VMD-L Mailing List

From: Heather Mayes (hmayes_at_hmayes.com)
Date: Wed May 02 2012 - 15:50:28 CDT

Axel and Joe,

Thank you both very much for your responses. This will save me much tedium!!

-Heather

On Tue, May 1, 2012 at 6:13 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> 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.