur when a ''donor'' atom donates its covalently bonded hydrogen atom to an electronegative ''acceptor'' atom. Typical donor atoms are the oxygens in -OH (e.g. the sidechains of Ser, Thr, Tyr), HOH, and the nitrogen in -NH3+ (as in the sidechains of Lys, Arg) or -NH- (as in the main chain peptide bond, and the sidechains of Trp, His, Arg, and nucleotide bases). The lone electron pairs on these same donors can serve as hbond acceptor sites. So can those on carbonyl oxygens =O (as in the protein main chain) or nitrogens with three covalent bonds =N- (as in the sidechains of His, Trp, or in nucleotide bases). Lacking hydrogens, these latter cannot serve as donors.

==Distances and Energies==
The mean donor-acceptor distances in protein secondary structure elements are close to 3.0 Å, as are those between bases in Watson-Crick pairing (Jeffrey<ref name='jeffrey' />, pp. 191, 200). Jeffrey<ref name='jeffrey'>Jeffrey, George A., An introduction to hydrogen bonding, Oxford University Press, 1997.</ref> (page 12) categorizes hbonds with donor-acceptor distances of 2.2-2.5 Å as "strong, mostly covalent", 2.5-3.2 Å as "moderate, mostly electrostatic", and 3.2-4.0 Å as "weak, electrostatic". Energies are given as 40-14, 15-4, and <4 kcal/mol respectively. Most hbonds in proteins are in the moderate category. Strong hbonds require moieties or conditions that are rare within proteins. The hydrogen atoms in moderate hbonds often do not lie on the straight line connecting the donor to acceptor, so donor-acceptor distance slightly underestimates the length of the hbond (Jeffrey<ref name='jeffrey' />, p. 14).

==Finding and Visualizing Hbonds==
Few, if any, free molecular visualization programs show hbonds as rods or sticks between atoms. This is because determining the positions of hbonds with high confidence requires expert and detailed examination of the donor-acceptor chemistry and geometry. Instead, some molecular visualization programs display potential donor-acceptor pairs, deeming them "putatively" hbonded. [[Protein Explorer]] and [[FirstGlance in Jmol]] have ''Contacts'' dialogs that show putatively hbonded donors and acceptors based simply on the chemical elements and interatomic distances. [[PyMOL]] likewise displays "polar contacts" using dashed bonds between the involved atoms, leaving further assessment of hydrogen bonding to the user.

Since many [[PDB file|PDB files]] lack [[Hydrogen in macromolecular models|hydrogen atoms]], the possibility of an energetically significant hydrogen bond exists when donor and acceptor atoms are within about 3.5 Å of each other. However, before rigorously concluding that a hydrogen bond is present in a macromolecular crystal structure, viewers should first:

* Consider the overall coordinate error implied by the resolution of the structure.
* Survey local temperature factor values to see if the involved model coordinates are well-determined.
* Factor in corroborating evidence such as involvement in surrounding elements of secondary structure.
* Inspect the electron density, if available, to confirm that the model coordinates are actually in density.
* Assess whether or not nearby side chain conformations make sense (ASN, GLN, and HIS must often be flipped).
* Evaluate the local electrostatic potential to confirm that it is consistent with the assumed ionization states.
* If the putative hydrogen bond involves a small-molecule ligand, check that the ligand donors and acceptors have been correctly assigned (hydroxy vs. ketone, amine vs. imine, etc.).

[[FirstGlance in Jmol]] has a ''Contacts'' dialog, where you can select any moiety by clicking on it. (The moiety can be a chain, a segment of a chain, a single residue or ligand, or a single atom.) All the likely non-covalent bonds to the designated target moiety are then shown automatically. The putatively non-covalently bonded atoms can be hidden or shown in any combination of seven subsets: hydrogen bonds not involving water, hydrogen bonds involving water, water bridges, hydrophobic interactions, salt bridges, cation-pi orbital interactions, metal and miscellaneous interactions. This display defines "likely hydrogen bonded bonded" oxygens and nitrogens (shown as balls) as those within 3.5 Å of other oxygens or nitrogens.

''An interactive example in Jmol is needed here.''

==Content Attribution==

The text initially provided on this page was adapted by [[User:Eric Martz|Eric Martz]] from the ''hydrogen bonds'' entry that he wrote several years earlier for the glossary in [http://proteinexplorer.org ProteinExplorer.Org].

==References==
<references />

Hydrogen bonds

2008-11-10T16:54:35Z

Warren DeLano:

==Donor and Acceptor Atoms==
<table align='right' border='0' width='184' cellpadding='10' bgcolor='#d0d0d0' hspace='8'><tr><td rowspan='2'> </td><td bgcolor='#e8e8e8'>
[[Image:Hbond.gif]]</td></tr><tr><td bgcolor='#e8e8e8'><div style='color: white; background-color: black;'>   Elements: {{Template:ColorKey_Element_C}}, {{Template:ColorKey_Element_H}}, {{Template:ColorKey_Element_N}}, {{Template:ColorKey_Element_O}}.</div>A hydrogen bond (dotted white line) between a <font color='#6565b4'><b>nitrogen donor</b></font> and an <font color='red'><b>oxygen acceptor</b></font>. Distances shown in Å are typical for those found in proteins.</td></tr></table>

Hydrogen bonds ("hbonds") are non-covalent bonds that occur when a ''donor'' atom donates its covalently bonded hydrogen atom to an electronegative ''acceptor'' atom. Typical donor atoms are the oxygens in -OH (e.g. the sidechains of Ser, Thr, Tyr), HOH, and the nitrogen in -NH3+ (as in the sidechains of Lys, Arg) or -NH- (as in the main chain peptide bond, and the sidechains of Trp, His, Arg, and nucleotide bases). The lone electron pairs on these same donors can serve as hbond acceptor sites. So can those on carbonyl oxygens =O (as in the protein main chain) or nitrogens with three covalent bonds =N- (as in the sidechains of His, Trp, or in nucleotide bases). Lacking hydrogens, these latter cannot serve as donors.

==Distances and Energies==
The mean donor-acceptor distances in protein secondary structure elements are close to 3.0 Å, as are those between bases in Watson-Crick pairing (Jeffrey<ref name='jeffrey' />, pp. 191, 200). Jeffrey<ref name='jeffrey'>Jeffrey, George A., An introduction to hydrogen bonding, Oxford University Press, 1997.</ref> (page 12) categorizes hbonds with donor-acceptor distances of 2.2-2.5 Å as "strong, mostly covalent", 2.5-3.2 Å as "moderate, mostly electrostatic", and 3.2-4.0 Å as "weak, electrostatic". Energies are given as 40-14, 15-4, and <4 kcal/mol respectively. Most hbonds in proteins are in the moderate category. Strong hbonds require moieties or conditions that are rare within proteins. The hydrogen atoms in moderate hbonds often do not lie on the straight line connecting the donor to acceptor, so donor-acceptor distance slightly underestimates the length of the hbond (Jeffrey<ref name='jeffrey' />, p. 14).

==Finding and Visualizing Hbonds==
Few, if any, free molecular visualization programs show hbonds as rods or sticks between atoms. This is because determining the positions of hbonds with high confidence requires expert and detailed examination of the donor-acceptor chemistry and geometry. Instead, some molecular visualization programs display potential donor-acceptor pairs, deeming them "putatively" hbonded. [[Protein Explorer]] and [[FirstGlance in Jmol]] have ''Contacts'' dialogs that show putatively hbonded donors and acceptors based simply on the chemical elements and interatomic distances. [[PyMOL]] likewise displays "polar contacts" using dashed bonds between the involved atoms, leaving further assessment of hydrogen bonding to the user.

Since many [[PDB file|PDB files]] lack [[Hydrogen in macromolecular models|hydrogen atoms]], the possibility of an energetically significant hydrogen bond exists when donor and acceptor atoms are within about 3.5 Å of each other. However, before rigorously concluding that a hydrogen bond is present in a macromolecular crystal structure, viewers should first:

* Consider the overall coordinate error implied by the resolution of the structure.
* Survey local temperature factor values to see if the involved model coordinates are well-determined.
* Factor in corroborating evidence such as involvement in surrounding elements of secondary structure.
* Inspect the electron density, if available, to confirm that the model coordinates are actually in density.
* Assess whether or not nearby side chain conformations make sense (ASN, GLN, and HIS must often be flipped).
* Evaluate the local electrostatic potential to confirm that it is consistent with the assumed ionization states.

