(Thu, 12/13/2018 - 09:35 | 4 comments)
Let band.Add work even if all origin, +x, and y atoms are on the same protein segment
|Opened on:||Thursday, December 13, 2018 - 09:35|
|Last modified:||Monday, September 7, 2020 - 14:00|
The other day I was debugging a Foldit LUA recipe with lines like below in it: jn,jca,jc,jo=1,2,3,4 -- backbone atoms N,CA,C,O have atom #'s 1-4 respectively tryb=band.Add(nmid,nmid,nmid,0.001,0,0,jca,jc,jn) -- The above uses atoms on residue nmid to set up xyz coordinates for -- a band to space. Here, nmid's CA is the origin, nmid's C is along -- the +x axis, and nmid's N lies in the xy plane with N having y>0. -- The band to space will be from nmid's CA to 0.001 A along the +z axis. -- -- 12/11/18 You can't have the segment for the origin & +x axis -- be the same, even if you're using different atom #'s. I got a message about needing different segment #'s for the origin and +x axis (here both the same, namely nmid), but the atom #'s I chose for the origin, +x axis, and y axis were all different (namely, nmid's alpha-carbon CA, backbone C, and backbone N). Seems like band.Add was being a little too picky about when it would work. Shouldn't it be enough to specify 3 different non-collinear atoms (like N,CA,C in the protein backbone, which generally form an angle around 111 degrees, making these 3 atoms non-collinear) to set up the xyz coordinates for a band to space? Why must all the atoms be on different amino acid segments? Also, I used the 0.001 A distance along the +z axis because I suspected band.Add would fail if I used 0 instead. It would be nice if 0 instead of 0.001 would let band.Add work here, after all, my goal was to make a zero-length band to space. I was able to work around the case above, but it cost me time and wasn't as intuitive or simple as I originally intended. I would appreciate it if you let band.Add accept a wider variety of inputs. See http://foldit.wikia.com/wiki/Foldit_Lua_Function_band.Add for details.