VMD-L Mailing List

From: James Kress (jimkress_58_at_kressworks.org)
Date: Thu Feb 19 2015 - 12:23:51 CST

Can’t you combine the pdb files into one pdb file? Then you can use the Graphics Representation menu to define the display for all frames at once.

 

Jim

 

James Kress Ph.D., President

The KressWorks Foundation ©

An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization

"Improving Lives One Atom At A Time" TM

(248) 605-8770

 

Learn More and Donate At:

 <http://www.kressworks.org/> http://www.kressworks.org

 

Confidentiality Notice | This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or proprietary information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, immediately contact the sender by reply e-mail and destroy all copies of the original message.

 

From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of jing liang
Sent: Thursday, February 19, 2015 8:26 AM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: script for displaying multiple frames

 

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.