[[FirstGlance in Jmol]] has a ''Contacts'' dialog, where you can select any moiety by clicking on it. (The moiety can be a chain, a segment of a chain, a single residue or ligand, or a single atom.) All the likely non-covalent bonds to the designated target moiety are then shown automatically. The putatively non-covalently bonded atoms can be hidden or shown in any combination of seven subsets: hydrogen bonds not involving water, hydrogen bonds involving water, water bridges, hydrophobic interactions, salt bridges, cation-pi orbital interactions, metal and miscellaneous interactions. This display defines "likely hydrogen bonded bonded" oxygens and nitrogens (shown as balls) as those within 3.5 Å of other oxygens or nitrogens.

''An interactive example in Jmol is needed here.''

==Content Attribution==

The text initially provided on this page was adapted by [[User:Eric Martz|Eric Martz]] from the ''hydrogen bonds'' entry that he wrote several years earlier for the glossary in [http://proteinexplorer.org ProteinExplorer.Org].

==References==
<references />

Hydrogen bonds

2008-11-10T16:52:55Z

Warren DeLano: /* Finding and Visualizing Hbonds */

==Donor and Acceptor Atoms==
<table align='right' border='0' width='184' cellpadding='10' bgcolor='#d0d0d0' hspace='8'><tr><td rowspan='2'> </td><td bgcolor='#e8e8e8'>
[[Image:Hbond.gif]]</td></tr><tr><td bgcolor='#e8e8e8'><div style='color: white; background-color: black;'>   Elements: {{Template:ColorKey_Element_C}}, {{Template:ColorKey_Element_H}}, {{Template:ColorKey_Element_N}}, {{Template:ColorKey_Element_O}}.</div>A hydrogen bond (dotted white line) between a <font color='#6565b4'><b>nitrogen donor</b></font> and an <font color='red'><b>oxygen acceptor</b></font>. Distances shown in Å are typical for those found in proteins.</td></tr></table>

Hydrogen bonds ("hbonds") are non-covalent bonds that occur when a ''donor'' atom donates its covalently bonded hydrogen atom to an electronegative ''acceptor'' atom. Typical donor atoms are the oxygens in -OH (e.g. the sidechains of Ser, Thr, Tyr), HOH, and the nitrogen in -NH3+ (as in the sidechains of Lys, Arg) or -NH- (as in the main chain peptide bond, and the sidechains of Trp, His, Arg, and nucleotide bases). The lone electron pairs on these same donors can serve as hbond acceptor sites. So can those on carbonyl oxygens =O (as in the protein main chain) or nitrogens with three covalent bonds =N- (as in the sidechains of His, Trp, or in nucleotide bases). Lacking hydrogens, these latter cannot serve as donors.

==Distances and Energies==
The mean donor-acceptor distances in protein secondary structure elements are close to 3.0 Å, as are those between bases in Watson-Crick pairing (Jeffrey<ref name='jeffrey' />, pp. 191, 200). Jeffrey<ref name='jeffrey'>Jeffrey, George A., An introduction to hydrogen bonding, Oxford University Press, 1997.</ref> (page 12) categorizes hbonds with donor-acceptor distances of 2.2-2.5 Å as "strong, mostly covalent", 2.5-3.2 Å as "moderate, mostly electrostatic", and 3.2-4.0 Å as "weak, electrostatic". Energies are given as 40-14, 15-4, and <4 kcal/mol respectively. Most hbonds in proteins are in the moderate category. Strong hbonds require moieties or conditions that are rare within proteins. The hydrogen atoms in moderate hbonds often do not lie on the straight line connecting the donor to acceptor, so donor-acceptor distance slightly underestimates the length of the hbond (Jeffrey<ref name='jeffrey' />, p. 14).

==Finding and Visualizing Hbonds==
Few, if any, free molecular visualization programs show hbonds as rods or sticks between atoms. This is because determining the positions of hbonds with high confidence requires expert and detailed examination of the donor-acceptor chemistry and geometry. Instead, some molecular visualization programs display potential donor-acceptor pairs, deeming them "putatively" hbonded. [[Protein Explorer]] and [[FirstGlance in Jmol]] have ''Contacts'' dialogs that show putatively hbonded donors and acceptors based simply on the chemical elements and interatomic distances. [[PyMOL]] likewise displays "polar contacts" using dashed bonds between the involved atoms, leaving assessment of hydrogen bonding to the user.

