Hi Garib, > Are these related to the side chain of ARG? In the monomer library sigmas are > capped from below - 1.5degree. > In the PDB these sigmas might be very small and tiny differences could be > given > as outliers. > Another reason might be that in the monomer library these two angles are > identical (they are considered graph-equivalent, however, rotating around NE- > CZ may make them non-equivalent in 3D space): > ARG NE CZ NH1 120.052 1.50 > ARG NE CZ NH2 120.052 1.50 The chi-5 angle is not really freely rotatable due to the 1.33 bond order. It does give away more than say, a peptide bond with 1.5 bond order. Anyway, NH2 and NH1 have E/Z differences if you assume the bond is not freely rotatable.
> In the PDB they may be considered different with small differences and very > small sigmas. I'm using ARG NE CZ NH1 121.5 1.00 ARG NE CZ NH2 119.2 0.90 From https://pubmed.ncbi.nlm.nih.gov/27326702/ > I personally do not think that these differences are significant or important. > However, to make pdb validation happy you can change the sigmas and make > the angles different. Then NH1 and NH2 will become inequivalent and you have > to change your coordinates (it could be done automatically if somebody writes > a tiny program) Because chi-5 was freely rotatable in O (against convention) there is a check for this in WHAT_CHECK. AFAIK the atom naming is fixed in pdb-redo based on that. We can build in into flipper. Cheers, Robbie > > If the problem is not related with this then I need more info. > > Regards > Garib > > > > On 20 Oct 2022, at 12:33, Bernhard Rupp > <hofkristall...@gmail.com <mailto:hofkristall...@gmail.com> > wrote: > > Hi Fellows/Garib, > > I notice unexplained discrepancies between the PDB validation report > and the Refmac log file: > > a. If I set in ‘Monitoring and Output Options’ the angle sigma for > the log output reporting option to the PDB 5 sigma cutoff, > > I get zero angle deviations (i.e., no angle deviation printout at all > in the > log), even at improbably low sigma levels such as 2.0 or 1.0 > > monitor MANY torsion 5.0 distance 5.0 angle 1.0 plane 5.0 > > > b. PDB informs me that there are up to 10 sigma outliers on > multiple (and almost exclusively) ARG N-C-N angles (how to fix this we address > later). > > > Garib, I can send you a link to the complete log, below the header for > versions (windows) : > > #CCP4I VERSION CCP4Interface 8.0.005 > > #CCP4I SCRIPT LOG refmac5 > #CCP4I DATE 20 Oct 2022 13:17:07 > #CCP4I USER 'UNKNOWN' > #CCP4I PROJECT data_mono > #CCP4I JOB_ID 13 > #CCP4I SCRATCH C:/Users/br/AppData/Local/Temp > #CCP4I HOSTNAME BR-WORK > #CCP4I PID 10064 > > <B><FONT COLOR="#FF0000"> > > <hr><font size="-5"><br></font> > </FONT></B> > <B><FONT COLOR="#FF0000"> > > > > ############################################################### > ############################################################ > ### > ############################################################ > ### > ### CCP4 8.0.005: Refmac version 5.8.0352 : 05/31/22## > ############################################################ > ### > > Thx, BR > ----------------------------------------------------------------- > Bernhard Rupp > k.k. Hofkristallamt > 001 (925) 209-7429 > +43 (676) 571-0536 > b...@ruppweb.org <mailto:b...@ruppweb.org> > hofkristall...@gmail.com <mailto:hofkristall...@gmail.com> > http://www.hofkristallamt.org/ <http://www.hofkristallamt.org/> > ----------------------------------------------------------------- > Doors and corners – that’s where they get you > ----------------------------------------------------------------- > > > > > ________________________________ > > > 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/
