File formats/Ray Tracing - Revision history

GregE at 23:58, 29 October 2013

2013-10-29T23:58:02Z

GregE at 00:21, 27 October 2013

2013-10-27T00:21:07Z

GregE at 00:19, 27 October 2013

2013-10-27T00:19:30Z

GregE: /* POV-Ray for Mac */

2013-10-25T21:17:08Z

‎POV-Ray for Mac

GregE: /* POV-Ray for Mac */

2013-10-24T03:10:37Z

‎POV-Ray for Mac

GregE at 02:16, 18 October 2013

2013-10-18T02:16:19Z

GregE at 06:14, 17 October 2013

2013-10-17T06:14:28Z

GregE at 00:02, 15 October 2013

2013-10-15T00:02:27Z

AngelHerraez: moving POV-Ray information to a new subpage - Also, new info on Tachyon

2010-02-06T13:11:41Z

moving POV-Ray information to a new subpage - Also, new info on Tachyon

New page

{{File_Formats}}
= File Formats for Ray Tracing Images Exported from Jmol =

Recent versions of Jmol application and signed applet can export models to several high-quality image formats that can be displayed and edited in ray tracing programs like POV-Ray and Tachyon.

== POV-Ray ==
Jmol can export, with limited features, the current view of a model into POV-Ray format. This can be done from script or from the pop-up menu, but is better controled using the top menu in the Jmol application, which opens a dialog with options.

Please, note that two files will be written: the main file and an additional one with a <code>.ini</code> extension appended (a typical example would be {{file|xxx.pov}} and {{file|xxx.pov.ini}}).

* [http://www.povray.org/ Home page] for POV-Ray, the Persistence of Vision Raytracer.
* Information on [[:en:POV-Ray|POV-Ray]] on Wikipedia.

<div style="float:right;padding-left:1ex;">
[[Image:POV-RayExportDialog.png|POV-Ray export dialog]]
</div>
=== Saving from Jmol application ===
The application's top menu bar has
<br />
<code>File > Export > Render in POV-Ray</code>
<br />
which produces images that can be displayed and edited in this ray tracing program (using a dialog with options).

There is also a button in the toolbar that invokes the same dialog.
[[Image:POV-RayExportToolbar.png|POV-Ray export from toolbar]]

{{clear}}
=== Saving from Jmol application and signed applet ===

The pop-up menu also allows in these cases (not in the normal, unsigned applet) to save a snapshot of the model in <code>POV-Ray</code> format. Open the pop-up menu (right-click, or Ctrl+click, or click on Jmol frank) and choose <code>File > Save</code> (or directly <code>Save</code> in older versions). After choosing a format, a dialog will open to choose the location and filename.
In this method, no other options for the export will be offered.

You can also export using a script (e.g. from the console) with the <code>write</code> command (see the [{{ScriptingDoc}}#writeexport scripting documentation]).

== Tachyon ==
Jmol can export, with limited features, the current view of a model into Tachyon format. Currently this can only be done from script.

* [http://jedi.ks.uiuc.edu/~johns/raytracer/ Home page] for Tachyon, a Parallel / Multiprocessor Ray Tracing System.
* [http://jedi.ks.uiuc.edu/~johns/raytracer/papers/tachyon.pdf File format specification].

