Tim, I have checked in code which calculates protein mainchain hbonds using the algorithm is RasMol 2.6 beta 2.
These hbonds are rendered as dotted lines or as segmented cylinders if a size is specified. in Jmol ... load samples/1crn.pdb hbonds .1 color hbonds lime select mainchain wireframe .1 trace ; color trace structure The RasMol algorithm only works on distance, it does not take angles into account. Therefore, it generates bonds which probably should not be there. A specific case with samples/1crn.pdb select 38,40 hbonds .2 ; color hbonds hotpink center selected ; zoom 1000 select (38,40) & (oxygen,nitrogen) label %r ; color label white It doesn't seem to me that this bond should be there. In any case, take a look at this hbond stuff and let me know what you think. Miguel ------------------------------------------------------- This SF.net email is sponsored by: IBM Linux Tutorials. Become an expert in LINUX or just sharpen your skills. Sign up for IBM's Free Linux Tutorials. Learn everything from the bash shell to sys admin. Click now! http://ads.osdn.com/?ad_id=1278&alloc_id=3371&op=click _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
