AtomSets - Revision history

AngelHerraez: ammending definition of "solvent" to include "ions"

2023-09-06T19:26:44Z

ammending definition of "solvent" to include "ions"

AngelHerraez: peptide

2018-02-07T08:44:59Z

peptide

AngelHerraez: new atomset words for types of elements

2016-05-18T09:57:35Z

new atomset words for types of elements

AngelHerraez: ammending mistakes in describing "ligand" atom set

2015-02-07T20:33:38Z

ammending mistakes in describing "ligand" atom set

AngelHerraez: alternative to "ligands"

2015-02-07T20:19:17Z

alternative to "ligands"

AngelHerraez: removing colons

2014-10-31T12:20:28Z

removing colons

AngelHerraez: warning about ligand set

2014-10-31T12:17:59Z

warning about ligand set

AngelHerraez: new definition of LIGAND - also moving aside old definitions of water and solvent

2011-08-30T14:58:44Z

new definition of LIGAND - also moving aside old definitions of water and solvent

AngelHerraez: /* By type of residue: */

2011-06-29T18:36:26Z

‎By type of residue:

AngelHerraez: carbohydrate atom set

2011-06-29T18:32:51Z

carbohydrate atom set

@@ Line 71: / Line 71: @@
 * <tt>solvent</tt>
-: This includes <tt>water</tt> (in its extended definition) and also UREA groups.
+: This includes <tt>water</tt> (in its extended definition), UREA groups and also <tt>ions</tt> (PO4 and SO4 by their residue/group name in the pdb file).
 * <tt>ligand</tt>

@@ Line 43: / Line 43: @@
 :* Case 2:
 :: If the group has exactly 1 atom whose name is CA then it is considered protein. The purpose of this is to pick up alpha-carbon-only models
 * <tt>nucleic</tt>

← Older revision		Revision as of 09:57, 18 May 2016
Line 16:		Line 16:

	Note: Jmol 10.2 has a bug by which it may read calcium as alpha carbon based on its ID, although identification by element name works properly. It's been fixed for Jmol 11.		Note: Jmol 10.2 has a bug by which it may read calcium as alpha carbon based on its ID, although identification by element name works properly. It's been fixed for Jmol 11.
		+
		+	== By type of element ==
		+	:''(new in Jmol 14.6)''
		+	* <tt>nonMetal</tt>: H; B; C, Si; N, P, As; O, S, Se, Te; F, Cl, Br, I, At; noble gases
		+	* <tt>metal</tt>: all except <tt>nonMetal</tt>
		+	* <tt>metalloid</tt>: B, Si, Ge, As, Sb, Te ''(note it overlaps with both metal and metalloid)''
		+	* <tt>alkaliMetal</tt>: from Li down to Fr
		+	* <tt>alkalineEarth</tt>: from Be down to Ra
		+	* <tt>nobleGas</tt> from He down to Rn
		+	* <tt>transitionMetal</tt>: from Sc to Zn, from Y to Cd, from Hf to Hg, from Rf to Cn
		+	* <tt>lanthanide</tt>: La, from Ce to Lu
		+	* <tt>actinide</tt>: Ac, from Th to Lr

	== By type of molecule ==		== By type of molecule ==

@@ Line 59: / Line 59: @@
 * <tt>ligand</tt>
 :: ''Note: <code>ligand</code> will, in some occasions, '''not''' match what you expect.''
-: The new definition (Jmol 12.2) includes atoms that do not belong to protein, nucleic or solvent. As a consequence,
+: The new definition (Jmol 12.2) includes atoms that do not belong to protein, nucleic or water. As a consequence,
-:* <tt>water</tt>, other <tt>solvent</tt>, <tt>ions</tt> and <tt>carbohydrate</tt> '''are''' considered <code>ligands</code>.
+:* <tt>ions</tt> and <tt>carbohydrate</tt> '''are''' considered <code>ligands</code>.
 :* Nonstandard amino acids are '''''not''''' considered <code>ligands</code>.
 :* Nonstandard nucleotides are '''''not''''' considered <code>ligands</code>.
-:* Isolated nucleotides (e.g. ATP, GTP, AMP...) are '''''not''''' considered <code>ligands</code> (despite being understood by us as ligands; this is due to them being part of the <code>nucleic</code> atom set). To account for this, you may choose to use <code>polymer=0 and not solvent</code> instead of <code>ligand</code> ''(this works only in most recent versions like 14.3.12)''
+:* Isolated nucleotides (e.g. ATP, GTP, AMP...) are '''''not''''' considered <code>ligands</code> (despite being understood by us as ligands; this is due to them being part of the <code>nucleic</code> atom set). To account for this, you may choose to use <code>polymer=0 and not water</code> instead of <code>ligand</code> ''(this works only in most recent versions like 14.3.12)''
 : Ligand was clasically defined as <tt>hetero</tt> and not <tt>solvent</tt> (and so not always what you would expect from the word ligand, either).

@@ Line 63: / Line 63: @@
 :* Nonstandard amino acids are '''''not''''' considered <code>ligands</code>.
 :* Nonstandard nucleotides are '''''not''''' considered <code>ligands</code>.
-:* Isolated nucleotides (e.g. ATP, GTP, AMP...) are '''''not''''' considered <code>ligands</code> (despite being understood by us as ligands; this is due to them being part of the <code>nucleic</code> atom set)
+:* Isolated nucleotides (e.g. ATP, GTP, AMP...) are '''''not''''' considered <code>ligands</code> (despite being understood by us as ligands; this is due to them being part of the <code>nucleic</code> atom set). To account for this, you may choose to use <code>polymer=0 and not solvent</code> instead of <code>ligand</code> ''(this works only in most recent versions like 14.3.12)''
 : Ligand was clasically defined as <tt>hetero</tt> and not <tt>solvent</tt> (and so not always what you would expect from the word ligand, either).

