Hallo Elaine, Im sorry to waste your time with such a thing, in chimera 1.4 it is really allright. I worked with .py sessions made in 1.3 release and these session even in chimera 1.4 showed gap - missing ser183 in ribbon repr. Thank you very much for your kind answers, Tomas
Hi Tomas, I don't see any missing ribbon loop when I look at the structure. I see one continuous protein ribbon for residues 56-195 of chain A. There is also a short peptide, residues 10-14 of chain Q. However, chains A and Q are separate molecules so they should not be connected, if that is what you meant.
The only weird things I can see in the display are - Glu 89 in chain A is broken into two parts because it does not have a CG atom - Asn 185 in chain A is broken into two parts because it does not have a CB atom
However, neither of these things affects the ribbon because all of the backbone atoms are there. Maybe you are seeing the sidechain pieces of these two residues?
I looked at the structure in both the current 1.4 release candidate and the current 1.5 daily builds of Chimera. Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 2, 2009, at 3:38 AM, klumpler@sci.muni.cz wrote:
Dear Elaine, I think PDB is alright, I send it as a attachment. Could you help me with the editing? Thank you very much Tomas