VMD-L Mailing List
From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Wed May 05 2004 - 01:28:00 CDT
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>>> "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?
hello,
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:
<http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part3.html#chap5_sect3>
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: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de 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 http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/ ======================================================================= If you make something idiot-proof, the universe creates a better idiot.
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- In reply to: Edward J. Smiley Jr.: "Coloring with an XYZ file"
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