@@ Line 24: / Line 24: @@
-The 3.7 Unofficial release appears to utilise 2 cores fully. It runs the model.pov and model.pov.ini files generated by Jmol 13.0.18 and produces fine images.
+The MegaPOV 3.7 Unofficial release appears to utilise 2 cores fully. It runs the model.pov and model.pov.ini files generated by Jmol 13.0.18 and produces fine images.
 The technique which has worked for me on 10.6.8 is:
@@ Line 38: / Line 38: @@
 Some examples are at http://ptmgallery.s3.amazonaws.com/list.html
-I will try to find and document a command-line technique to do all the above, and to allow the direct Render button from the Jmol standalone app to work.
+Using 2 cores (see the Render Pefererences panel, Bounding and Threads) only drops the render time from say 5 seconds to 4 seconds for a small molecule (amino acid) and not much different for a larger one (eg. 1GFL.pdb). You can see the two threads at times, when one falls behind the other on a time-consuming piece of the scene, and the checkerboard updates separately.
-Update 17oct13: My research is showing that there is no command-line version of (Mega)POV-Ray Unofficial 3.7. Ie. running the app always launches into the full Gui version. You ''may'' be able to write basic settings to a scene.pov.ini file and launch the app to obey that, I have not attempted that yet.
+There appears to be no command-line version of (Mega)POV-Ray Unofficial 3.7. Ie. running the app always launches into the full Gui version.
-The Unix/Linux version can obviously run on Mac as well, and has command-line abilities. Useful discussion is at:
+The Unix/Linux version of POV-Ray can run on Mac as well, and has command-line abilities. Useful discussion is at:
 http://news.povray.org/povray.unix/   and
-http://news.povray.org/povray.macintosh/  I have not put time into this yet.
+http://news.povray.org/povray.macintosh/  It would need to be built from source, which can vary greatly in difficulty depending mainly on how far the libraries needed have changed from the set used at the time (2007/8/9) . I have not put time into this.
 ===POV-Ray for Windows===
@@ Line 50: / Line 50: @@
 An update for POV-Ray on Windows, Oct 2013.  The following was tested on Windows 7, under Parallels 7 on Mac OS X 10.6.8.
-The standard latest POV-Ray Windows release is 3.6. Can be downloaded from http://www.povray.org/download/#binaries . I used the 32 bit version. Release 3.7 is a beta of the SMP version. There is possibly little galn from SMP on Jmol images, they are not render-intensive in a ray-tracing sense. The SMP code only drops the render time from say 5 seconds to 4 seconds for a simple small molecule, in MegaPOV-Unoffical-3.7 (described above).
+The standard latest POV-Ray Windows release is 3.6.2. Can be downloaded from http://www.povray.org/download/#binaries . I used the 32 bit version.
 Install POV-Ray 3.6 wherever you prefer, then run Jmol as a standalone app (by clicking in Windows Explorer, or java -jar Jmol.jar mymodel.pdb).  The POV-Ray icon on the menubar will bring up the dialog shown below. Fill in the location of the POV-Ray executable (pvengine.exe).
@@ Line 56: / Line 56: @@
 Hit Go. A dialog may pop up asking for special permission to read the Jmol.pov file, answer yes. (This is a POV-Ray security check, read the Help in the dialog for details). The molecule will then render.
-POV-Ray 3.7 and MegaPOV were not tested here.
+POV-Ray 3.7 Beta adds SMP facilities. It worked fine and reduced render times by about 20%. I used the 32-bit version.

@@ Line 50: / Line 50: @@
 An update for POV-Ray on Windows, Oct 2013.  The following was tested on Windows 7, under Parallels 7 on Mac OS X 10.6.8.
-The standard latest POV-Ray Windows release is 3.6. Can be downloaded from http://www.povray.org/download/#binaries . Release 3.7 is a beta of the SMP version. There is possibly little galn from SMP on Jmol images, they are not render-intensive in a ray-tracing sense. The SMP code only drops the render time from say 5 seconds to 4 seconds for a simple small molecule, in MegaPOV-Unoffical-3.7 (described above).
+The standard latest POV-Ray Windows release is 3.6. Can be downloaded from http://www.povray.org/download/#binaries . I used the 32 bit version. Release 3.7 is a beta of the SMP version. There is possibly little galn from SMP on Jmol images, they are not render-intensive in a ray-tracing sense. The SMP code only drops the render time from say 5 seconds to 4 seconds for a simple small molecule, in MegaPOV-Unoffical-3.7 (described above).
 Install POV-Ray 3.6 wherever you prefer, then run Jmol as a standalone app (by clicking in Windows Explorer, or java -jar Jmol.jar mymodel.pdb).  The POV-Ray icon on the menubar will bring up the dialog shown below. Fill in the location of the POV-Ray executable (pvengine.exe).

