Re: [ccp4bb] Anomalous atom or ligand?
Respected Mam, I used Cadmium at home source 1.54179Ang. For detecting the anomalous peaks CAD and FFT was used. It has Se also. So while refining the occupancies of Cd, Se, S and P are also refined. Thanking you Respectfully Kavya > Not sure I follow you completely.. You dont say what anom scatterer you > expect, or what the wavelength is. > > 1) How did you find the anomalous peaks? If from an anomalous difference > Fourier there will inevitably be noise. > In practice when there are S to check this can be very helpful in deciding > on noise levels. You can be pretty sure > that SG and SD are indeed S, and if the wave length is appropriate, that > they should show some anom. signal. > > One often finds the well defined S show up well. then there is a grey area > wher they are down amongst noise but still appear. It often highlights how > many MET are in alternate conformations.. > > If possible I like to use these as bench marks for P. But in my experience > the P are often even weaker - maybe the ligand is not fully occupied, or > the P temp. factors are higher? > > > > > > > > > On 24 April 2013 10:56, Kavyashree Manjunath > wrote: > >> Dear users, >> >> After detecting the anomalous peaks in a data, Is it >> necessary that there will be an anomalous atom in most >> of the peaks? >> >> In a particular case, a low ranking peak was assigned >> an anomalous atom because it was present in the native >> structure, while a peak with a rank higher than this >> one did not correspond to anomalous position in native >> structure. >> >> For eg. Peak 15 in ligand bound structure corresponds to >> the anomalous position in native structure, so anomalous >> atom was assigned. >> But Peak 3,4 in ligand bound structure does not correspond >> to anomalous position in native structure but it is present >> near the ligand which is beta and gamma Phosphates of ATP. >> The question is whether It is ATP or AMP and 2 anomalous >> atoms? >> >> Thanking you >> Regards >> Kavya >> >> >> -- >> This message has been scanned for viruses and >> dangerous content by MailScanner, and is >> believed to be clean. >> > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Re: [ccp4bb] Anomalous atom or ligand?
Not sure I follow you completely.. You dont say what anom scatterer you expect, or what the wavelength is. 1) How did you find the anomalous peaks? If from an anomalous difference Fourier there will inevitably be noise. In practice when there are S to check this can be very helpful in deciding on noise levels. You can be pretty sure that SG and SD are indeed S, and if the wave length is appropriate, that they should show some anom. signal. One often finds the well defined S show up well. then there is a grey area wher they are down amongst noise but still appear. It often highlights how many MET are in alternate conformations.. If possible I like to use these as bench marks for P. But in my experience the P are often even weaker - maybe the ligand is not fully occupied, or the P temp. factors are higher? On 24 April 2013 10:56, Kavyashree Manjunath wrote: > Dear users, > > After detecting the anomalous peaks in a data, Is it > necessary that there will be an anomalous atom in most > of the peaks? > > In a particular case, a low ranking peak was assigned > an anomalous atom because it was present in the native > structure, while a peak with a rank higher than this > one did not correspond to anomalous position in native > structure. > > For eg. Peak 15 in ligand bound structure corresponds to > the anomalous position in native structure, so anomalous > atom was assigned. > But Peak 3,4 in ligand bound structure does not correspond > to anomalous position in native structure but it is present > near the ligand which is beta and gamma Phosphates of ATP. > The question is whether It is ATP or AMP and 2 anomalous > atoms? > > Thanking you > Regards > Kavya > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. >
[ccp4bb] Anomalous atom or ligand?
Dear users, After detecting the anomalous peaks in a data, Is it necessary that there will be an anomalous atom in most of the peaks? In a particular case, a low ranking peak was assigned an anomalous atom because it was present in the native structure, while a peak with a rank higher than this one did not correspond to anomalous position in native structure. For eg. Peak 15 in ligand bound structure corresponds to the anomalous position in native structure, so anomalous atom was assigned. But Peak 3,4 in ligand bound structure does not correspond to anomalous position in native structure but it is present near the ligand which is beta and gamma Phosphates of ATP. The question is whether It is ATP or AMP and 2 anomalous atoms? Thanking you Regards Kavya -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
