Hello Ruchi, I know that when you use non-crystallographic averaging there is a possibility of the starting with positive density and ending up with negative, the enantiomorph, or the negative enantiomorph density. In order to shift back to the correct phases you can apply a simple formula. This is the math that i recall:
positive structure alpha negative structure alpha + 180 enantiomorphic structure -alpha negative enantiomorphic structure -alpha + 180 The recollection comes from a paper in methods in enzymology that i don't recall the author or year of at the moment. I know your case has nothing to do with averaging but the math should hold true. In this case, you can switch between the enantiomorphs by multiplying the phases by -1. I don't know if this holds a solution to your case. It may be worth a quick shot just to multiply the phase column by -1. I may be far off base here but i think i am correct. This of course is assuming that you have the correct space group and that you have the enantiomorphic phases. If i am totally off on this, someone please correct me. I'm really sticking my neck out late on a friday, eh! Good Luck- todd -----Original Message----- From: CCP4 bulletin board on behalf of Ruchi Anand Sent: Fri 3/30/2007 5:31 PM To: [email protected] Subject: Re: [ccp4bb] Right Handedness of Density Dear All, We are working with a DNA binding protein with 4 Zn sites in in ASU. Using SnB and then CNS we were able to get a map using MAD phasing and could visualize the density for the double helix of the DNA but it was a left handed spiral instead of the usual right handed one. The space group which yielded the result was P3(2). We tried to flip the sites and change the space group to P3(1) but we are not able to generate a sensible map. Any advice regarding the best way to proceed will be very helpful. The resolution is around 3.2. Thanks Ruchi This email was scanned with Mcafee's Anti-Virus appliance, but this is no guarantee that no virus exists. You are asked to make sure you have virus protection and that it is up to date.