Since many [[PDB file|PDB files]] lack [[Hydrogen in macromolecular models|hydrogen atoms]], the possibility of an energetically significant hydrogen bond exists when donor and acceptor atoms are within about 3.5 Å of each other. However, before rigorously concluding that a hydrogen bond is present in a macromolecular crystal structure, viewers should first:

* Consider the overall coordinate error implied by the resolution of the structure.
* Survey local temperature factor values to see if the involved atom coordinates are well-determined.
* Factor in corroborating evidence such as involvement in surrounding elements of secondary structure.
* Inspect the electron density, if available, to confirm that the model coordinates are actually in density.
* Assess whether or not nearby side chain conformations make sense (ASN, GLN, and HIS must often be flipped).
* Evaluate the local electrostatic potential to confirm that it is consistent with the assumed ionization states.

[[FirstGlance in Jmol]] has a ''Contacts'' dialog, where you can select any moiety by clicking on it. (The moiety can be a chain, a segment of a chain, a single residue or ligand, or a single atom.) All the likely non-covalent bonds to the designated target moiety are then shown automatically. The putatively non-covalently bonded atoms can be hidden or shown in any combination of seven subsets: hydrogen bonds not involving water, hydrogen bonds involving water, water bridges, hydrophobic interactions, salt bridges, cation-pi orbital interactions, metal and miscellaneous interactions. This display defines "likely hydrogen bonded bonded" oxygens and nitrogens (shown as balls) as those within 3.5 Å of other oxygens or nitrogens.

''An interactive example in Jmol is needed here.''

==Content Attribution==

The text initially provided on this page was adapted by [[User:Eric Martz|Eric Martz]] from the ''hydrogen bonds'' entry that he wrote several years earlier for the glossary in [http://proteinexplorer.org ProteinExplorer.Org].

==References==
<references />

PyMOL

2008-11-08T16:34:18Z

Warren DeLano:

[http://pymol.org PyMOL] is a stand-alone [[Molecular modeling and visualization software|molecular visualization]] program that is very popular with protein crystallographers because of the high quality of its rendering, its speed and versatility. A large percentage of the figures in journal publications reporting new macromolecular structures are created using PyMOL. PyMOL is the creation of [http://www.delanoscientific.com/ Warren DeLano]. It has an innovative license: it is open source, but not free in all forms: the author's current ready-to-run downloads (binaries) and up-to-date documentation require payment of modest annual subscription fees. However, a current [http://pymol.org/educational.html free version] is available to students and educators for classroom use, old out-of-date binary builds can be [http://delsci.com/rel/099 freely downloaded] by anyone, and some Linux distributions provide [http://packages.debian.org/stable/pymol PyMOL packages] compiled from the open-source code.

PyMOL has a strong user community which interacts via the [http://sourceforge.net/mail/?group_id=4546 PyMOL-Users] mailing list and operates the [http://pymolwiki.org PyMOL Wiki] documentation site. The "Py" in PyMOL refers to the [http://python.org Python language], an integral part of the package. Python enables users to automate PyMOL with simple command scripts and to develop plugins with their own custom user interfaces.

==See Also==
*[http://pymol.org PyMOL.Org], the official download and information home of PyMOL.
*[[Molecular modeling and visualization software]]
*[http://molvisindex.org World Index of Molecular Visualization Software]

PyMOL

2008-11-08T16:31:51Z

Warren DeLano:

[http://pymol.org PyMOL] is a stand-alone [[Molecular modeling and visualization software|molecular visualization]] program that is very popular with protein crystallographers because of the high quality of its rendering, its speed and versatility. A large percentage of the figures in journal publications reporting new macromolecular structures are created using PyMOL. PyMOL is the creation of [http://www.delanoscientific.com/ Warren Delano]. It has an innovative license: it is open source, but not free in all forms: the author's current ready-to-run downloads (binaries) and up-to-date documentation require payment of modest annual subscription fees. However, a current [http://pymol.org/educational.html free version] is available to students and educators for classroom use, old out-of-date binary builds can be [http://delsci.com/rel/099 freely downloaded] by anyone, and some Linux distributions provide [http://packages.debian.org/stable/pymol PyMOL packages] compiled from the open-source code.

