VMD-L Mailing List

From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Thu Feb 19 2015 - 15:10:19 CST

Why do you need to load them info separate molecules if this is the same enzyme? Simply load them into a single molecule (vmd -m ... ), create representation you want and proceed as needed.

Maxim

> On Feb 19, 2015, at 7:26 AM, jing liang <jingliang2015_at_gmail.com> wrote:
>
> hi,
>
> I have multiple pdb files of an enzyme called frame1.pdb, frame2.pdb, ... and
> so on.
>
> I want to display the whole structure of the enzyme with "lines" but some
> amino acids and ions with "cpk" ("segid ami" and "segid ion") .
>
> Dealing with a single frame is not a problem because I can use the graphics
> representation tool to select the drawing method "lines" for the enzyme
> and then use the "cpk" after creating a new representation.
>
> My problem is when I have to do the same for 30 frames. What I am doing is
> to open the frames with
>
> vmd -f frame1.pdb -f frame2.pdb -f frame3.pdb ... -f frame30.pdb
>
> and then I need to do the steps I already mentioned with the graphics
> representation tool.
>
> Is there any way to accomplish this task more efficiently? Is it possible to
> do that with the tcl scripting of VMD?
>
> thanks.
>
>
>