From: Axel Kohlmeyer (
Date: Wed May 05 2004 - 01:28:00 CDT

>>> "ES" == Edward J Smiley, <Edward> writes:

ES> Hello all,
ES> I am having some trouble trying to figure out how to color with this
ES> new user field. I have an xyz file (well, xmol actually) that is made
ES> up of numerous frames with the following format.

>> 530590
>> Time = 0
>> C9 166.23 164.11 6.53 1.00
>> C9 167.14 163.06 6.96 1.00
>> etc. to line 530592
>> 530590
>> Time = 1
>> C9 166.23 164.11 6.53 1.00
>> C9 167.14 163.06 6.96 0.00
>> etc.

ES> The last column represents the direction of the atom. If it is a 1
ES> then it is moving down, if it is a 0 then it is not moving or moving
ES> up. I have tried to figure out where this last column is put when VMD
ES> "converts" it from an XYZ. The user field only lists 0.00 and no other
ES> field list 1and 0. How does VMD handle a xyz file, does it convert it
ES> to a PDB somehow or just read it straight?


vmd reads the xyz file straight away, but since there are so many
conventions on what to store in the 5th to the n-th column, it simply
ignores that additional data.

in your case you would have to set the user data
separately. e.g. extract 1/0 data into a separate file and
then read it in and set the user field from that via a vmd script.
please have a look at the example in:


it uses the charge property, but the process is the same.

good luck,
     axel kohlmeyer.

ES> You guys have a great program here!
ES> Thanks for any help,
ES> Ed Smiley

Axel Kohlmeyer       e-mail:
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum
If you make something idiot-proof, the universe creates a better idiot.