I forgot to mention: from looking at the images, I would say the Chimera results are more reasonable, because that's how beta-sheets form, with strand-strand hydrogen bonds. In the VMD view, some strands lack H-bonds to the next strand in the sheet, or only have one. Of course, these statements are only qualitative, but it was my first impression. Elaine On Jan 28, 2010, at 2:36 PM, snoze pa wrote:
Hi Elaine, Thanks for your help. But somehow I am getting different number of bonds in vmd and chimera. A snap shot of the figure is shown below.
http://img191.imageshack.us/img191/9084/screenshotva.png
In VMD the Hbonds are calculated by show Hbonds and protein. Vms shows 24 hbonds while chimera shows 38 hbonds. I don't know how to justify this. I will highly appreciate your help. A snapshot is shown in the link http://img191.imageshack.us/img191/9084/screenshotva.png
Thanks s