Yes, you can provide your own bulk solvent model as a "partial
structure" to REFMAC.
http://www.ysbl.york.ac.uk/~garib/refmac/docs/keywords/xray-principal.html#labin_fparti_phiparti
http://www.ysbl.york.ac.uk/~garib/refmac/docs/keywords/xray-general.html#scpa
http://www.ysbl.york.ac.uk/~garib/refmac/docs/keywords/xray-principal.html#solv
Once you have an electron density map for the bulk solvent that you are
happy with, use the CCP4 program SFALL to convert that map into
structure factors:
sfall mapin my_better_solvent.map hklout my_better_solvent.mtz << EOF
mode sfcalc mapin
EOF
SFALL will output FC and PHIC, but since these names are sort of
"taken" inside of REFMAC, you may want to re-name them to be Fsolv and
PHIsolv using CAD. While you are at it, you might as well combine Fsolv
PHIsolv with your input MTZ file (the one that contains your observed
data. REFMAC only takes one input MTZ file. For example:
cad hklin1 old_refme.mtz hklin2 my_better_solvent.mtz hklout
new_refme.mtz << EOF
labin file 1 E1=FP E2=SIGFP E3=FreeR_flag
labin file 2 E1=FC E2=PHIC
labou file 2 E1=Fsolv E2=PHIsolv
scale file 2 1 0
EOF
Next, you want to alert REFMAC to the "partial structure" you are
providing. Do this by assigning them to FPART1 and PHIP1. My input
usually looks like this:
refmac5 hklin new_Refme.mtz xyzin best_model_yet.pdb hklout
refmacout.mtz xyzout refmacout.pdb << EOF
LABIN FP=FP SIGFP=SIGFP FREE=FreeR_flag FPART1=Fsolv PHIP1=PHIsolv
SCPART 1
SOLVENT NO
EOF
The "SCPART 1" is required if you want REFMAC to refine a scale and B
factor for your bulk solvent like it does with the bulk solvent it makes
automatically. If the map you input into SFALL used "1" to define a
"solvent" map voxel and "0" to define vacuum, then the "scale factor"
you will find under "Partial structure 1: scale" in the refmac output
log will be your refined bulk solvent electron density (k_sol), which
has units of electrons/Angstrom^3.
Note that I am using "SOLVENT NO" in the above example to turn off the
"built-in" bulk solvent model. If you don't do this, REFMAC will make
its own bulk solvent as usual, but refine it as an additional partial
structure. Then you will have two bulk solvent masks! REFMAC actually
supports multiple partial structures (up to four, I think), but my
experience with this is that it gets unstable rather quickly.
That's the mechanics of it anyway. It is a pity that phenix.refine
doesn't support external partial structures like this, but perhaps it
will soon.
One thing to beware is that MSKOUT may or may not be on any particular
scale. If you want to actually recover the "refined" bulk solvent map,
you need to first re-scale the mskout.map so that it ranges from 0 to 1
in value (check this with MAPDUMP), before you feed it to SFALL. Then,
during the CAD step above apply an appropriate scale and B factor to
Fsolv using "SCALE FILE 1":
http://www.ccp4.ac.uk/html/cad.html#scale
You will find appropriate scale and B factor values printed out on the
last "Partial structure 1:" entry in your last refmac log.
Now, of course, you have the finer detail problem of what, exactly, to
do to the "default" bulk solvent mask to make it better. Simply adding
the Fo-Fc map is not only cheating; it doesn't work! By default, the
Fo-Fc map does not contain structure factors flagged as part of the FREE
set. So, if you "edit" your bulk solvent by adding Fo-Fc, you will
immediately get an Rwork of zero, but will see no change to Rfree. This
is because all the "free" structure factors used to make the Fo-Fc map
were zero.
Finding some way to "transfer" information from the differences in the
working set into the free set is challenging, and indeed this is the
central problem of model building.
-James Holton
MAD Scientist
On 1/11/2015 11:05 AM, Alastair Fyfe wrote:
A related/follow-on question, hopefully on the same topic:
When mask-based solvent modeling leads to problems caused by
calculation of an inappropriate mask (eg inclusion of disordered loops
or inaccessible pockets as bulk-solvent volume) it seems that a
feasible workaround is to (a) output the calculated mask via MSKOUT
(b) edit it to remove spurious regions (c) calculate partial structure
factors for the new solvent region using refmac's previous kSol, bSol
estimates (d) include the partial structure factors in a second round
of refinement by specifying "SOLVENT NO", FPART and SCPART.
However, this does not re-calculate kSol and bSol to reflect the
modified mask. Is there a way to simply supply the mask to be used
rather than have refmac calculate it ?
Thanks,
Alastair Fyfe
On 01/11/2015 08:04 AM, Eleanor Dodson wrote:
Yes. If the model is incomplete it is obviously not sensible to use the
mask based solvent - you will tend to lose the unmodelled features.
It also
gives unrealistically low R factors for a crystal with high solvent
content. However the best test would be to analyse maps and try to
decide
if & when the different procedures work best.. A project for a student
dissertation perhaps??
Eleanor
On 9 January 2015 at 20:13, Roberts, Sue A - (suer)
<s...@email.arizona.edu>
wrote:
I always try both methods - usually there is little difference.
However,
For CueO (multicopper oxidase) where there are about 25 disordered
(unseen) residues in a loop, using Babinet scaling instead of the
default
refmac scaling reduced the R factors by about 2% (both R and Rfree) and
improved the quality of the maps substantially.
From Dirk's comment, I'd guess this is because the mask-based solvent
model is putting solvent where there is (disordered) protein, which is
different from real bulk solvent.
Sue
Dr. Sue A. Roberts
Dept. of Chemistry and Biochemistry
University of Arizona
1306 E. University Blvd, Tucson, AZ 85721
Phone: 520 621 4168
s...@email.arizona.edu
-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Armando Albert
Sent: Friday, January 09, 2015 12:56 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Bulk solvent
Dear all,
Is there any reason for using Babinet scaling for bulk solvent
correction
instead of mask based scaling?
Armando
