File formats/Export - Revision history

AngelHerraez: Exporting for augmented reality

2023-08-25T16:34:29Z

Exporting for augmented reality

AngelHerraez: /* Special image files PNGJ */

2021-03-09T17:14:13Z

‎Special image files PNGJ

AngelHerraez: details of export to PNGJ

2021-03-09T16:28:34Z

details of export to PNGJ

AngelHerraez: preventing line breaks that may confuse reading the syntax

2021-03-09T16:07:28Z

preventing line breaks that may confuse reading the syntax

AngelHerraez: /* show() chemical function */

2018-11-17T11:33:10Z

‎show() chemical function

AngelHerraez: /* show() chemical function */

2018-11-16T23:26:41Z

‎show() chemical function

AngelHerraez: /* show() chemical function */

2018-11-16T23:25:26Z

‎show() chemical function

AngelHerraez: /* show() chemical function */

2018-11-16T21:02:25Z

‎show() chemical function

AngelHerraez: show() chemical

2018-11-16T17:19:29Z

show() chemical

AngelHerraez: expanding on the write command and functon

2017-12-11T11:46:55Z

expanding on the write command and functon

@@ Line 232: / Line 232: @@
 :Note 2: by default, molecular state is included in the file, unless <code>set imageState</code> has been previously set to <code>false</code> or <code>off</code>.
 :Note 3: in the case of png files (not pngj), the molecular model file and any isosurface files involved must be in the same folder as the png file in order for the state to be interpreted.
@@ Line 242: / Line 241: @@
 :<code>a._IMAGE_ = b._DATA_;</code> puts the binary data making image "B" into the image section of data from file "A" (replacing the existing image data)
 :<code>write var a "fileC.png";</code> saves the new combination stored in variable "a", i.e. molecular data from file "A" and image from file "B", into a new PNGJ file

@@ Line 200: / Line 200: @@
 === Special image files PNGJ ===
-Jmol can export to a PNG file that, in addition of a snapshot of the current molecular rendering, includes all the information of atomic coordinates, rendering style and state.
+Jmol can export to a PNG file that, in addition of a snapshot of the current molecular rendering, includes the state with all the information of rendering style (PNG) and, optionally, the data of the molecular model (PNGJ).
 These files appear as regular image files to any software but, when loaded back in Jmol (or drag-and-dropped) will reproduce the exact state of the 3D molecular model.

← Older revision		Revision as of 16:28, 9 March 2021
Line 195:		Line 195:
	=== Save isosurface ===		=== Save isosurface ===
	The pop-up menu entry will svae the last isosurface selected or generated. More flexibility is allowed by using the [{{ScriptingDoc}}#writeobject <code>write isosurface</code>] command.		The pop-up menu entry will svae the last isosurface selected or generated. More flexibility is allowed by using the [{{ScriptingDoc}}#writeobject <code>write isosurface</code>] command.
		+
		+	== Saving Jmol-specific files ==
		+
		+	=== Special image files PNGJ ===
		+
		+	Jmol can export to a PNG file that, in addition of a snapshot of the current molecular rendering, includes all the information of atomic coordinates, rendering style and state.
		+	These files appear as regular image files to any software but, when loaded back in Jmol (or drag-and-dropped) will reproduce the exact state of the 3D molecular model.
		+
		+
		+
		+	''New feature:'' Allows replacement of PNG data in PNGJ
		+	(available since version 14.31.34)
		+	:<code>write "fileA.png" as pngj;</code> saves a file containing both the image, the model data and the state
		+	:<code>a = load("fileA.png",true);</code> loads the file contents into a (binary) variable
		+	:<code>b = load("fileB.png");</code> loads a regular image file into another (binary) variable
		+	:<code>a._IMAGE_ = b._DATA_;</code> puts the binary data making image "B" into the image section of data from file "A" (replacing the existing image data)
		+	:<code>write var a "fileC.png";</code> saves the new combination stored in variable "a", i.e. molecular data from file "A" and image from file "B", into a new PNGJ file

@@ Line 34: / Line 34: @@
 write v2000 myFile.myExt
 write myFile.myExt as mol
-write myFile.myExt as v2000</pre>
+write&nbsp;myFile.myExt&nbsp;as&nbsp;v2000</pre>
 | {{file|mol-v2000}}  format
 |-
 | <pre>write v3000 myFile.myExt
-write myFile.myExt as v3000</pre>
+write&nbsp;myFile.myExt&nbsp;as&nbsp;v3000</pre>
 | {{file|mol-v3000}}  format
 |-
@@ Line 69: / Line 69: @@
 | {{file|mol-v2000}}  format
 |-
-| <pre>write coord v3000 myFile.myExt</pre>
+| <pre>write&nbsp;coord&nbsp;v3000&nbsp;myFile.myExt</pre>
 | {{file|mol-v3000}}  format
 |}
@@ Line 98: / Line 98: @@
 | exports to {{file|xyz}} format, original untransformed coordinates
 |-
-| <pre>a = write("coord","mol")</pre>
+| <pre>a&nbsp;=&nbsp;write("coord","mol")</pre>
 | exports transformed coordinates to {{file|mol-v2000}} or {{file|mol-v3000}} format, respectively
 |-

