From: Linda Ravazzano (
Date: Tue Apr 26 2022 - 09:10:39 CDT

Hi everybody,

I have just started to use vmd and I'm interested in obtaining pdb files of crystals composed of multiple copies of a defined unit cell.

I have a pdb file of the unit cell that has the following structure:


REMARK Unit cell dimensions:
REMARK a1 9.4214
REMARK a2 9.4214
REMARK a3 6.8814
REMARK Basis vectors:
REMARK basisVector1 1.0 0.0 0.0
REMARK basisVector2 0.5 sqrt(3.)/2. 0.0
REMARK basisVector3 0.0 0.0 1.0
REMARK replicationCount 1 1 1
ATOM 1 CAL CAL 1 1.132 14.255 12.038 1.00 0.00 Ca
ATOM 2 CAL CAL 2 4.712 13.603 6.889 1.00 0.00 Ca
ATOM 3 CAL CAL 3 2.357 16.269 8.599 1.00 0.00 Ca

To multiply the unit cell and to obtain a proper pdb file I used the
script 'replicateCrystal.tcl' that I found in your official Tutorial
When running the code on VMD TkConsole, I obtain this error: can't read "a1": no such variable
I would like to know if this is due to the peculiar structure of the unit cell pdb file I'm using.
In the Tutorial script, I just changed the input file, output name and crystal parameters.

Thanks in advance for your time and availability.
Kind regards.

Linda Ravazzano