@@ Line 15: / Line 15: @@
 === POV-Ray for Mac ===
-The following concerns POV-Ray for Mac, as of Oct 2013. The latest official release for Mac from POV-Ray is 3.6, dating from somewhere around 2007. It runs only on Power PC Macs, not on Intel Macs, ie. it is not a Mac OS X Universal Binary (containing IBM Power-PC and Intel binaries).
+The following updates POV-Ray for Mac, as of Oct 2013. The latest official release for Mac from POV-Ray is 3.6, dating from somewhere around 2007. It runs only on Power PC Macs, not on Intel Macs, ie. it is not a Mac OS X Universal Binary (containing IBM Power-PC and Intel binaries).
 For Windows, POV-Ray Release 3.7 is available, the main addition being SMP abilities, ie. it can run on all cores of a chip - useful for a ray-tracer which is an "embarrassingly parallel" type of code. This appears to date from about 2009.
@@ Line 45: / Line 45: @@
 http://news.povray.org/povray.unix/   and
 http://news.povray.org/povray.macintosh/  I have not put time into this yet.

@@ Line 15: / Line 15: @@
 === POV-Ray for Mac ===
-The following concerns POV-Ray for Mac, as of Oct 2013. The latest official release for Mac from POV-Ray is 3.6, dating from somewhere around 2007. It runs only on Power PC Macs, not on Intel Macs, ie. it is not a Mac OS X Universal Binary (containing IBM Power-PC and Intel binaries).  Release 3.7 is available for Windows, and introduces SMP abilities, ie. can run on all cores of a chip. This appears to date from about 2009.
+The following concerns POV-Ray for Mac, as of Oct 2013. The latest official release for Mac from POV-Ray is 3.6, dating from somewhere around 2007. It runs only on Power PC Macs, not on Intel Macs, ie. it is not a Mac OS X Universal Binary (containing IBM Power-PC and Intel binaries).
-Mac OS X 10.6 can allegedly have the Rosetta IBM Power-PC emulator installed, see  http://support.apple.com/kb/ph6531  This was on by default in 10.5 and earlier, and was the means by which older Power-PC apps could be run on the Intel Macs. It is being phased out by Apple and I believe it could be problematic at 10.6.
+For Windows, POV-Ray Release 3.7 is available, the main addition being SMP abilities, ie. it can run on all cores of a chip - useful for a ray-tracer which is an "embarrassingly parallel" type of code. This appears to date from about 2009.
-However MegaPOV which is much more active has released a "3.7 Unofficial" release for Mac in 2013. Available at  http://megapov.inetart.net/povrayunofficial_mac/index.html  This runs ok on Mac OS X 10.6.8 (Snow Leopard) and allegedly later, ie. 10.7 Lion and 10.8 Mountain Lion. If you search for "povray 3.7 unofficial mac" you will find the announcements and some discussion.
+Prior to OS X 10.6 (Snow Leopard) Macs used the Rosetta emulator to run Power-PC apps on the later Intel chips. However this is defaulted off in 10.6. It can be installed, see  http://support.apple.com/kb/ph6531 .  However I believe that it is somewhat problematic at 10.6 or later.
 The 3.7 Unofficial release appears to utilise 2 cores fully. It runs the model.pov and model.pov.ini files generated by Jmol 13.0.18 and produces fine images.
-The technique which has worked for me is:
+The technique which has worked for me on 10.6.8 is:
 * Adjust Jmol window size to 800x600
 * Get your Jmol scene how you want it.
@@ Line 31: / Line 33: @@
 * Also in that panel, Tick 'Use Ini File', and specify scene.pov.ini
 * Also in that panel, if any standard POV-ray include files are needed, specify <path>/POV-Ray 3.7Unofficial/include as a search path for includes.
-* In the panel Image & Quality, select 800x600. (This laborious matching of 800x600 is not fully necessary but it will get you going).
+* In the panel Image & Quality, select 800x600. (This laborious matching of 800x600 is not fully necessary but it will get you going. Later you can play with sizes and aspect ratios).
 * In Misc, you can also set a path for all output images, which overrides setting (*) above.
@@ Line 38: / Line 40: @@
 I will try to find and document a command-line technique to do all the above, and to allow the direct Render button from the Jmol standalone app to work.
-Update 17oct13: My research is showing that there is no command-line version of (Mega)POV-Ray Unofficial 3.7. Ie. running the app always launches into the full Gui version. You -may- be able to write basic settings to a scene.pov.ini file and launch the app to obey that, I have not succeeded yet.
+Update 17oct13: My research is showing that there is no command-line version of (Mega)POV-Ray Unofficial 3.7. Ie. running the app always launches into the full Gui version. You ''may'' be able to write basic settings to a scene.pov.ini file and launch the app to obey that, I have not attempted that yet.
 The Unix/Linux version can obviously run on Mac as well, and has command-line abilities. Useful discussion is at:
 http://news.povray.org/povray.unix/   and
-http://news.povray.org/povray.macintosh/
+http://news.povray.org/povray.macintosh/  I have not put time into this yet.

