VMD-L Mailing List

From: Joe Huang (HCHuang_at_uh.edu)
Date: Fri May 02 2003 - 16:23:54 CDT

Dear Justin,
Actually, I haven't really solved the problems yet about the "Memory
problems with TCL scripts in VMD" that I mentioned on Thu Mar 20 2003
-13:02:48 CST. So I wonder what you mean by saying that you have found
and corrected the problem that was leading to the out of memory
condition from Thomas' script. Do you mean there is a bug in the
program and you have debugged it or ...?

Best regards,

H.-C. (Joe) Huang 

-- 
 *****************************************
 Hung-Chung Huang, M. T., M. Sc., Ph. D.
 Department of Biology and Biochemistry
 University of Houston, Houston, TX 77204
 Tel: (713) 743-8365, Fax: (713) 743-8351
 e-mail: HCHuang_at_uh.edu
 http://prion.bchs.uh.edu/~jhuang
 *****************************************
Justin Gullingsrud wrote:
>Thomas,
>
>Thanks for letting us know about this problem.  We've found and corrected
>the problem that was leading to your out of memory condition.
>
>I might also suggest:
>
>  
>
>>proc rmsd_resid { frame } {
>>
>>	global time_betw_frame selection rmsd_selec fid20 reference1 num_resid
>>
>>	# the selection and frame used for fitting
>>       	set compare1 [atomselect top $selection frame $frame]
>>    
>>
>
>Since compare1 is always the same selection, just with a different frame
>it will be much faster to create compare1 only once, then call
>
>  $compare1 frame $frame
>
>to set the frame.  This will also make it unnecessary to delete the selection
>below.
>
>  
>
>>	# compute the transformation
>>       	set trans_mat1 [measure fit $compare1 $reference1]
>>
>>	$compare1 delete
>>	unset compare1
>>    
>>
>
>Cheers,
>Justin
>
>  
>