Blueprint-folded residues do not show in right place on rama map

Case number:954892-2003005
Topic:Developer Preview
Opened by:Susume
Opened on:Thursday, October 27, 2016 - 05:27
Last modified:Thursday, October 27, 2016 - 05:27

After using blueprint to make the turns between structures, the rama dots of some turn residues do not match the current shape of those residues.

Shared solution "1299dev s1 1st wig froz" with scientists. This was constructed using SS and Ideal SS to make the sheets and helices, blueprint to make the turns, then one long wiggle at ci 0.2 with structures frozen, loops unfrozen, and the bands you see to pull the sheets together.

In selection interface with rama map open, select residue 38 ASN. Drag its rama dot a tiny bit in each of the four cardinal directions, undoing in between drags. All four tiny drags make the pair of sheets and the N-terminal helix jump more than a tiny bit, in the *same direction*. Those four moves should move that end of the protein in four *different* directions. This tells me the beginning dot is incorrect - it does not describe the beginning shape. The beginning shape is one some distance away on the map, from which all four of those tiny moves make approximately the same change.

The same thing happens with residue 57 GLY. The adjacent residues 37 ASP and 58 ASP show a little jump when you move their dots a tiny bit. Other loop residues seem unaffected. There were two places where I put the turn template down on the wrong spot in the sequence and then dragged it one residue to the side - I don't recall which two turns those were. Maybe these are those two spots?

(Thu, 10/27/2016 - 05:27  |  0 comments)


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