VMD-L Mailing List

From: Daniel Gaston (daniel.gaston_at_DAL.CA)
Date: Tue Apr 21 2009 - 12:02:29 CDT

Also an excellent solution. Thank you very muxh experienced VMDers for
all your assistance. It is much appreciated.

Dan

Axel Kohlmeyer wrote:
> On Tue, 2009-04-21 at 12:29 -0300, Daniel Gaston wrote:
>
>> Thank you for the reply,
>>
>
> daniel,
>
> you can retrieve and set the secondary structure codes
> at you liking via the script interface and atom selections.
>
> set fixme [atomselect top "residue XX to YY and name CA"]
> $fixme set structure L
>
> those will override the output of stride.
>
> cheers,
> axel.
>
>
>> In regards to option b, I should have mentioned that I have already
>> subjected these structures to minimzation and and MD tun (1.5 ns or so
>> worth). The beta sheet predicted structure in that case has been reduced
>> but not eliminated entirely, at least when done in a water sphere. I
>> believe when I minimize and do the MD in a vacuum (done initially by
>> mistake) that it was resolved.
>>
>> Option A does work. Ideally I would like to break and resolve that loop
>> altogether. Oddly enough this is a case where I submit the same
>> alignment to Swiss-Model using the same template structure (a homodimer)
>> and only change which Chain is used as the template (A versus B). The A
>> chain model works perfectly, it is only on the B chain that this loop
>> appears to be modeled incorrectly.
>>
>> Thanks for the help. Any further suggestions/comments from users would
>> be appreciated.
>>
>> Dan
>>
>>
>>
>> L. Michel Espinoza-Fonseca wrote:
>>
>>> Hi Daniel,
>>>
>>> There are two options I can think of:
>>>
>>> (a) You can use the 'new ribbons' rendering instead of the 'new
>>> cartoon' one. You can change the thickness of the ribbons to make it
>>> look like a cartoon but without worrying about the sheet depiction.
>>>
>>> (b) This option is more difficult, but better in terms of cleansing of
>>> incorrect geometries/contacts. Probably what you could do is to relax
>>> your protein using MD and minimize the final coordinates. This should
>>> give you an improved geometry. Remember that homology modeling often
>>> produces 'dirty' geometries. In this case STRIDE is just processing
>>> what you're giving to it, whether is correct or not.
>>>
>>> Cheers,
>>> Michel
>>>
>>> On Tue, Apr 21, 2009 at 4:25 PM, Daniel Gaston <daniel.gaston_at_dal.ca> wrote:
>>>
>>>
>>>> Hi all,
>>>>
>>>> I am wondering if there is a method to override STRIDE's secondary structure
>>>> prediction (and thus how VMD displays it in New Cartoon format) for only a
>>>> specified portion of a structure file? I have a Homology Model from
>>>> Swissprot where one loop region in only one chain of a homodimer is show as
>>>> as anti-parallel beta-sheet instead of the loop region that it should be.
>>>> Because only this one portion is incorrect (and because Swissprot homology
>>>> models contain only coordinates and not a secondary structure section) I
>>>> would like to override the representation only for that one area of the
>>>> structure without needing to create a secondary structure entry in the PDB
>>>> for the entire protein. Is this possible?
>>>>
>>>> Thank you,
>>>>
>>>> Dan Gaston
>>>>
>>>> --
>>>> Daniel Gaston
>>>> PhD Candidate, Dr. Andrew Roger Lab
>>>> Department of Biochemistry and Molecular Biology
>>>> Dalhousie University, Nova Scotia, Canada
>>>>
>>>>
>>>>
>>>>
>
> 

-- 
Daniel Gaston
PhD Candidate, Dr. Andrew Roger Lab
Department of Biochemistry and Molecular Biology
Dalhousie University, Nova Scotia, Canada