Jmol/PDB file editing with Jmol

The Jmol.jar application can be used to edit the contents of PDB files. For example, you could change atom serial numbers, names of chains, change sequence numbers, and so forth. A command script file can be written to make specific changes, following the principles outlined below.

Put the PDB file in a variablePut the PDB file in a variable

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

load =1d66 # No space between = and the 4-character PDB code.

After you have the PDB file loaded and the molecule is displayed:

mypdb = getproperty("filecontents")

mypdb now has one long string (with newlines) for the entire PDB file, unmodified, including the header.

Edit line by lineEdit line by line

It is usually easiest to loop through the PDB file line by line. So:

mypdblines = mypdb.lines

Now, mypdblines is an array with one PDB line per element. So you can loop line by line:

for (i=1; i<=mypdblines.length; i++)

{

  mypdblines[i] ...

}

Jmol has plentiful commands for finding lines, and editing them. For example, to operate only on lines beginning "ATOM ...",

if (mypdblines[i].find("^ATOM ", "")) ...

The second parameter "" signals that the first parameter should be interpreted as a regular expression, where "^" means "beginning of the line".

Most of Jmol's built in functions for operations on character strings are listed in this section of the Jmol documentation.

Since PDB format has fixed column positions, you can, for example, change the chain name, which is in column 22:

if ((mypdblines[i])[22][23] == "G") {(mypdblines[i])[22][23] = "D";}

(The atom property "chain" is not writable in Jmol, nor are "resno" nor "seqcode". So you can't simply assign new values to these properties.)

Write a PDB file containing the edited linesWrite a PDB file containing the edited lines

When finished, you write the PDB file like this:

write var @mypdblines "filename.pdb"

"Var" means you are writing the contents of a variable into a disk file.

It is important to note that the command

write "filename.pdb"

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

Saving key information in the headerSaving key information in the header

Custom information can be inserted into the header section of mypdblines. 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 mypdblines like this:

HEADER TRANSCRIPTION/DNA 06-MAR-92 1D66

@ Custom information in lines beginning "@ ".

TITLE DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX

Jmol uses the first line of a PDB file to recognize PDB format, so it is important not to put your custom lines first. Not only Jmol, but PyMOL and Chimera and likely other popular molecular visualization apps (including FirstGlance) happily ignore lines in a PDB file that do not begin with a recognizable record name such as REMARK or ATOM. (FirstGlance recognizes lines beginning "!" as custom information from the ConSurf server.)

It is even possible to put Jmol scripts (perhaps to define a function, or specify custom variable values [variables are not saved in PDB nor in PNGJ files]) for later use. For example, this could be inserted into the header of mypdblines:

@ # Jmol script.

@ myvar = 12.6

@ function f1()

@ {

@   print _arguments

@ }

@ # End Jmol script.

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 with "script inline @variable".

Writing a PNGJ file containing the edited linesWriting a PNGJ file containing the edited lines

PNGJ files contain a PNG (Portable Network Graphics) static image of the scene Jmol was displaying when the PNGJ file was written, and also the complete information to reproduce the scene in Jmol. When you drag a PNGJ file and drop it into Jmol's graphics window, the scene appears in interactive form that can be rotated, zoomed, and further modified with Jmol commands.

In addition to a PDB file, you can save a PNGJ file with customized PDB lines and a customized header, tho 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:

# Customize mypdblines as desired previous to this line.

zap # Deletes all atoms and defined atom sets. Preserves variables and functions.

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

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

write filename.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.

A PDB file editing server?A PDB file editing server?

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 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). See the link "Export Animated Image" under any JSmol in Proteopedia.Org. In collaboration with Prilusky, User:Eric Martz adapted these server routines to make such animations within FirstGlance.Jmol.Org (with a simplified user interface). There, under JSmol, click "Save Image or Animation for Powerpoint".

If you know of any PDB file editing servers, please link them here!