Tutorial-l Mailing List

From: Chris Harrison (charris5_at_gmail.com)
Date: Thu Jul 09 2009 - 15:49:42 CDT

Two ideas:
1) did you actually type: "$ubq writepdb ubq.pdb" and not just "writepdb
ubq.pdb"?

2) after doing your atomselection, try "$ubq num". This should return the #
of atoms of the $ubq selection. If not, there's a problem in the
atomselection command .....

Chris 

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char               Fax: 217-244-6078
On Thu, Jul 9, 2009 at 1:51 PM, Corey Fugate <fugate_at_hawaii.edu> wrote:
>        Page 9 of the Unix/Mac NAMD tutorial step 4.  I have 1UBQ.pdb open
> in vmd, I open the Tk console and type (while in the 1-1-build dir) -
> set ubq [atomselect top protein]  (press enter)
>
> atomselect0 is printed to the screen.  After using writepdb ubqp.pdb the
> pdb file is written, n=but is completely empty.
>
>                Am I missing something?
>
>
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