[gmx-users] make_ndx for do_dssp

[Justin A. Lemkul]

Paymon Pirzadeh wrote:
> I assumption was that when provide the index file, do_dssp will do the
> analysis for the protein but prints out the results only for the
> designated residues. All I wanted was a better resolution on the final

When prompted for only one group, that group is used for calculation and output.

> xpm plot to see the secondary structure of the protein at those residues
> of interest. Any suggestions on how we can increase the resolution of
> dssp plot and enlarging the axis of residues?

Yes, use an .m2p file to adjust the matrix spacing.  This was discussed several 
days ago.

> By the way, what would the option -nice do here?
> 

Likely nothing.  Nice levels are irrelevant for most tasks.

-Justin

> Paymon 
> 
> 
> On Wed, 2010-10-06 at 15:29 -0400, Justin A. Lemkul wrote:
>> Paymon Pirzadeh wrote:
>>> Justin,
>>> I produced the index file based on your suggestion, but when I ran the
>>> do_dssp, a completely different result was spit out comparing to what
>>> the whole protein analysis had given. Any ideas on why that might have
>>> happened?
>>>
>> That depends on what "completely different" means.  I have no idea.  If you're 
>> only analyzing a subset of the residues, you're going to get a discontinuous 
>> plot that's probably going to look a whole lot different from any analysis done 
>> on the whole protein.  What's more, if you're only considering small fragments 
>> of the protein, then omitting surrounding residues from the analysis probably 
>> won't permit DSSP to find hydrogen bonding partners that are necessary to 
>> determine the correct secondary structure.
>>
>> -Justin
>>
>>> Paymon
>>>
>>> On Wed, 2010-10-06 at 14:42 -0400, Justin A. Lemkul wrote:
>>>> Paymon Pirzadeh wrote:
>>>>> Hello, I want to check the secondary structure of protein at particular
>>>>> residues. Since dssp needs all main chain atoms, does the following command
>>>>> at the make_ndx prompt makes the correct index file? 
>>>> You can answer that yourself by looking at the resulting index file.
>>>>
>>>>> 5 | r 1 | r 10-11 |r 14-17 | r 20-21 | r 26-32 | r 42 | r 45
>>>>>
>>>> To get these groups to merge, I think you probably need to do 5 & r 1 | ...
>>>>
>>>> -Justin
>>>>
>>>>> (Main chain atom of particular residues). regards,
>>>>>
>>>>> Paymon
>>>>>
>>>> -- 
>>>> ========================================
>>>>
>>>> Justin A. Lemkul
>>>> Ph.D. Candidate
>>>> ICTAS Doctoral Scholar
>>>> MILES-IGERT Trainee
>>>> Department of Biochemistry
>>>> Virginia Tech
>>>> Blacksburg, VA
>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>
>>>> ========================================
>>>
>> -- 
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================