2008/4/28 Mauricio Carrillo Tripp <[EMAIL PROTECTED]>: > > We currently have a repository of viral capsid structures at > http://viperdb.scripps.edu > > We also dealt with this issue a while ago. We also found it "problematic" to > show the > whole biological unit, full capsid (because of the likely high number of > atoms for some entries > and the possible memory limitations on the clients). We concluded that it is > not necessary > to do so for spherical capsids and that it suffices if only the neighboring > units to the central > icosahedral asymmetric unit, CIAU (on the VIPERdb convention), are shown, > in order to appreciate > the interfaces and interactions generated upon capsid assembly. > > At first we tried to use the biomat info (translation+rotation matrices) > from the PDB as you have > suggested. Then we realized there was an alternative for the case of > spherical capsids; we > know the cage vertices (vectors) the biounit is 'inscribed' into (VIPERdb > convention), and the > angles that relates all the copies around these vertices. Therefore, we can > use a 'rotateSelected' > command to create all the needed 'duplicates' (we got a lot of help from Bob > on this ;) > > An excerpt from the code to manage one of the 5-fold symmetry related > copies, for example, follows: > > set echo top center;echo Calculating|Duplicates;refresh; > select :*.Ca/2.1; > n_models = getProperty("modelInfo","modelCount"); > ini = n_models + 1; > fin = n_models + 4; > x = data("selected", "pdb"); > subu_count = 0; > for (var i = ini; i <= fin; i = i + 1) > subu_count = subu_count + 1; > DATA "append @x"; > m = "*/"+i+".1"; > select @m; > ang = 72.0 * subu_count; > rotateSelected MOLECULAR AXISANGLE {0.0,87.9,142.2} @ang; > trace 0.5; > end for > set drawHover TRUE; > draw five_fold_01 "5-fold Axis" ARROW 110 DIAMETER 1 {0.0,0.0,0.0} > {0.0,87.9,142.2}; > frame all;display displayed;refresh;select none;set echo off; > > A couple of 'live' examples of this can be found here: > a T=1 virus > http://viperdb.scripps.edu/info_page_big_jmol.php?VDB=1a34 > or a T=3 virus > http://viperdb.scripps.edu/info_page_big_jmol.php?VDB=2bbv
Out of interest, do you check the results for 'clashes' between interface atoms? The presence of many clashes would indicate that something had gone wrong in the process. If I understand correctly this could happen if the ASU were incorrectly specified. > Please note that the user interface and the options provided are still in > development, but still you can get a good idea > of how it works. > > This is just an alternative and I am aware this tactic can not be used in > all general cases, or at least > no as straight forward, but perhaps it can help someone else in the mean > time the biomat info can be of use. > > -- > 0 | Mauricio Carrillo Tripp, PhD > / | Department of Molecular Biology, TPC6 > 0 | The Scripps Research Institute > \ | 10550 North Torrey Pines Road > 0 | La Jolla, California 92037 > / | [EMAIL PROTECTED] > 0 | http://www.scripps.edu/~trippm > > ** Aut tace aut loquere meliora silentio ** > ------------------------------------------------------------------------- > This SF.net email is sponsored by the 2008 JavaOne(SM) Conference > Don't miss this year's exciting event. There's still time to save $100. > Use priority code J8TL2D2. > > http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- hello ------------------------------------------------------------------------- This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
