Yes - the RMS for the map is weighted by sin beta
Here is the comment:
C Mean RMS need to be weighted by sin beta, to allow for distortions
c in Eulerian space.
c On the last section, if beta = 90, the weight is 1/2 because of
c symmetry. Here we only need to test for last
Is ' U ' now the standard vs ' U' ? I'm used to right justified letters for
RNA residues in the residue field.
This is with a recent refinement with refmac 5.6.0117 .
And of course this switch in naming convention breaks compatibility with
molprobity (which requires right justified letters
Is there finally, at long last, one convention for nucleic acids? I wonder how
many cumulative person-years of exasperation this @#$% issue has caused?
And please note, even Mother Nature herself, let alone synthetic chemists,
occassionally attaches U to deoxyribose or T to plain ribose.
Hi Garib
Thanks for the quick reply!
Refmac however is writing my pdb's as with the residue letter in the centered
position.
Is the newest pdb requiring centered residue letters for RNA?
F
On Sep 12, 2011, at 1:05 PM, Garib N Murshudov wrote:
Refmac will read right or left justified
Yes, new version of the dictionary uses U. Refmac will read right or left
justified residue names, however pdb may use only one of them.
There are some backward compatibility code/dictionary elements. For example
Ad/Ar are also accepted. However it is encouraged to use new pdb v2.3
Hi Francis
Is that newer version of refmac?
regards
Garib
On 12 Sep 2011, at 20:09, Francis E Reyes wrote:
Hi Garib
Thanks for the quick reply!
Refmac however is writing my pdb's as with the residue letter in the
centered position.
Is the newest pdb requiring centered residue
Hi Paul,
I am running the centos5 build. After a couple of yum installs it seems to be
happy...
Except I cannot maximize the window for some reason.
Thanks for the reply.
Yuri
