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 relating somehow all pairs of residues i<>j in the N-mer. Sorry ... I do not know what this means ... Q: What is N-mer? > This is flat text file (any format, user is responsible for it) > > GOAL: > c. Load the protein to Jmol as usual. > > d. Tell Jmol that the NxN file related to the protein should be loaded to > say internal matrix M (Menu item) > > e. Create a window WM (WM is connected to the protein plot in Jmol window > see below) with contour plot of the profile defined by M and allow user to > vary the z-axis threshold (goal: If maxima of M-defined profile is what I > need to see, it would be nice to have a slider with Zmax-Zmin interval, > that I can drag and the contours would start from the z-threshold thus > defined..optimally, one can move both lower and upper threshold to see a > "slice"). I am not a chemist ... I do not understand the terminology ... I am lost. > f. If I (left-?)-click on the feature in WM, the i and j coordinates (in > real units, i.e. in the indices of monomers i and j, corresponding to the > selected element of M) are read, and transferred to the "select i,j" > command issued for the protein. At the same time, the selection should be > somehow visualized, either by immediate (automatic) coloring of the > residues i and j or by rendering them in stick or CPK. Toggle by > right-click this would de-select the residues in mol. plot and restore > previous rendering of them. > g. If I drag a rectangle in WM window, the boundaries of that rectangle > would be identified as i and j and transferred to protein structure plot > by > "select i-j" with the similar visualization (color, residue rendering). > Somehow then I should be able to de-select the region again from the WM > window (say by left click inside the rectangle?). > > Any one knows about a viewer with such a functionality? VM had something > like that but not very flexible and handy. The only piece of molecular visualization software I am familiar with is Jmol. > What I am using to emulate this functionality is sort of "off-line" > combination of a script in R which I run parallel to Jmol. R reads the > matrix, generates the plot, allows me to do the z-clipping and reads-out > the features in terms of residue i, residue j pairs with printing them in > R-text window as "select i,j" or "select i-j". I then copy/paste those to > Jmol/Rasmol command line window + some additional clicking. > > If this sounds doable, where to start? Not much experience with Jmol code, > so most probably I need to learn a lot first.... 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 ------------------------------------------------------- SF email is sponsored by - The IT Product Guide Read honest & candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://productguide.itmanagersjournal.com/ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