@@ Line 8: / Line 8: @@
 :''Technical note'': most of these are set in [http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/viewer/JmolConstants.java?view=markup src/org/jmol/viewer/JmolConstants.java]
-== By element name: ==
+== By element name ==
 <tt>carbon</tt>, <tt>oxygen</tt>, <tt>hydrogen</tt>, <tt>sulphur</tt>, etc.
@@ Line 17: / Line 17: @@
 Note: Jmol 10.2 has a bug by which it may read calcium as alpha carbon based on its ID, although identification by element name works properly. It's been fixed for Jmol 11.
-== By type of molecule: ==
+== By type of molecule ==
-* <tt>amino</tt>:
+* <tt>amino</tt>
 : This is based only upon group name and has nothing to do with the actual atoms that make up the group.
 : This set is composed of all groups with one of these names: ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL, ASX, GLX, UNK.
 : This will usually be the 20 canonical proteinogenic amino acids, plus ambiguous Asp/Asn (ASX), ambiguous Glu/Gln (GLX) and 'unknown' (UNK).
-* <tt>protein</tt>:
+* <tt>protein</tt>
 : The 'protein' set in Jmol is based solely on the atoms that make up the group. It is independent of the group name and independent of whether the atoms are defined in ATOM records or HETATM records.
 : This has the advantage that modified groups and interesting things that are not amino acids can still be identified as part of the protein.
@@ Line 32: / Line 32: @@
 :: If the group has exactly 1 atom whose name is CA then it is considered protein. The purpose of this is to pick up alpha-carbon-only models
-* <tt>nucleic</tt>:
+* <tt>nucleic</tt>
 : A group is considered 'nucleic' if it contains atoms with all of these names: C3*, O3*, O5*, N1, C2, N3, C4, C5, C6 (asterisk may be substituted by prime/apostrophe). It is independent of the group name and independent of whether the atoms are defined in ATOM records or HETATM records.
-* <tt>rna</tt>:
+* <tt>rna</tt>
 : A group is 'rna' if it is <tt>nucleic</tt> and it also contains an atom named O2* (or O2').
-* <tt>dna</tt>:
+* <tt>dna</tt>
 : A group is 'dna' if it is <tt>nucleic</tt> and it '''does not''' contain an atom named O2* (or O2').
-* <tt>carbohydrate</tt>:
+* <tt>carbohydrate</tt>
 : This is based only upon group name.
 : This set is composed of all groups which name is in a (not comprehensive) list corresponding to common mono-, di- and trisaccharides ([[AtomSets/Carbohydrate|full list and identities]]).
-* <tt>water</tt>:
+* <tt>water</tt>
 : Any molecule chemically interpreted as water (an oxygen atom connected to two hydrogen, deuterium or tritium atoms), plus groups named HOH, DOD, or WAT.
 :: The original implementation of this set was only the named groups.
-* <tt>ions</tt>:
+* <tt>ions</tt>
 : This set is not what might seem, but it's just composed of groups named PO4 or SO4.
 :: ''Explanation'': Both are common ions in protein crystals for X-ray diffraction, and this special set (which is RasMol syntax) is kept for backward compatibility.
-* <tt>solvent</tt>:
+* <tt>solvent</tt>
 : This includes <tt>water</tt> (in its extended definition) and also UREA groups.
 :: The original implementation of this was <tt>water</tt> or <tt>ions</tt>.
-* <tt>ligand</tt>:
+* <tt>ligand</tt>
 :: ''Note: <code>ligand</code> will, in some occasions, '''not''' match what you expect.''
 : The new definition (Jmol 12.2) includes atoms that do not belong to protein, nucleic or solvent. As a consequence,
@@ Line 66: / Line 66: @@
 : Ligand was clasically defined as <tt>hetero</tt> and not <tt>solvent</tt> (and so not always what you would expect from the word ligand, either).
-== By type of residue: ==
+== By type of residue ==
 Inclusion in these sets is mostly determined by residue id (only as far as it is written in the adequate field in the molecular coordinate file, usually PDB format). A few cases are also included based on their chemical structure and the presence of a distinguishing atom name.
@@ Line 82: / Line 82: @@
 * <tt>hetero, carbohydrate, ions, ligand, water, solvent</tt> (see above)
-== By structure of the polymer: ==
+== By structure of the polymer ==
 * <tt>helix, sheet, turn</tt>
 * <tt>bonded</tt>
-== Parts in proteins: ==
+== Parts in proteins ==
 === <tt>Backbone</tt> or <tt>Mainchain</tt> ===
 Inclusion in this set is determined by '''atom id'''*, as follows:
@@ Line 108: / Line 108: @@
 A set defined by '''atom id''' <tt>CA</tt>.
-== Parts in nucleic acids: ==
+== Parts in nucleic acids ==
 === <tt>Backbone</tt> or <tt>Mainchain</tt> ===
 Inclusion in this set is determined by '''atom id'''*, as follows:

@@ Line 73: / Line 73: @@
 ** <tt>polar, nonpolar, hydrophobic (Ala,Gly,Ile,Leu,Met,Phe,Pro,Trp,Tyr,Val), neutral, charged, acidic, negative, basic, positive,</tt> ...
 ** <tt>buried (Ala,Cys,Ile,Leu,Met,Phe,Trp,Val), surface</tt>
-* <tt>hetero, ions, ligand, water, solvent</tt> (see above)
+* <tt>hetero, carbohydrate, ions, ligand, water, solvent</tt> (see above)
 == By structure of the polymer: ==