If I may expand on what Eleanor said. The issue is not the atom labels, but that the atom labels are in the right place (i.e. the refer to the right atoms).
There is an IUPAC convention on the torsion of CB-CG-CD-OE1 (for GLU). The torsion should be between -90 and +90. Yours is not. Therefore the atom labels for OE1 and OE2 should be swapped. Many molecular graphics or model manipulation programs can fix this. In Coot, one would use the fix-nomenclature-errors function. Hope that is clearer, Paul. On Fri, Aug 10, 2007 at 07:19:44PM +0800, Jiamu Du wrote: > Dear Eleanor: > But in my structure, the atom labelles are all right. > Such as GLU A 15 : > > ATOM 55 N GLU A 15 -59.930 -39.249 -9.123 1.00 30.10 > N > ATOM 56 CA GLU A 15 -60.573 -38.776 -7.889 1.00 30.54 > C > ATOM 57 CB GLU A 15 -61.533 -37.599 -8.146 1.00 31.08 > C > ATOM 58 CG GLU A 15 -61.014 -36.528 -9.124 1.00 35.70 > C > ATOM 59 CD GLU A 15 -61.459 -36.784 -10.589 1.00 40.21 > C > ATOM 60 OE1 GLU A 15 -60.561 -36.946 -11.467 1.00 40.16 > O > ATOM 61 OE2 GLU A 15 -62.701 -36.815 -10.851 1.00 41.17 > O > ATOM 62 C GLU A 15 -61.334 -39.901 -7.182 1.00 29.34 > C > ATOM 63 O GLU A 15 -61.335 -39.989 -5.947 1.00 29.37 > O > > I think the labbels are all right. > > Thanks. > > On 8/10/07, Eleanor Dodson <[EMAIL PROTECTED]> wrote: > > > > There are conventions on which atoms is labelled OE1 and which OE2 for > > example > > > > It doesnt change the electron density of structure calns an iouta but > > conventions are conventions! > > > > Eleanor > > > > Jiamu Du wrote: > > > Dear All: > > > I have refined a structure. When I run procheck, a messege apears in > > > the log file as below: > > > > > > Average value of CA-N-C-CB angle is 33.83 > > > Standard deviation is 1.85 > > > * Side chain atoms swapped for residues: > > > * GLU A 15 ARG A 24 TYR A > > > > > > I have checked the density and the geometry of these residues. All > > > this residues are all right. > > > Is there anyone who have the same experience? How to deal with this > > > situation? > > > > > > Thanks. > > > > > > -- > > > Jiamu Du > > > State Key Laboratory of Molecular Biology > > > Institute of Biochemistry and Cell Biology Shanghai Institutes for > > > Biological Sciences > > > Chinese Academy of Sciences (CAS) > > > > > > > -- > Jiamu Du > State Key Laboratory of Molecular Biology > Institute of Biochemistry and Cell Biology Shanghai Institutes for > Biological Sciences > Chinese Academy of Sciences (CAS)
