>>I found this bug and fixed it ... at least I *think* I fixed it :-) >> >>Code is checked in. >> >> > Hi Miguel, > nice, but there where missing interconnections between the first fused > helices in px73313. > with kind regards, Jan
Jan, I noticed this last night after I mailed you the email. I do not know how to handle this situation and I need your help. Here is the way I filed the bug report on it: If one helix cylinder joins another directly, then there is no rope segment which hooks the two together. The problem is that sizes are effectively associated with the alpha carbon atoms. So the last alpha carbon of one helix has a size. And the first alpha carbon of the next nelix has a size. There is no place to store (or specify) the size of the rope which joins the two. The problem is difficult to describe, so I will try asking the question several different ways. The problem is, that this 'diameter/size' is associated with the alpha carbon atom itself, not with the segment between the alpha carbons. When you say: select 1 and alpha; cartoon 2.0 Are you setting the size of the cartoon at the alpha carbon? How do you select the segments between alpha carbon atoms to give them a size? The problem is similar to the behavior of 'backbone' ... but is different. 'backbone' behaves like a bond, and the selection criteria follow the bondmode and/or but 'backbones' terminate at the alpha carbon atoms that is not the case with cartoons. with cartoons, the alpha carbon atoms are in the center of the residue. so the residue extends from one side of the alpha carbon to the other side. Q: Where should a residue start and where should it end? Q: In the case of two fused helixes, in cartoon representation, how do you describe the segment that runs between the end of one alpha carbon and the beginning of the next? Q: How would you pick/specify a size for this segment of 'rope'? 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
