File formats - Revision history

AngelHerraez at 22:56, 26 January 2020

2020-01-26T22:56:00Z

2009-04-25T17:34:15Z

content was moved to subpages

2009-04-23T18:57:56Z

new link to Molecular Formats Converter

2009-04-23T18:40:28Z

‎Exporting coordinates

2009-04-19T19:18:28Z

online converters; charge and isotope support, others

2009-04-19T01:05:25Z

inline scripts in CIF files

2009-04-19T00:48:32Z

link update

2009-04-19T00:29:16Z

‎Script inline within a molecular coordinates file

2009-04-19T00:20:57Z

multiple models in a single MOL2 file

2009-04-18T17:28:56Z

fix link

@@ Line 15: / Line 15: @@
 * Online:
 ** [http://www.vcclab.org/lab/babel/start.html E-BABEL Interactive Molecular Structure Formats Interconversion Program]. Part of the Virtual Computational Chemistry Laboratory; uses the Open Babel engine.
 ** [http://www.molecular-networks.com/online_demos/convert_demo.html Online demonstration of the CONVERT program] by Molecular Networks.

@@ Line 489: / Line 489: @@
 = Exporting coordinates =
-Jmol has a limited capability for writing molecular coordinates, including only the selected set of atoms.
+Jmol has a limited capability for writing molecular coordinates, including only the currently selected set of atoms. (This allows to save the whole model, maybe in a format different from the original one, or to extract a subset of the atoms in the original model).
 Due to Java security restraints, only the [[Jmol_Application | application]] and the [[Jmol_Applet#Unsigned_vs._Signed_Applet_.26_Data_Access | signed applet]] can write to files on disk.
-The unsigned applet can display the exported data in the console window, from where you can copy it, paste into a text editor and save it to file.
+The unsigned applet can however display the exported data in the console window, from where you can copy it, paste into a text editor and save it to file.
 Only '''MOL, XYZ and PDB''' formats are supported for export. The method is to use the [{{ScriptingDoc}}#write <code>write</code> command] (from script or from the console).

@@ Line 91: / Line 91: @@
 Crystallographic Information File, the official format from the International Union of Crystallography. [http://www.iucr.org/iucr-top/cif/standard/cifstd1.html Original documentation], Acta Cryst. (1991). A47, 655-685, and the [http://www.iucr.org/iucr-top/cif/spec/version1.1/ 2003 update].
-CIF files may contain anywhere an [[#Script_inline_within_a_molecular_coordinates_file | inline script]] starting with <code>jmolscript:</code>.
+CIF files may contain an [[#Script_inline_within_a_molecular_coordinates_file | inline script]] starting with <code>jmolscript:</code>.
 == mmCIF ==
@@ Line 424: / Line 424: @@
 * In a MOL file (both v2000 and v3000), use <code>jmolscript:</code> in the '''third line''', followed by the script commands in the same line.
 * In an XYZ file, use <code>jmolscript:</code> in the '''second line''', followed by the script commands in the same line.
-* In a CIF file, use <code>jmolscript:</code> in any line, followed by the script commands in the same line.
+* In a CIF file, use <code>#jmolscript:</code> followed by the script commands in the same line. It may be in any line as long as it does not interfere with the data structure, so it is better to put it either at the beginning or the end of the file.
 In all cases, the script will be applied after the whole molecule has loaded and after whatever script commands may have been set using <code>set defaultLoadScript</code>.

@@ Line 89: / Line 89: @@
 == CIF ==
 Jmol reads CIF files.
-Crystallographic Information File, the official format from the International Union of Crystallography. [http://www.iucr.org/iucr-top/cif/standard/cifstd1.html Original documentation], Acta Cryst. (1991). A47, 655-685, and [http://www.iucr.org/iucr-top/cif/spec/version1.1/index.html 2003 update].
+Crystallographic Information File, the official format from the International Union of Crystallography. [http://www.iucr.org/iucr-top/cif/standard/cifstd1.html Original documentation], Acta Cryst. (1991). A47, 655-685, and the [http://www.iucr.org/iucr-top/cif/spec/version1.1/ 2003 update].
 CIF files may contain anywhere an [[#Script_inline_within_a_molecular_coordinates_file | inline script]] starting with <code>jmolscript:</code>.
 == mmCIF ==

@@ Line 42: / Line 42: @@
 Original from Tripos.
 Contains atom coordinates, bonds, partial charge, substructure information.
 Official document: http://www.tripos.com/data/support/mol2.pdf
 == PDB ==

@@ Line 62: / Line 62: @@
 XYZ header lines:
 * The first line is reserved for the number of atoms.
-* The second line is for comments, and may contain an [[#Script_inline_within_a_molecular_coordinates_file inline script]] starting with <code>jmolscript:</code>.
+* The second line is for comments, and may contain an [[#Script_inline_within_a_molecular_coordinates_file | inline script]]  starting with <code>jmolscript:</code>.
 [http://local.wasp.uwa.edu.au/~pbourke/dataformats/xyz/ Example] by Paul Bourke.
@@ Line 85: / Line 85: @@
 </pre>
 :where <code>Sym</code> is either an element symbol (C, Fe, Si) or an element symbol preceded by an isotope number (2H, 13C, etc.)
 == CIF ==