VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Oct 05 2021 - 23:42:45 CDT

Chris,

This is not a plugin but just a script with some functions written in
VMD/Tcl. And the script from the URL you quote will still work if you make
a tiny adjustment (it works for me with the provided example): there is
some location that points to the membrane plugin version 1.0. This plugin
is in version 1.2 in my VMD installation, so I needed to edit the file
accordingly. but other than that i just followed the instructions,
downloaded the PDB file, uncompressed it. launched VMD, sources the tcl
script. loaded the pdb file, then ran the command and then loaded the final
pdb file. It is complaining about poorly guessed coordinates, but the atoms
are still there.

Axel.

On Tue, Oct 5, 2021 at 11:50 PM Chris Taylor <christay_at_usc.edu> wrote:

> Hello, I ran across this old mailing list post:
>
> https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/8118.html
>
>
>
> It mentions using a plugin
> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/mergemultiframepdb/
> that doesn’t seem to be part of the distribution any more. The post
> describes something I’d like to do, for instance downloading the 5IRE
> “Biological Assembly 1” file from the RCSB.org protein databank and using
> the plugin to create a new structure with frames of trajectory 0-59
> represented. Then, in VMD I could manipulate the icosahedral assembly as
> one structure. Is there an up to date way to do this? I was able to
> download an old version of the plugin from somewhere but I got lots of
> errors when I ran it. Thanks,
>
> Chris
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!qT8xn5S8y77W2Wjr-B5eOSKVxQjNG2QL8HkNPi0x_jNDaIyzECcHoEkCjoqc_z2XwQ$ 
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.