[gmx-users] percentage of secondary structure

[Mark Abraham]

On 5/01/2011 12:35 AM, ahmet yıldırım wrote:
> I get the residue versus time ( secondary structure graph) using 
> do_dssp tool. I want to get the percentage value(alpha helix, beta 
> sheet, coil ...) of secondary structure. 

Please say this in the *first* email. Giving a full description of what 
you have done and what you got as output and why it isn't yet suitable 
runs a much lower risk of wasting the time of everyone who reads your 
email and has to guess what help you want. See 
http://www.gromacs.org/Support - had you followed these steps you'd have 
probably had an answer from Justin in one email.

Mark

> For example:
>
> Secondary structure percentage (%):
> Helix:51.6
> B-sheet:0
> Random coil:24.0
> Turn:24.4
>
> 04 Ocak 2011 14:59 tarihinde Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> yazdı:
>
>     On 4/01/2011 11:38 PM, ahmet yıldırım wrote:
>>     Dear Mark,
>>
>>     I will do by using the g_analyze tool but I do not know how to
>>     use it.
>
>     There's a section in Appendix D of the manual for each tool, or
>     you can use the -h argument to the tool to get the same information.
>
>     Either way, you haven't got the right tool. Hint: it's a "protein
>     specific analysis"
>
>     Mark
>
>
>>
>>     Thanks
>>
>>     2011/1/4 Mark Abraham <Mark.Abraham at anu.edu.au
>>     <mailto:Mark.Abraham at anu.edu.au>>
>>
>>         On 4/01/2011 8:33 PM, ahmet yıldırım wrote:
>>
>>             Hi,
>>
>>             How can I calculate the percentages (alpha helix, beta
>>             sheet, coil ...) of secondary structure?
>>
>>
>>         Look in manual section 7.4 for a suitable tool.
>>
>>         Mark
>>         -- 
>>         gmx-users mailing list gmx-users at gromacs.org
>>         <mailto:gmx-users at gromacs.org>
>>         http://lists.gromacs.org/mailman/listinfo/gmx-users
>>         Please search the archive at
>>         http://www.gromacs.org/Support/Mailing_Lists/Search before
>>         posting!
>>         Please don't post (un)subscribe requests to the list. Use the
>>         www interface or send it to gmx-users-request at gromacs.org
>>         <mailto:gmx-users-request at gromacs.org>.
>>         Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>>     -- 
>>     Ahmet YILDIRIM
>
>
>     --
>     gmx-users mailing list gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at
>     http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>     Please don't post (un)subscribe requests to the list. Use the
>     www interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
> -- 
> Ahmet YILDIRIM

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110105/54fce914/attachment.html>