VMD-L Mailing List

From: Eduard Schreiner (eduard.schreiner_at_gmail.com)
Date: Tue Nov 30 2010 - 19:44:55 CST

Hi Luke,

2010/11/30 JhonY. I. <yijhon_at_hotmail.com>:
> I've studied TCL script in tutorial of VMD and it was vuluable really.
> But I'd like to ask your advice on some points as follows.
>
> 1. Would you let me know what command I should use to load "i" th frame from
> DCD file of multi-frame?
>

Check out the "mol addfile" command in the manual. I will be something like

mol addfile YOURDCD.dcd type dcd first YOURSTEP last YOURSTEP step 1
filebonds 1 autobonds 1 waitfor all

> 2. Does DCD file have also similar column to B factor column of pdb file?

no

> If so, what is it?
> If I'd like to assing "mag" (it is vector having length of total atom
> number) to B factor-like column of DCD file, what should I do?

if you have a list mag containing all the data, you can do something like

set a [atomselect top all]
$a set beta $mag

Check the User's Guide for examples, e.g., p. 98 or p. 175.
The issue was also already discussed on this list, so you may want to
check that too.

eddi
>
>
> Best regards,
>
>   Luke
>
> 

-- 
--
=============================================================================
Eduard Schreiner
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
Phone: 217-244-4361
Fax: 217-244-6078
http://www.ks.uiuc.edu/~eschrein/
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