Hi Miguel. Suggestions:
Strongly advocate for being able to label polymers by residue/monomer strings/indices via <label> menu that one gets by right click. More "user-friendly". Currently, to get amino acid labels on protein structure requires "lots of work" on console (:-)) : <select carbon and backbone and alpha> <label %n%r> If one renders via<Render> <Structures><something> and then changes her/his mind and repeats the <Render><Structures><something else>, the previous rendering remains, so one generates overlay of the two renderings. To get the "pure" second type, one needs to switch the Structures rendering off and re-enter the new one. The coloring schemes of those different types implemented "sequentially" behave in funny, i.e. non-systematic way. Sometimes they "inherit" the color scheme of the previous (e.g.Trace from Cartoon), sometimes one needs to re-enter the required color scheme. <Structures><backbone> does not behave as <trace> or <cartoon> e.g. once it is implemented, it does not go "off", so "to get rid of it", one needs to change to <render><scheme><wireframe> and then back to whatever is necessary.... Needless to say that sometimes having the overlay of cartoon with backbone is useful, though. I found not much info about toolbar buttons, so experimenting with the toolbar button [arrow] with pop-up [Select atom or region] I assumed that I will be able to select atoms or sequences of atoms "on screen" with result similar to issuing <select a> or <select a-b> on the console. Instead, the function is "only" [Highlights those already selected atoms or regions]. Perhaps modification of the pop-up text might be appropriate, believe or not, I spent some time clicking and hitting ctrl, alt etc.and browsing through doc's to make sure that the "advertised" function is not there (Or is it?) I would vote for something like that to be implemented eventually (i.e. with that button pressed, whatever is clicked, or - for more atoms-residues - shift-clicked or "lassoed" by mouse become selected, highlighted by yellow "halloo" and subsequent commands act on that selection) In atom expressions, Rasmol had <within( distance, mol_selection)> command - allowing to select say active site or drug binding region. Is this available? On similar theme, is there any way to select bonds longer then user-defined threshold? Might be useful for getting rid of non-real bonds calculated automatically in cases the coordinates allow that. Re linking "correlation" matrix to protein structure rendering - I have program that converts my matrices to xyz file and the Jmol rendering is just fine (I am finalizing the color scheme). You hinted, that there might be a solution how to transfer the picked "atoms" in the "correlation matrix rendering" to the protein picture? Thanks Petr Dr. Petr Pancoska Department of Pathology SUNY Stony Brook, NY 11794 phone: (631)-444-3030 ****************************************************************************** This e- mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by e-mail and destroy all copies of the original. ****************************************************************************** ------------------------------------------------------- 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