@@ Line 107: / Line 107: @@
 === <code>show() chemical</code> function ===
-The same information that would be exported to a file may be put into a variable using this function.
+The same information that would be exported to a file may be put into a variable using this function. It uses the NCI CACTVS Resolver web service for format conversion, and hence it needs a live internet connection to work.
-:Note: ''If only a subset of the full model has been selected, only the currently selected atoms will be included in the exported model. Since the procedure involves a query to the NCI CACTVS Resolver, and their server tries to interpret it as a full molecule, the result may then not be what you expect. Example: <code>select _N; show("chemical pdb")</code> returns pdb-formatted data for ammonia, no matter which was the original molecule with several N atoms.''
+:''Available since Jmol version 14.6.0''
-:Note: ''available since Jmol version 14.6.0''
+:Note: ''If only a subset of the full model has been selected, only that subset will be included in the exported model. Since the procedure involves a query to the Resolver, and their server tries to interpret it as a full molecule, the result may then not be what you expect. Example: <code>select _N; show("chemical mol")</code> returns mol-formatted data for ammonia, no matter which was the original molecule containing several N atoms.''
 Formats available are:
@@ Line 172: / Line 172: @@
 The syntax is like this:
-  x = show("chemical xyz")
+  d = show("chemical xyz")
-  x = show("chemical mol")
+  d = show("chemical mol")
-  x = show("chemical hyperchem")
+  d = show("chemical hyperchem")
 etc.
 === Pop-up menu ===

@@ Line 118: / Line 118: @@
 ! <code>[https://www.cambridgesoft.com/services/documentation/sdk/chemdraw/cdx/IntroCDXML.htm cdxml]</code>
 | XML-compliant version of ChemDraw's native file format
-| <code>cerius</code>
+! <code>cerius</code>
 | Cerius II from Accelrys/MSI
 |-
-| <code>[https://www.charmmtutorial.org/index.php/CHARMM:The_Basics#Molecule_Metadata charmm]</code>
+! <code>[https://www.charmmtutorial.org/index.php/CHARMM:The_Basics#Molecule_Metadata charmm]</code>
 | CHARMM (Chemistry at HARvard Macromolecular Mechanics)
-| <code>[[File_formats/Coordinates#CIF|cif]]</code>
+! <code>[[File_formats/Coordinates#CIF|cif]]</code>
 | Crystallographic Information File
-| <code>cml</code>
+! <code>cml</code>
 | Chemical Markup Language
 |-
-| <code>ctx</code>
+! <code>ctx</code>
 | Gasteiger group
-| <code>gjf</code>
+! <code>gjf</code>
 | Gaussian input
-| <code>[[File_formats/Coordinates#GROMACS|gromacs]]</code>
+! <code>[[File_formats/Coordinates#GROMACS|gromacs]]</code>
 | GROMACS
 |-
-| <code>hyperchem</code>
+! <code>hyperchem</code>
 | HIV / HIN format from Hyperchem
-| <code>[[File_formats/Chemical_Structure#JME|jme]]</code>
+! <code>[[File_formats/Chemical_Structure#JME|jme]]</code>
 | from the JME/JSME Molecular Editor
-| <code>[https://sites.google.com/a/srscicomp.com/maestro/data-analysis/data-file-format maestro]</code>
+! <code>[https://sites.google.com/a/srscicomp.com/maestro/data-analysis/data-file-format maestro]</code>
 | from SchrÃ¶dinger
 |-
-| <code>[[File_formats/Coordinates#MOL_and_SD_.28Symyx_MDL.29|mol]]</code>
+! <code>[[File_formats/Coordinates#MOL_and_SD_.28Symyx_MDL.29|mol]]</code>
 | Symyx MDL
-| <code>mol2</code>
+! <code>mol2</code>
 | Sybyl, Tripos
-| <code>sybyl2</code>
+! <code>sybyl2</code>
 | Sybyl, Tripos
 |-
-| <code>[http://onlinelibrarystatic.wiley.com/marvin/help/formats/mrv-doc.html mrv]</code>
+! <code>[http://onlinelibrarystatic.wiley.com/marvin/help/formats/mrv-doc.html mrv]</code>
 | Marvin format, from ChemAxon
-| <code>pdb</code>
+! <code>pdb</code>
 | from Protein DataBank, but nonstandard
-| <code>[[File_formats/Coordinates#MOL_and_SD_.28Symyx_MDL.29|sdf]]</code>
+! <code>[[File_formats/Coordinates#MOL_and_SD_.28Symyx_MDL.29|sdf]]</code>
 | Symyx MDL
 |-
-| <code>[[File_formats/Coordinates#MOL_and_SD_.28Symyx_MDL.29|sdf3000]]</code>
+! <code>[[File_formats/Coordinates#MOL_and_SD_.28Symyx_MDL.29|sdf3000]]</code>
 | Symyx MDL, V3000
-| <code>[https://pubs.acs.org/doi/abs/10.1021/ci7004687 sln]</code>
+! <code>[https://pubs.acs.org/doi/abs/10.1021/ci7004687 sln]</code>
 | SYBYL Line Notation
-| <code>[[File_formats/Chemical_Structure#SMILES|smiles]]</code>
+! <code>[[File_formats/Chemical_Structure#SMILES|smiles]]</code>
 | SMILES string
 |-
-| <code>[[File_formats/Coordinates#XYZ|xyz]]</code>
+! <code>[[File_formats/Coordinates#XYZ|xyz]]</code>
 | the traditional XYZ format
+|

