VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Thu May 28 2015 - 17:14:24 CDT

to your first question:

see fig 9 here:

https://www-s.ks.uiuc.edu/Training/Tutorials/science/timeline/tutorial_timeline-html/node4.html

or page 17 here:

http://www.ks.uiuc.edu/Training/Tutorials/science/timeline/tutorial_timeline.pdf

for your later question:

when the graph has popped up -- top write corner -

*File > Write data file*

this will convert the graphical to text format into something like this:

*residue|| Chain||some_val||frame number||secondary_structure_Code*

Then you can trace a residue's secondary structure state across frame
numbers ...

On Fri, May 29, 2015 at 4:21 AM, Jevgenij Raskatov <jraskato_at_ucsc.edu>
wrote:

> And one more thing, can one actually take this color-coded graph and turn
> it into numbers, e.g. how many distinct instances along the trajectory does
> the helical element appear?
>
> On Thu, May 28, 2015 at 9:14 AM, Jevgenij Raskatov <jraskato_at_ucsc.edu>
> wrote:
>
>> Thanks a lot, Ashar; how do I read the color code? I understand that H is
>> helix and C is likely coil, but what about T, E, B, G and I?
>>
>> Thank you!
>>
>> On Wed, May 27, 2015 at 7:54 PM, Ashar Malik <asharjm_at_gmail.com> wrote:
>>
>>>
>>> 1.
>>>
>>> Select *Extensions:Analysis:Timeline* from "VMD Main" window.
>>> 2.
>>>
>>> display a 2D graph of secondary structure vs. time, select
>>> Calculate:Calc Sec. Struct. from the "VMD Timeline" window. A color-coded
>>> map of secondary structure should appear. The horizontal axis is time
>>> (frame number), the vertical axis is residue number/chain.
>>>
>>> Source: http://www.ks.uiuc.edu/Research/vmd/plugins/timeline/
>>>
>>>
>>
>>
>> --
>> Dr. Jevgenij A. Raskatov
>> Assistant Professor in Chemistry and Biochemistry
>>
>> Tel.: +1-831-459-2978
>>
>> Department of Chemistry and Biochemistry
>> Physical Science Building 356
>> 1156 High Street
>> Santa Cruz, CA
>> 95064 USA
>>
>
>
>
> --
> Dr. Jevgenij A. Raskatov
> Assistant Professor in Chemistry and Biochemistry
>
> Tel.: +1-831-459-2978
>
> Department of Chemistry and Biochemistry
> Physical Science Building 356
> 1156 High Street
> Santa Cruz, CA
> 95064 USA
> 

-- 
Best,
/A