Well - I would stick in waters - they can be very well rdered in certain environments. Anecote: We have spent ages trying to put some interesting compound into a "feature" in maps, untill the crystals finally diffracted to 1.6A and in that map it is very clear there are 4 beautifully shaped waters, with lots of hydrogen bonds to the surrounding amino acides..
So all that intelligent interpretation was unnecessary! Eleanor On 3 November 2017 at 21:02, Abhishek Anan <rendezvous.a...@gmail.com> wrote: > Dear all, > > My apology for the confusion!! I did mean the map radius is "truncated" at > 5A. Poor choice of words :( > > Any thoughts on what this density could be are still welcome. > > Best regards, > Abhishek > > On Fri, Nov 3, 2017 at 9:21 PM, Joern Krausze < > j.krau...@tu-braunschweig.de> wrote: > >> Dear all, >> >> I think Abhishek means that the picture shows 5 A map radius. >> >> Best >> Joern >> >> On 3. Nov 2017, at 18:42, Pavel Afonine <pafon...@gmail.com> wrote: >> >> If by "it was truncated at 5A for clarity" you really mean you truncated >> all low-resolution data from 5A and lower then I am not surprised you see >> funny densities all over or don't see density where it is expected. Why? >> Consult a textbook for the answer. >> >> All the best, >> Pavel >> >> On Fri, Nov 3, 2017 at 3:10 AM, Abhishek Anan <rendezvous.a...@gmail.com> >> wrote: >> >>> Dear Prof Schreuder >>> >>> Here are another couple of perspectives from coot. The density is too >>> far and isolated from the peptide chain to be an alternate conformation or >>> conformational change. The density of the peptide chain does not look good >>> because it was truncated at 5A for clarity. >>> >>> Best regards >>> Abhishek >>> >>> On Fri, Nov 3, 2017 at 9:33 AM, <herman.schreu...@sanofi.com> wrote: >>> >>>> Dear Abhishek, >>>> >>>> >>>> >>>> To me, it looks like an alternative conformation of the peptide chain >>>> or maybe even a conformational change with respect to the starting model. >>>> The peptide chain does not look too well defined, despite high resolution >>>> electron density. >>>> >>>> >>>> >>>> Best, >>>> >>>> Herman >>>> >>>> >>>> >>>> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag >>>> von *Abhishek Anan >>>> *Gesendet:* Freitag, 3. November 2017 09:26 >>>> *An:* CCP4BB@JISCMAIL.AC.UK >>>> *Betreff:* [EXTERNAL] [ccp4bb] another unknown density problem >>>> >>>> >>>> >>>> Hi all, >>>> >>>> I have an "unknown" density in the map. I have tried to fit it to PEG >>>> but it doesn't fit very well. I was wondering if there are other >>>> PEG-related or other molecules I could try. >>>> >>>> The crystal grew in TRIS-HCl and PEG MME 2K. >>>> >>>> Thank you >>>> >>>> Abhishek >>>> >>> >>> >> >> >
