From: Jevgenij Raskatov (jraskato_at_ucsc.edu)
Date: Thu May 28 2015 - 17:31:48 CDT

Thank you!!

On Thu, May 28, 2015 at 3:29 PM, Barry Isralewitz <barryi_at_ks.uiuc.edu>
wrote:

> Hello,
>
> Here’s another way to see the secondary structure codes:
>
> In the “VMD Timeline” window menu, select:
> “Help” -> “Structure codes…”
>
> .
> Cheers,
>
> Barry
>
> On May 28, 2015, at 5:14 PM, Ashar Malik <asharjm_at_gmail.com> wrote:
>
> 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
>
>
> --
> Barry Isralewitz
> Theoretical and Computational Biophysics Group
> 3043 Beckman, University of Illinois at Urbana-Champaign
> Office Phone: (217) 244-1612
> email: barryi_at_ks.uiuc.edu http://www.ks.uiuc.edu/~barryi
>
>

-- 
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