@@ Line 15: / Line 15: @@
 === POV-Ray for Mac ===
-The following concerns POV-Ray for Mac, as of 15 Oct 2013. The latest official release for Mac from POV-Ray is 3.6, dating from somewhere around 2007. It runs only on Power PC Macs, not on Intel Macs, ie. it is not a Mac OS X Universal Binary (containing IBM Power-PC and Intel binaries).  Release 3.7 is available for Windows, and introduces SMP abilities, ie. can run on all cores of a chip. This appears to date from about 2009.
+The following concerns POV-Ray for Mac, as of Oct 2013. The latest official release for Mac from POV-Ray is 3.6, dating from somewhere around 2007. It runs only on Power PC Macs, not on Intel Macs, ie. it is not a Mac OS X Universal Binary (containing IBM Power-PC and Intel binaries).  Release 3.7 is available for Windows, and introduces SMP abilities, ie. can run on all cores of a chip. This appears to date from about 2009.
 Mac OS X 10.6 can allegedly have the Rosetta IBM Power-PC emulator installed, see  http://support.apple.com/kb/ph6531  This was on by default in 10.5 and earlier, and was the means by which older Power-PC apps could be run on the Intel Macs. It is being phased out by Apple and I believe it could be problematic at 10.6.
@@ Line 38: / Line 38: @@
 I will try to find and document a command-line technique to do all the above, and to allow the direct Render button from the Jmol standalone app to work.
-Update 17oct13: My research is showing that there is no command-line version of (Mega)POV-Ray Unofficial 3.7. Ie. running the app always launches into the full Gui version. You -may- be able to write basic settings to a scene.pov.ini file and launch the app to obey that, not succeeded yet.
+Update 17oct13: My research is showing that there is no command-line version of (Mega)POV-Ray Unofficial 3.7. Ie. running the app always launches into the full Gui version. You -may- be able to write basic settings to a scene.pov.ini file and launch the app to obey that, I have not succeeded yet.
 The Unix/Linux version can obviously run on Mac as well, and has command-line abilities. Useful discussion is at:
@@ Line 48: / Line 48: @@
 [[Image:POV-RayExportDialog.png|POV-Ray export dialog]]
 </div>
 === Saving from Jmol application ===
 The application's top menu bar has

@@ Line 11: / Line 11: @@
 * [http://www.povray.org/ Home page] for POV-Ray, the Persistence of Vision Raytracer.
 * Information on [[:en:POV-Ray|POV-Ray]] on Wikipedia.
 <div style="float:right;padding-left:1ex;">