Miguel, sorry - some sort of inverse effect.
I tried to be very explicit and the result is "Lost in translation".
Simplification (I hope ... :-)) ) is below in ################'s
Petr
Dr. Petr Pancoska
Department of Pathology
SUNY Stony Brook, NY 11794
phone: (631)-444-3030
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"Miguel"
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Subject
Re: [Jmol-users] How difficult this
12/23/2004 12:09 feature might be?
PM
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Petr wrote:
> Hello.
> Sorry for contributing not with the technical questions/solutions,
> but with "user would like to....".
No need to apologize ... customers are rather important :-)
> In your expert opinion how difficult would be to implement the following
> functionality to Jmol (polymers=proteins again, my nemesis):
>
> INPUT:
> a. pdb file of a protein (no indexing issues, ideal case) of N residues
> (amino acids).
> b. NxN matrix and somehow all pairs of residues i<>j in the N-mer.
Sorry ... I do not know what this means ...
Q: What is N-mer?
###################################
Ooops. N-mer = polymer of N-amino acids = protein.
Sorry. In plain words:
Jmol loads pdb file=protein.
Protein is (folded) chain of amino acids, indexed from 1 to N.
These indices 1..N are associated with each monomer=amino acid - usage e.g.
in residue labeling.
Now user has some external quantification how in say N=130-amino acid
protein is amino acid #25 similar to amino acid #56.
This is encoded in the external, user-defined file containing (in this
example) a 130x130 matrix M.
If user quantifies similarity of amino acids 25 and 56 by 1.0, then in that
matrix for our example, element M[25,56]=1.0 (and for the sake of
simplicity, all other elements but M[56,25] will be =0).
Goal is to have a UI showing graphically 130x130 plane with a contour
around x=25,y=56 and x=56,y=25. That contour should be clickable=by
clicking there, UI passes 25 and 56 to the rendering window.
The rendering window takes these and selects amino acid 25 and 56 and
immediately changes their rendering, so user has "real time" view of what
his/her 1.0 generated by some bioinformatics analysis of the sequence of
that protein means structurally.
You can stop here, below is why:
#######################################################
Holly grail for protein people is to take the (known) sequence of amino
acids (genome sequecing got them nearly all) and predict from them what
Jmol shows as the protein structure without relying on experiments that are
the sources of PDB files your program uses.
So - without experiments, in one type of predictive methodology, one has to
take a sequence and find out the relationships between all amino acids
i=1..N and j=1..N. Then, ideally, matrix M will contain the information
that amino acid 25 and 56 in our example protein have CA-CA distance 6A and
similar information for all other pairs.
If you are testing something like this, you have lots of M matrices and you
are trying to figure out how good/bad your i-j relations are by testing
them against known structures.
Thus - one "pretends" for a protein that its PDB file does not exist.
Then one takes the amino acid sequence of that "virtually unknown structure
protein" and does his "trial magic" with that sequence. Result is matrix M.
Then one wants to know, how good the M reflects the real structure
("re-discovered" for this testing).
So one "re-discovers" the PDB file, loads it in the Jmol, looks what 1's in
M mean structurally, get an idea how to improve "magic", and the cycle
continues.
Lots of select click, clicking....
######################################
It certainly sounds doable.
I may be mistaken, but this sounds to me like a specialized application.
The Jmol application has a plug-in mechanism for adding this type of
functionality.
I am sure that you understand that calculations.
For someone experienced in building user interface in Java the UI controls
would be very straightforward. (I would be reluctant to attempt to do it
with a student ... unless they can demonstrate that they can demonstrate
that they can write a java program to open a window with a slider control
in less than an hour).
>From within a plugin one can retrieve information about the molecule and
one can fully control the rendering.
Miguel
######################################
Thanks for the analysis, makes sense to me on the entry level.
######################################
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