On Sun, 2004-12-19 at 18:58 -0500, Miguel wrote: > > The files I was loading were modified versions of 1CRN - I only kept the > > first 3 > > residues. That might explain why theres no overlap > > If you can, please change it so that they are offset by only 2 or 3 > angstroms.
> I would like to know whether or not they will ever 'intercept'. I changed the coordinates of xxx.pdb by adding 3 to the x coordinate. Now loading the two PDB files in PyMOL does indeed lead to them partially overlapping > If you could make some specific recommendations on how Jmol should handle > multiple molecular models then that would be very helpful. OK, here are a few things that I think would be useful: 1) When loading a molecule ask if it should be centered or not rather than automatically centering a molecule (this could be in the preferences rather a question each time a molecule is loaded) 2) When multiple molecules are loaded how do we manipulate them individually and as a set? 2a) Selecting individual molecules - Here a first approach would be to have a menu option that lists the filenames. Selecting a name from this menu would select the corresponding structure. Then all rotations/translation/zooming would be applied to that molecule. Alternatively, Jmol currently allows the user to select an atom. An option could be added to 'extend the selection' to the whole molecule to which that atom belongs. (alternate uses of this is to select the whole residue to which that atom belongs, the whole chain to which that atom belongs and so on). Thus by extending the selection to the whole molecule, the resultant selected object would then be the focus of any geometric operations. 2b) Handling the coordinate systems - In this case, I feel that the origin should remain at the centroid of the set of molecules. I realize that this means that if the first molecule has coordinates of the order of 1 and the second molecule has coordinates of the order of 100, then when the second one is loaded one of the molecules will disappear (depending on whether we load the second one centered or not). However this problem can be alleviated by having 2 options: 1) center a molecule (as in PyMOL) - positions the specified molecule at the center of the screen or 2) zoom - basically calculate a zoom value such that if applied all molecules will be visible (even if one of them becomes just a speck!) One alternative to the abvoe is to transform the coordinates of evey molecule after the first such that the centroid of each molecule is the same as the first one. This results in overlapping structures - but with an intuitive selection mechanism, the molecules could be seperated. My preference is for the former option, as it seems that one would respect the specified coordinates in the file itself rather than transform them arbitrarily. 3) An option could also be made available to hide a given molecule (so that it is not visible) and a corresponding option to unhide it Right now these are things I'd think would be useful. Are there other aspects you'd like more input about? ------------------------------------------------------------------- Rajarshi Guha <[EMAIL PROTECTED]> <http://jijo.cjb.net> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- Got Mole problems? Call Avogadro at 6.02 x 10^23. ------------------------------------------------------- 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 [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
