Jmol/PDB file editing with Jmol: Difference between revisions

First, run the [[Jmol/Application|Jmol.jar Java application]], and load any PDB file. If you have a PDB file saved to your disk (for example, downloaded from [http://rcsb.org RCSB.Org]), drag it and drop into the Jmol graphics window. Alternatively, to load 1d66 directly from the [[PDB]]:

<code>mypdb</code> is a variable inside the Jmol scripting context that now has one long string (including newline characters) for the entire PDB file, unmodified, including the header.

It is usually easiest to loop through the PDB file line by line. So, let's define a new variable:

   &nbsp;  mypdblines[i] ... # do something with this

  write var mypdblines "someFileName.pdb"

It is important to note that another command you might think of using,

writes a file without the original header (and containing only the currently selected atoms). By using the variable <code>mypdblines</code>, you preserve the header and write all atoms.

Custom information can be inserted into the header section of <code>mypdblines</code>.  

 

===Method #1===

For example, if Jmol has calculated things that you would like to have available (without re-calculating) in the output PDB file, you can insert lines between the first and second lines of <code>mypdblines</code> like this:

After loading the saved PDB or PNGJ file with this in its header, you can drag and drop in a script file that (i) extracts the @ lines into a variable, (ii) removes the leading "@ " from each line, then (iii) executes the variable using "<code>script inline @variable</code>".

 

If you prefer your files to be closer to PDB format standards (and so prevent potential problems if those files are read into other software), any extra custom lines should always start with the PDB keyword <code>REMARK</code>. In fact, Jmol is designed to read and apply any Jmol scripts embedded in the file, when a line starts with <code>REMARK jmolscript:</code> (as described in [http://wiki.jmol.org/index.php/File_formats/Scripting#Script_inline_within_a_molecular_coordinates_file this page]). You must put your whole script of commands into that single line, but several such lines in a file are also supported. Taking the example above, this would look like:

In addition to a PDB file, you can save a PNGJ file with customized PDB lines and a customized header, though it is slightly more tricky. Unlike a PDB file, you can't save a PNGJ file from a variable. So here is one scripting method that works, using only 3 commands:

  load var mypdblines # loads the PDB file data contained in the variable, including header, optionally modified.

  # Render, color, center, orient and zoom as desired.

  write someFileName.pngj

The PNGJ file will have all the customized PDB lines as well as the view at the time it was saved. It does not include variables or functions that were defined at the time is was saved. If any of these are needed, define them in custom header @ lines and write a script to use them as described above, or use <code>REMARK jmolscript:</code> lines to include the definition of those variables.

 

 

For those who might be interested in writing a server to modify PDB files, JmolData.jar is a variant of Jmol that runs without a graphics window. It is perfect for these kinds of operations. [[User:Jaime Prilusky|Jaime Prilusky]] used it in Proteopedia.org to generate a series of image files after small rotations. These are then assembled into a multi-GIF movie using other free software (ImageMagick.org) in the web server. See the link "Export Animated Image" under any JSmol box in Proteopedia.Org. In collaboration with Prilusky, [[User:Eric Martz|Eric Martz]] adapted these server routines to make such animations within [http://FirstGlance.Jmol.Org FirstGlance.Jmol.Org] (with a simplified user interface). There, under JSmol, click "Save Image or Animation for Powerpoint".