From: George Madalin Giambasu (
Date: Tue Apr 21 2009 - 11:12:54 CDT


I want to add smth from the nucleic acids simulation side on the STRIDE
issue. We encounter frequently RNA structures (XRAY or MD) that cannot
be "understood" well by STRIDE and consequently displayed incompletely.

What I would think would really useful is to have a tcl function that
can take as arguments the secondary structure as a list, for example,
and be able to display the structure as ribbons/cartoon. The list can be
generated by the user and will avoid calling STRIDE.

I am sure that from the devleopers side the things might not be as easy,
but if the idea seems interesting I can provide lots of tricky to
display RNA structures.

all the best,


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 <> 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

George Madalin Giambasu                        PhD Student
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