Jmol prerelease 10.00.53 is now available for download from: http://www.jmol.org/files
This prerelease includes: * new 'connect auto' functionality, including support for hbonds. Details below. * change in 'hbond on' behavior * new JUnit tests (for developers) * improved chain support in mmCIF files We are still targeting an official 10.1 release within the next few days. Testing and bug reports are appreciated. Miguel connect and hbond enhancements ------------------------------ Jan pointed out several problems with hbonds. Investigation revealed some subtle interactions in calculated hbond behavior based upon whether or not the author-supplied file included hbonds and/or secondary structure definitions. Bob was instrumental in helping figure out the problems. Previous work by Tim to change the automatic secondary structure definitions to use phi/psi angles instead of DSSP-like hbond linkages provided us with a path out of the problem. comprehensive 'connect' control ------------------------------- All control over the creation and deletion of bonds has been consolidated under the 'connect' command. connect 'auto' -------------- A new 'auto' option has been added to the 'connect' command in order to control the internal Jmol distance-based connection algorithm. As with 'connect' variants, this command takes two sets as parameters, if either of the two sets is not supplied then it defaults to the 'selected' set. select *; connect delete; connect auto; select *; connect delete; connect auto (hydrogen) (carbon) select *; connect delete; connect auto (1)(1); # only within group 1 change in 'hbond' behavior -------------------------- Previously, the 'hbond on' or 'hbond 0.1' command would automatically calculate hbonds if and only if the underlying author-supplied file did not contain hbond definitions. So, this command was being used to 'create' hbonds as well as to control hbond size. As of this 10.00.53 release the 'hbond' command will only control hbond radius. This is consistent with the 'wireframe' command used to control bond radius. 'connect auto hbond' -------------------- If the 'hbond' option is passed to 'connect auto' then the internal algorithms will run to calculate hbonds. As with other 'connect' variants, source and target atoms are taken from two sets that are passed as parameters. If either of the two sets is not supplied then it defaults to 'selected'. Note that the internal 'autoHbond' calculations only attempt to calculate *classic* hbonds: 1. along protein backbone 2. between DNA/RNA strands This behavior is consistent with previous Jmol behavior (when it was triggered by 'hbond on'). This behavior may change in future releases of Jmol. Here are some examples: #short strand of DNA load 1D68.pdb; select *; connect auto hbond; # only between groups 38 and 40 load 1CRN.pdb; connect auto hbond (38) (40); hbond 0.1; color hbond lime; # only for the DNA, not for the protein load 1D66.pdb; select nucleic; connect auto hbond; Difference between 'connect hbond' and 'connect auto hbond' ----------------------------------------------------------- Recall that 'connect hbond' can be used to explicitly create hbonds ... single, double, triple, aromatic, & hbond. Recall that all pairs of atoms in the two sets are bonded, unless minimum and maximum distance criteria are specified. Therefore, one can easily create a 'highly connected graph' with tens of thousands of bonds. The 'connect auto hbond' command will run the internal autoHbond calculations, making determinations of (hopefully) valid hbonds. If you accidentally type 'connect hbond' instead of 'connect auto hbond' then you may be puzzled to see no change to the screen ... followed by a rat's next a few seconds later. I believe that this consolidation of bonding functionality under 'connect' is very good. Bob did a lot of work on it and is to be applauded. Bug reports/feedback appreciated. Miguel ------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid0944&bid$1720&dat1642 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
