Hi,
have a look into the supplement of the paper by Poul Nissen pointed out.
There are some shell scripts exactly for that purpose.
I had to adapt the scripts a bit, but the instructions are very well to
follow.
HTH
Guenter
Hi Pete
Thanks for the reply.
As for the transformation, I was going to use the refined mask operator (either
from the end of a DM run that produces a better map for features I know have
to be there, or from a correlation of the averaging mask from MAVE).
The interpolation is going to be a little more difficult. The 'good' solvent
mask output after a dmmulti run
has different gridding, extent, and cell than the mask output by the other
crystal forms.
However, the documentation for dmmulti says that SOLin can be on any grid or
axis ordering.. not quite sure about the extent.
Furthermore, it seems that Poul Nissen was able to put in a generic mask for
all his crystal forms
(http://journals.iucr.org/d/issues/2010/03/00/kw5018/index.html) without regard
for interpolation (unit cell, extent, or gridding) nor transformation. So I'm
not exactly sure how I'm getting an 'inconsistent cell info'.....
Maybe it's because I'm getting my masks from dm instead of generating it from a
my averaging mask (which came from a pdb).. hmmm.......
Anyone know of a wiki page that talks about maps/masks and a description of
their properties (gridding, extent, basically everything discussed in the
output of mapinfo?) A wiki with examples (images) of different settings for
these items would be especially useful.
F
On Oct 24, 2011, at 9:40 AM, Pete Meyer wrote:
Hi,
It's definitely possible, but the devil is in the details. It's a two-step
process: transform the coordinates of the mask so it's in the right spot in the
new cell, and interpolate the mask into the appropriate grid for the new
crystal form.
The last time I did this I was using O/PHASES masks (so I'm probably off on the details
for CCP4 stuff): maprot should be able to handle the transformation and interpolation,
but you may have to use a mask -> map -> maprot -> mask pathway. This isn't
ideal due to differences in mask interpolation vs map interpolation but could be a good
starting point.
Determining the transformation may be tricker - I'd try placing pseudo-atoms at
similar features in both maps and using lsqkab to get the transformation
matrix; but this approach would probably need tuning to get a good alignment.
Good luck,
Pete
Francis E Reyes wrote:
Hi all
I'm using dmmulti and one of my crystal forms seems to have a better solvent
mask (after outputting it with solout) than the other. (Probably due to better
phased reflections at low res for the first crystal form). Is it possible to
take the better solvent mask and use it as input for the solvent mask for the
other? How's this done? (a direct input of the better xtal1 mask to xtal 2
gives 'inconsistent cell info'). Thanks!
F
---------------------------------------------
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
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Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
