Hello, When I further refine my structure the N+1 is gone and it becomes a normal N again. So it is very much possible this is related to geometry. Thanks everyone (Esp. to Jon) for the input!
Sam On Fri, 16 Oct 2020 at 19:31, Jon Cooper <jon.b.coo...@protonmail.com> wrote: > Hello Sam > > thanks for the pictures. It looks like the guanidinium group of the first > Arg is not very planar. I don't know the detailed nuts-and-bolts of how > Coot and Refmac handle this but the problem may arise from the initial > geometry at the affected nitrogen being off-target. > > Best wishes, Jon Cooper. jon.b.coo...@protonmail.com > > > > > > -------- Original Message -------- > On 16 Oct 2020, 06:57, Sam Tang < samtys0...@gmail.com> wrote: > > > Dear all > > I attach herewith the Arg concerned. I actually saw no issue in Coot when > I checked residue info. The issue was repeatable using both Refmac from > Coot and from CCP4i. I rectified the issue simply by changing "N+1" back to > "N" using a word editor, but would surely be glad to know more about the > cause of the problem. > > > https://drive.google.com/file/d/137Q0CybNynOlI0R-b-3-OL2eWk7f6L2a/view?usp=sharing > > Best Regards > > Sam > > > On Fri, 16 Oct 2020 at 00:51, Jon Cooper <jon.b.coo...@protonmail.com> > wrote: > >> Hello, can you possibly show us a couple of screenshots with atom labels >> of the affected side chain and a normal one? >> >> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com >> >> >> >> >> >> -------- Original Message -------- >> On 15 Oct 2020, 15:07, Sam Tang < samtys0...@gmail.com> wrote: >> >> >> Dear colleagues >> >> I am trying to refine a structure with Refmac and the work completes >> without any warning. However I am a bit puzzled for one single N atom on an >> Arg residue the element type becomes N+1. This doesn't happen on my another >> NCS chain and the input PDB seems fine. Could anyone kindly point me to the >> possible cause? >> >> Thanks in advance! >> >> BRS >> >> Sam >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