@@ Line 114: / Line 114: @@
 {| class="wikitable"
 |-
-| <code>[[File_formats/Coordinates#Alchemy_.28Tripos.29|alc]]</code>
+! <code>[[File_formats/Coordinates#Alchemy_.28Tripos.29|alc]]</code>
 | Alchemy (Tripos)
-| <code>[https://www.cambridgesoft.com/services/documentation/sdk/chemdraw/cdx/IntroCDXML.htm cdxml]</code>
+! <code>[https://www.cambridgesoft.com/services/documentation/sdk/chemdraw/cdx/IntroCDXML.htm cdxml]</code>
 | XML-compliant version of ChemDraw's native file format
 | <code>cerius</code>

@@ Line 74: / Line 74: @@
 === <code>write()</code> function ===
-This function in the Jmol Scripting Language allows to place the output of the write command into a variable, rather than saving to a file. The data can later be loaded using <code>load var a</code>
+This function in the Jmol Scripting Language allows to place the output of the write command into a variable, rather than saving to a file. The data can later be loaded using <code>load var a</code>.
 First parameter in the function is the format, second if needed is some qualifier, both matching what would be used in the command.
@@ Line 84: / Line 85: @@
+!
 |-
-| <pre>a = write("xyz")
+| <pre>a = write("xyz")</pre>
-a = write("pdb")</pre>
+| exports to {{file|xyz}} format
-| incorrect, not implemented, do not work
+|-
 |-
 | <pre>a = write("mol")
@@ Line 103: / Line 106: @@
 |}
 === Pop-up menu ===

@@ Line 45: / Line 45: @@
 write myFile.myExt as sdf</pre>
 | {{file|sdf-v2000}}  format
 |}
 All of the above commands will save the original cooordinates of each atom as they were in the input file.
-There is also the choice (only in MOL format) of saving the '''modified coordinates''' as in the current state of the model:
+There is also the choice (only in MOL format) of saving the '''transformed coordinates''' as they are in the current state of the model:
 {| class="wikitable"
 |-
 ! commands (synonymous)
 ! export the currently selected set of atoms,
-with modified coordinates, using this format:
+with transformed coordinates, using this format:
 |-
 | <pre>write coord myFile.mol
@@ Line 65: / Line 74: @@
 === <code>write()</code> function ===
-This function in the Jmol Scripting Language allows to put in a variable data equivalent to what the <code>write</code> command would save to a file.
+This function in the Jmol Scripting Language allows to place the output of the write command into a variable, rather than saving to a file. The data can later be loaded using <code>load var a</code>
 First parameter in the function is the format, second if needed is some qualifier, both matching what would be used in the command.
-Examples:
+Common examples:
- a = write("xyz") #incorrect, not implemented, does not work
+{| class="wikitable"
- a = write("pdb") #incorrect, not implemented, does not work
+|-
- a = write("mol") #exports to MOL v2000, original untransformed coordinates
+! commands
- a = write("v3000") #exports to MOL v3000, original untransformed coordinates
- a = write("coord") #exports to XYZ, original untransformed coordinates
+|-
- a = write("coord","mol") #exports to MOL v2000, transformed coordinates
+| <pre>a = write("xyz")
- a = write("coord","v3000") #exports to MOL v3000, transformed coordinates
+a = write("pdb")</pre>
 === Pop-up menu ===
@@ Line 89: / Line 115: @@
   File > Export > Export PNG+JMOL image
-The 2nd and 4th are equivalent and contain, in compressed form, a snapshot PNG image, the coordinates file and the state script file.
+The 2nd and 4th are equivalent and contain, packed in a single file, a snapshot PNG image, the coordinates file and the state script file.
 === Save isosurface ===
 The pop-up menu entry will svae the last isosurface selected or generated. More flexibility is allowed by using the [{{ScriptingDoc}}#writeobject <code>write isosurface</code>] command.