VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 06 2022 - 00:11:44 CDT

Hi,
  I'm not familiar with the specific script you're using in that
tutorial, but just reading the tutorial page you referenced, it is
clear that the variable "a1" should have been set by this command:
  set a1 [vecscale $l1 $basisVector1]

You'll likely need to edit/customize the script if you're trying to
use something from a tutorial in a more general case with different
input files.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Apr 26, 2022 at 02:10:39PM +0000, Linda Ravazzano wrote:
> 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
> page: [1]https://www.ks.uiuc.edu/Training/Tutorials/science/bionano/bionano-tutorial-html/node3.html#scr:replicateCrystal
> 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
>
> References
>
> Visible links
> 1. https://www.ks.uiuc.edu/Training/Tutorials/science/bionano/bionano-tutorial-html/node3.html#scr:replicateCrystal 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/