Thank you all. I think i know the difference. This is quite a interesting case.
On 8/10/07, Paul Emsley <[EMAIL PROTECTED]> wrote: > > > > 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) > -- Jiamu Du State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS)
