Re: [Chimera-users] missing ribbon loop
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
Hello, My guess is there is something strange about the structure or the format of the input file -- for example, maybe the residues don't all have the same chain ID, or the backbone atoms do not have the expected names (N,CA,C,O). If Chimera does not show a ribbon at that position even though you told it to show ribbons for everything, it is probably necessary to edit the input file to fix the problem. I couldn't be more specific without seeing the file. Best, 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 Nov 27, 2009, at 2:16 AM, klumpler@sci.muni.cz wrote:
Hallo, please, can you tell me how to create missing part of ribbon representation of loop?
Using "ball and stick" representation is peptide chain complete without gap, but in "ribbon" representation is one residue missing and forms the gap.
Thank you very much
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
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
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Elaine Meng -
klumpler＠sci.muni.cz