Dear All,
I checked the Mg2+ B factor, and it was around 22. So, were the values for F
atoms. For AlF3, it was more than 50 for Al and more than 40 for F atoms. I
will take care about the occupancy. I hope that will fix the small negative
density.
When I inserted MgF in COOT using the code MGF (get monomer), it did appear but
looked fragmented. It remained fragmented after refinement as well (as shown in
the previously attached fig). But, there was no warning about bond breaking in
the Refmac log file. Even the density of MgF3- looked better (2Fo-Fc).
If I see the structure in Chimera or CCP4MG, it does not look fragmented.
So, is it a problem of display in COOT? Is the exploded MgF3 form, not actually
a broken form, since the refinement log file does not show any such indication?
regards,Ansuman
On Monday, 19 January 2015 2:15 PM, Mark van Raaij
<mjvanra...@cnb.csic.es> wrote:
It could be a mixture of Mg2+ and Al3+Mark J van Raaij
CNB-CSIC
www.cnb.csic.es/~mjvanraaijOn 16 Jan 2015 20:07, ansuman biswas
<bubai_...@yahoo.co.in> wrote:
Dear users,
I have a data at 2.2 A resolution. I am able to model AlF3 into the electron
density (fig attached). However after one cycle of refinement the AlF3 molecule
is exploding and the atoms move apart (fig2).
AlF3 is already present in refmac library. First, I used that. But it broke up
after refinement.
Then, I extracted AlF3 coordinate from already published PDB and prepared the
cif file. But, it also failed. I modified the cif file by changing the bond
lengths according to the broken AlF3 structure but it was of no help.Kindly
suggest how to carry out the refinement.
regards,Ansuman
