Hi Nat,
Thanks for your help! I just have one more question: when you say "having an anomalous scatterer", do you mean add anomalous signal on the native crystal (Such as Br-derivative)? Like for my case, I have ~90 bp DNA duplex in one unit cell, how many Br do you think I should use to ensure the anomalous signal is strong enough? Any reasonable guess from you will be quite helpful!
Again, thanks a lot.
Sincerely,
Xiang
----- Original Message -----
From: "Nathaniel Echols"
I am working on two datasets of the similar crystal design. In one of the datasets, there is an extra guest protein (might be considered as a ligand) docked in one unit cell. The two crystals have very similar unit cell size and same symmetry. I want to calculate the Fo-Fo map to see whether I could figure out where the protein is. But I got error says the symmetry of the two datasets are not the same. I have never used the "isomorphous difference map" in GUI before. Can anyone help me to figure out where I did wrong please? I have attached the mtz file that I want to compare.
Your datasets differ by 3Å along the C edge, which is usually enough to be considered "non-isomorphous". At this low resolution, perhaps it won't matter, but you should be very cautious about interpreting the results, and pay special attention to the R-factors between the datasets. You can disable the symmetry check by clicking the box labeled "Ignore non-isomorphous unit cells"; it will simply use the symmetry from the first dataset. (Which is what the phasing model should also correspond to.)
Btw, if the protein is not very rigidly linked with the crystal framework (~2 free residues linkage), am I supposed to see the density of the protein? Or are there any better ways for me to identify the protein?
It depends on how large and how well ordered it is, but the only way to know for sure is to try. If you don't see the density you're expecting/hoping for, there could be multiple explanations. As always, having an anomalous scatterer helps a lot (but at this resolution, sulfur certainly doesn't count). -Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb