VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Dec 13 2012 - 06:30:54 CST

On Thu, Dec 13, 2012 at 11:48 AM, Pawel Siuda <siuda.pawel_at_gmail.com> wrote:
> Hello everyone,
>
> I would really appreciate if someone would be able to help me to find a way
> to ascribe time-varying atom descriptors to user field.

simple. check out: pages 10 to 12 of this document:

https://sites.google.com/site/akohlmey/redirect/cpmd-vmd.pdf?attredirects=0&d=1

> I was trying to use beta field of pdb file to do so. In script library there
> is a pdbbfactor.tcl script, which is supposed to do the job, but is not

ouch. this seems very complicated.

> working (user values are not being changed). I was also trying to write a

the script below makes assumptions about a pdb format file,
that may not be true and thus many standard conforming .pdb
files will not be read correctly. this is overkill anyway.

> script on my own, but as I am kind of new to Tcl, there is still sth wrong
> with it. I would really appreciate if any of you could help me out.

there is an excellent Tcl tutorial on www.tcl.tk
http://www.tcl.tk/man/tcl8.5/tutorial/tcltutorial.html

axel.

> Regards,
> Paweł
>
> here is my code:
> display projection orthographic
>
> set dane [open "hyd.pdb" r]
> set numframes [molinfo top get numframes]
> set sel [atomselect top "all"]
> for {set i 0} {$i<$numframes} {incr i} {
>
> $sel frame $i
> gets $dane
> gets $dane
> gets $dane
> gets $dane
> gets $dane
> for {set j 0} {$j < 15875} {incr j} {
> gets $dane war
> set lst [split $war " "]
> set k [llength $lst]
> set l [expr {$k - 1}]
> set z "[lindex $lst $l]"
> $sel set user $z
> }
> gets $dane
> gets $dane
> $sel frame $i
> }
> $sel delete
>
> mol representation VDW 20.500000 40.000000
> mol color Name
> mol material Opaque
> mol selection {user >= 4}
> mol addrep top
> set molid 0
> set n [molinfo $molid get numreps]
> for {set i 0} {$i < $n} {incr i} {
> mol selupdate $i $molid on
> }
> animate goto start
> 

--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.