PyMOL has a strong user community which interacts via the [http://sourceforge.net/mail/?group_id=4546 PyMOL-Users] mailing list and operates the [http://pymolwiki.org PyMOL Wiki] documentation site. The "Py" in PyMOL refers to the [http://python.org Python language], an integral part of the package. Python enables users to automate PyMOL with simple command scripts and to develop plugins with their own custom user interfaces.

==See Also==
*[http://pymol.org PyMOL.Org], the official download and information home of PyMOL.
*[[Molecular modeling and visualization software]]
*[http://molvisindex.org World Index of Molecular Visualization Software]

PyMOL

2008-11-08T16:23:37Z

Warren DeLano:

[http://pymol.org PyMOL] is a stand-alone [[Molecular modeling and visualization software|molecular visualization]] program that is very popular with protein crystallographers because of the high quality of its rendering, its speed and versatility. A large percentage of the figures in journal publications reporting new macromolecular structures are created using PyMOL. PyMOL is the creation of [http://www.delanoscientific.com/ Warren Delano]. It has an innovative license: it is open source, but not free in all forms: the author's current ready-to-run downloads (binaries) and up-to-date documentation require payment of modest annual subscription fees. However, a [http://pymol.org/educational free version] is available to students and educators for classroom use, out-of-date binary builds can be freely downloaded, and some Linux distributions provide PyMOL packages compiled from the open-source code.

PyMOL has a strong user community which interacts via the [http://sourceforge.net/mail/?group_id=4546 PyMOL-Users] mailing list and operates the [http://pymolwiki.org PyMOL Wiki] documentation site. The "Py" in PyMOL refers to the [http://python.org Python language], an integral part of the package. Python enables users to automate PyMOL with simple command scripts and to develop their own custom user interfaces.

==See Also==
*[http://pymol.org PyMOL.Org], the official download and information home of PyMOL.
*[[Molecular modeling and visualization software]]
*[http://molvisindex.org World Index of Molecular Visualization Software]

PyMOL

2008-11-08T16:19:05Z

Warren DeLano:

[http://pymol.org PyMOL] is a [[Molecular modeling and visualization software|molecular visualization]] stand-alone program that is very popular with protein crystallographers because of the high quality of its rendering, its speed and versatility. A large percentage of the figures in journal publications reporting new macromolecular structures are created using PyMOL. PyMOL is the creation of [http://www.delanoscientific.com/ Warren Delano]. It has an innovative license: it is open source, but not free in all forms: the author's current ready-to-run downloads (binaries) and up-to-date documentation require payment of modest annual subscription fees. However, a [http://pymol.org/educational free version] is available to educators for use in teaching students, out-of-date binary builds can be freely downloaded, and some Linux distributions offer PyMOL packages compiled from the open-source code.

PyMOL has a strong user community which interacts via the [http://sourceforge.net/mail/?group_id=4546 PyMOL-Users] mailing list and operates the [http://pymolwiki.org PyMOL Wiki] documentation site. The "Py" in PyMOL refers to the [http://python.org Python language], an integral part of the package. Python enables users to automate PyMOL with simple command scripts and to develop their own custom user interfaces.

==See Also==
*[http://pymol.org PyMOL.Org], the official download and information home of PyMOL.
*[[Molecular modeling and visualization software]]
*[http://molvisindex.org World Index of Molecular Visualization Software]

PyMOL

2008-11-08T16:00:26Z

Warren DeLano:

[http://pymol.org PyMOL] is a [[Molecular modeling and visualization software|molecular visualization]] stand-alone program that is very popular with protein crystallographers because of the high quality of its rendering, its speed and versatility. A large percentage of the figures in journal publications reporting new macromolecular structures are created using PyMOL. PyMOL is the creation of [http://www.delanoscientific.com/ Warren Delano]. It has an innovative license: it is open source, but not necessarily free: current ready-to-run downloads (binaries) and up-to-date documentation require payment of modest annual subscription fees. However, a free version is available to educators for use in teaching students, and out-of-date binary builds can be freely downloaded as well.

The "Py" in PyMOL refers to the [[http://python.org Python language]] an integral part of the Package. Python enables users to control PyMOL with simple command scripts or to develop plugins and programs with their own custom user interfaces.

==See Also==
*[http://pymol.org PyMOL.Org], the official download and information home of PyMOL.
*[[Molecular modeling and visualization software]]
*[http://molvisindex.org World Index of Molecular Visualization Software]