I'm probably speaking too quickly without thinking (and tired from a deadline yesterday), but....
In my case, it's a single modification, and I just needed to see the coordinates for a grant app, so I'm sure the error will be resolved by the time I come back to this job. But, regardless, it is an important point, in that, I would likely get better refinement results if I split a shell of residues around the modification such that each of the residues within a sphere around the modification does have 2 conformations. As in... for both of our cases, we do have 2 proteins occupying the same volume. In my case, it's just a one residue difference. In your case, at a 5% total difference, would having a complete molecule "A" and molecule "B" be warranted? I tried doing this once with a case of twinning or pseudosymmetry where I could fly in the two overlapping molecules - it did not work very well (that obviously could be due to a lot of things). But in your case... where the molecules are occupying the same volume, and the spacegroup is likely right... could it be useful??? On Wed, Nov 6, 2013 at 3:59 PM, David Shin <[email protected]> wrote: > HI all, > > Just went back to a project and oddly having about the same problem (which > I do not think existed before): > > Coot 0.8-pre revision 4792 on 10.6.8 > > I have a modified residue, but has partial occupancy, so the residues have > different names for A and B. > > Just thought I'd share (and Scott - who is this person?). > > Thanks, > > Dave > > ############## > Error: > ERROR 39 READ: Duplicate sequence number and insertion code. > LINE #4250 > ATOM 1597 N ACYS A 238 30.800 -10.177 46.748 0.29 15.31 > N > > Spacegroup: C 2 2 2 > There was a coordinates read error > > ############## > What's in the .pdb file around line 4250: > > ATOM 1596 H BCSO A 238 30.629 -10.803 47.321 0.71 16.21 > H > ATOM 1597 N ACYS A 238 30.800 -10.177 46.748 0.29 15.31 > N # <--- line 4250 > ANISOU 1597 N ACYS A 238 1771 1072 2973 141 534 201 > N > > > > > > > > On Wed, Nov 6, 2013 at 3:27 PM, Scott Classen <[email protected]> wrote: > >> Hello COOTers, >> >> A colleague (not on the coot mailing list… shame on him) has a problem. >> His heterodimer is composed of alpha and beta subunits that are 95% >> identical, and because of his chosen space group, end up packing in the >> crystal lattice such that some residue positions (the 5% that are not >> identical and that are sufficiently well ordered to see differences) have >> mixtures of two different amino acids at the same position. How should he >> deal with this in coot? >> >> Thanks, >> Scott >> >> >> >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> Scott Classen, Ph.D. >> SIBYLS Beamline 12.3.1 >> sibyls.als.lbl.gov >> Advanced Light Source >> Lawrence Berkeley National Laboratory >> 1 Cyclotron Rd >> MS6R2100 >> Berkeley, CA 94720 >> cell 510.206.4418 >> desk 510.495.2697 >> beamline 510.495.2134 >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> >> > > > -- > David Shin, Ph.D > Lawrence Berkeley National Labs > 1 Cyclotron Road > MS 83-R0101 > Berkeley, CA 94720 > USA > > > > -- > David Shin, Ph.D > Lawrence Berkeley National Labs > 1 Cyclotron Road > MS 83-R0101 > Berkeley, CA 94720 > USA > -- David Shin, Ph.D Lawrence Berkeley National Labs 1 Cyclotron Road MS 83-R0101 Berkeley, CA 94720 USA
