First choose the molecule you mask as the one with the best and most
complete density and give all the matrices relative to that copy.
Anything which is masked out will certainly not return..
You only need one mask in one of the crystals; the matrices will
transform that into the otjer crystal form too, providing you specify
them correctly!
Eleanor
Jianghai Zhu wrote:
Thanks for the suggestions. However, in two different space groups, I
know the NCS contacts are similar, but the symmetry-related contact
can be different. Should I generate different masks for different
crystals? or it is not a big deal.
Another question. In my model, there is one domain which is fixed in
one molecule (good density, lots of lattice contacts) but flexible in
all other 5 molecules (no density, lacking lattice contacts). When I
left this domain out of the mask, the density of the domain was gone
after dmmulti. What should I do with this particular domain?
Thanks.
Jianghai
On Feb 22, 2007, at 4:59 AM, Kevin Cowtan wrote:
Two things:
1. You can do overlap removal in NCSMASK using the OVERLAP keyword.
2. You shouldn't be using 6 masks anyway - you only need one mask.
Dmmulti generates the rest internally.
On Feb 22, 2007, at 4:54 AM, Eleanor Dodson wrote:
You just need one mask for your master molecule, which will be
transferred by the matrices you give to all the other copies.
I make the mask from the crude model, with a generous border round it
- the program will also prune it to get rid of overlaps..
Eleanor
Jianghai Zhu wrote:
Dear all,
I have two low resolution (3.8 A) MAD data sets from two different
space groups. There are 4 copies of my molecule in one space group
and 2 copies in the other. The density-modified maps from these
data sets are poor, but still allow me to build a crude model on
them. All the domains should be at the right or close to right
orientations and positions. I would like to try multi-crystal
averaging to improve my maps. Since I already have the model, I
used NCSMASK to make 6 masks for the 6 copies of my model. Then I
used DMMULTI to perform the multi-crystal averaging. The maps came
out of DMMULTI showed great improvement. Some densities were not
seen before showed up nicely. However, after I read the manual
carefully, I realize that DMMULTI would not take care of the mask
overlap. So some regions in my density map between the NCS-related
and symmetry- related molecules must be messed up. Could any
expert out there give me some suggestions about how to make proper
NCS masks for DMMULTI? Thanks at advance.
Jianghai
