Hmm - of course heavy atoms will affect the sigma level of a map, but that is easily adjusted - just scroll till the electron density looks sensible for some well defined protein atoms. (Ideally I guess we should contour at some absolute density level but choosing that to take account of resolution is tricky..)
But ripples around heavier atoms are more likely due to some error. Data incompleteness? (not so common nowadays). Wrong occupancy for heavier atoms? That should show up as a residual peak or hole in the difference map.. I like to look at the plot of <Fobs> & <Fcalc> v resolution - it is in the REFMAC log after the rfactor v resolution. If there are gross differences between the two means that indicates a problem - maybe measurement - maybe scaling.. And of course that will be reflected ni the map Eleanor On Wed, 10 Jun 2020 at 10:06, LEGRAND Pierre < [email protected]> wrote: > Dear Vito, > In that case, and from what I can see from the picture you shared, I would > guess that it is mainly the effect of the low occupancy of this I3C. The > peak height of the iodide atoms seems low. > Pierre > > > *De :* CCP4 bulletin board [[email protected]] de la part de Vito > Calderone [[email protected]] > *Envoyé :* mercredi 10 juin 2020 10:54 > *À :* [email protected] > *Objet :* [ccp4bb] R: [ccp4bb] R: [ccp4bb] Heavy atom vs light atoms > density > > Dear John, > > I would say that in that case the FoFc is basically flat. > > > > Vito > > > > *Da:* CCP4 bulletin board <[email protected]> *Per conto di *John R > Helliwell > *Inviato:* mercoledì 10 giugno 2020 10:40 > *A:* [email protected] > *Oggetto:* Re: [ccp4bb] R: [ccp4bb] Heavy atom vs light atoms density > > > > Dear Vito, > > The I3C isn't like the platins as a challenge to the 2Fo-Fc map. > > It maybe is more akin to the situation we described here:- > > https://onlinelibrary.wiley.com/doi/abs/10.1107/S0907444903004219 > > ie what does your Fo-Fc map, with three iodines placed, at the correct > occupancy, look like? > > Best wishes, > > John > > Emeritus Professor John R Helliwell DSc > > > > > > > > On 10 Jun 2020, at 09:34, Vito Calderone <[email protected]> wrote: > > Dear Pierre, > I was in particular talking of 2FoFc refinement maps. > In the attached picture for example you can see the 2FoFc map contoured at > 1 > sigma level of an I3C molecule bound to a protein where for I3C the only > visible density is that of iodines whereas the density of the other atoms > of > the ligand is insignificant. > Best regards > > Vito > > -----Messaggio originale----- > Da: CCP4 bulletin board <[email protected]> Per conto di LEGRAND > Pierre > Inviato: mercoledì 10 giugno 2020 09:31 > A: [email protected] > Oggetto: Re: [ccp4bb] Heavy atom vs light atoms density > > Dear Vito, > Could you precise in what kind of maps are you experiencing these effects: > 2FoFc refinement maps or experimental phasing ? > I had this kind of effects long ago in experiemental phasing due to Fourier > transform ripple effects. This could be due to scaling problems, low > resolution truncation or incompletness (maybe intensity overloads). > Another source condition could be local X-ray dose degradation due to the > high absoption of the metals. > Best regards, > Pierre Legrand > PROXIMA-1, SOLEIL > ________________________________________ > De : CCP4 bulletin board [[email protected]] de la part de Vito > Calderone [[email protected]] Envoyé : mercredi 10 juin 2020 08:42 > À : > [email protected] Objet : [ccp4bb] Heavy atom vs light atoms density > > Dear All, > many of us have probably experienced that, in the diffraction > of protein ligands containing heavy atoms (cisPt, I3C, etc), the > overwhelming electron density of the metal can totally flatten that of the > light atoms around (or rather make it look insignificant). > Is anyone aware of an article/review (to use as a reference) in which this > is clearly stated/pointed out? > Best regards > > Vito Calderone > > > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?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/ > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?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/ > > <I3C_3.png> > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?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/
