VMD-L Mailing List
From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue May 01 2012 - 19:13:11 CDT
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On Tue, May 1, 2012 at 6:18 PM, Heather Mayes <hmayes_at_hmayes.com> wrote:
> I tried a couple things. The one I thought would be successful was
> copying the sample in a cpmd-vmd tutorial (below) and putting it in my
o dear. the sins of my youth are coming back to haunt me. ;)
> vim.rc (I'm using Windows). I saved and reopened VMD and then a
> molecule the result was a null result: the same display behavior
> (default lines) as if I had not added anything to my vim.rc. I have
> successfully made other changes to my vim.rc which do show a
> different display, such as adding the line "mol default style {VDW 0.3
> 15}".
> # delete the default visualization and create another one
> proc my_def_viz {args} {
> lassign $args fname molid
> mol delrep 0 $molid
> mol color Type
> mol representation CPK 1.000000 0.300000 19.000000 16.000000
> mol addrep $molid
> }
> # add 'default visualization' hack for the first three molecules.
> trace variable vmd_read_trajectory(0) w my_def_viz
> trace variable vmd_read_trajectory(1) w my_def_viz
> trace variable vmd_read_trajectory(2) w my_def_viz
>
> Does this look like it should work? As I said, it did not for me.
this was developed and tested with a *much* older version of VMD.
apparently there were some changes to the syntax and how
variable traces are handled. please try using the following code
instead that i just tested with a current version of VMD. it is a
bit more complicated, but also more robust and will work on
the molecule loaded at startup.
good luck,
axel.
proc reset_viz {molid} {
# operate only on existing molecules
if {[lsearch [molinfo list] $molid] >= 0} {
# delete all representations
set numrep [molinfo $molid get numreps]
for {set i 0} {$i < $numrep} {incr i} {
mol delrep $i $molid
}
# add new representations
mol color Name
mol representation VDW 0.3 15.0
mol selection all
mol material Opaque
mol addrep $molid
mol representation DynamicBonds 1.6 0.3 6.0
mol selection {name C}
mol addrep $molid
mol representation DynamicBonds 1.2 0.3 6.0
mol selection {name C H}
mol addrep $molid
}
}
proc my_def_viz {args} {
foreach {fname molid rw} $args {}
eval "after idle {reset_viz $molid}"
}
trace variable vmd_initialize_structure w my_def_viz
# take care of the molecule loaded on startup.
after idle {reset_viz 0}
> Thank you,
> -Heather
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA.
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- Reply: Heather Mayes: "Re: Make "Load all at once" the default? Adding representations?"
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