NOTE: If you feel strongly about default hydrogen bond behavior then you should read the end of this message
>> There is some subtle interaction with some of the old >> rasmol-compatibility hbond code. >> >> I will investigate. I found the problem ... see below ... >> This is a broader question but ... >> >> Q: Is there ever a reason why someone would want hbonds turned off? > yes, normally they are not shown (simplify the image, less confusing > network), this can be done by > select NoHbondsPart > hbonds off Correct. >> Q: Why should hbonds ever be treated differently from normal bonds? >> > these are weak interactions, but numerous OK >> Q: If you read in a file that contains hbonds, do you want them >> displayed by default? > yes, predefined hbonds should be seen on load pdb file. Previously, hbonds were not displayed when a file was loaded until someone said 'hbonds on'. I assume that I did it this way for RasMol compatibility. It certainly seems to me that if there are hbonds defined in the file then they should be displayed. As you said above, the user can turn them off with 'hbonds off'. I just checked in code which changes hbond behavior. hbonds are now created with the default bond radius rather than with a default radius of 0. NOTE: If you feel that hbonds should NOT be displayed by default then please post a message arguing your position. You can update an rebuild from the current svn repository OR you can wait and get the next prerelease which I will make in a few hours. 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
