Re: [ccp4bb] another unknown density problem
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 >>>> >>> >>> >> >> >
Re: [ccp4bb] another unknown density problem
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 >>> >> >> > >
Re: [ccp4bb] another unknown density problem
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 > <mailto: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 > <mailto: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 > <mailto:CCP4BB@JISCMAIL.AC.UK>] Im Auftrag von Abhishek Anan > Gesendet: Freitag, 3. November 2017 09:26 > An: CCP4BB@JISCMAIL.AC.UK <mailto: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 > > >
Re: [ccp4bb] another unknown density problem
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 >> > >
Re: [ccp4bb] AW: Re: [ccp4bb] another unknown density problem
If you mean you truncated the low resolution data to 5 angstrom, I wouldn't recommend that. On Fri, Nov 3, 2017 at 12:24 PM, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote: > That map does not look like a 5A map? > I guess you mean something else.. > Eleanor > > On 3 November 2017 at 11:00, <herman.schreu...@sanofi.com> wrote: >> >> You are right. In this case, I would put some waters in it, refine and see >> if the density gets any clearer. However, since from this perspective the >> density is quite far away from the protein, it could be a very disordered >> PEG, which, even at high resolution, might be impossible to fit. >> >> >> >> Best, >> >> Herman >> >> >> >> Von: Abhishek Anan [mailto:rendezvous.a...@gmail.com] >> Gesendet: Freitag, 3. November 2017 11:10 >> An: Schreuder, Herman /DE >> Cc: CCP4BB@jiscmail.ac.uk >> Betreff: [EXTERNAL] Re: [ccp4bb] another unknown density problem >> >> >> >> 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 >> >> > >
Re: [ccp4bb] AW: Re: [ccp4bb] another unknown density problem
That map does not look like a 5A map? I guess you mean something else.. Eleanor On 3 November 2017 at 11:00, <herman.schreu...@sanofi.com> wrote: > You are right. In this case, I would put some waters in it, refine and see > if the density gets any clearer. However, since from this perspective the > density is quite far away from the protein, it could be a very disordered > PEG, which, even at high resolution, might be impossible to fit. > > > > Best, > > Herman > > > > *Von:* Abhishek Anan [mailto:rendezvous.a...@gmail.com] > *Gesendet:* Freitag, 3. November 2017 11:10 > *An:* Schreuder, Herman /DE > *Cc:* CCP4BB@jiscmail.ac.uk > *Betreff:* [EXTERNAL] Re: [ccp4bb] another unknown density problem > > > > 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 > > >
[ccp4bb] AW: Re: [ccp4bb] another unknown density problem
You are right. In this case, I would put some waters in it, refine and see if the density gets any clearer. However, since from this perspective the density is quite far away from the protein, it could be a very disordered PEG, which, even at high resolution, might be impossible to fit. Best, Herman Von: Abhishek Anan [mailto:rendezvous.a...@gmail.com] Gesendet: Freitag, 3. November 2017 11:10 An: Schreuder, Herman /DE Cc: CCP4BB@jiscmail.ac.uk Betreff: [EXTERNAL] Re: [ccp4bb] another unknown density problem 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<mailto: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<mailto:CCP4BB@JISCMAIL.AC.UK>] Im Auftrag von Abhishek Anan Gesendet: Freitag, 3. November 2017 09:26 An: CCP4BB@JISCMAIL.AC.UK<mailto: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
[ccp4bb] AW: [ccp4bb] another unknown density problem
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
