On the whole it is good practice to refine the 7 molecules you have - correct
sequence etc etc, all with NCS restraints a 3A, then if you like use one of
your improved molecules as the search model. But don't you have some NC
symmetry such as dimers or tetramers - if so take one of the complete units and
fit over the partner of the missing molecule - it is very probable then that
you have positioned the lost one.
Or if you want to be completely automated - use the dimer/tetramer whatever as
the search model..
Eleanor
MOLREP is good at this -
On 30 Oct 2012, at 14:53, Mark J van Raaij wrote:
if you are sure about it's position, why not put the 8th molecule by hand?
why believe what a program does more than you can see by eye?
(this is nothing against Phaser, it is a great program)
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij
On 30 Oct 2012, at 15:44, Jacob Wong wrote:
Dear all, I have this (3.0 A) structure that has 8 molecules per ASU -
Phaser was able to find 7 molecules correctly, but not the last one, as
indicated by the .sol file (TFZ=5.1) below and the resultant density map. I
tried to delete the entry of the last molecule and give the truncated .sol
file for another round of MR but Phaser returned with the same solution that
has the 8th molecule misplaced. I am tempted to place the 8th molecule by
hand but before that would like to learn from you a better way of handling
it. One thing I could think of is to refine/rebuild the partial structure
with the 7 molecules so as to resolve any potential packing clashes due to
model/structure variations and then let Phaser find/position the 8th one for
me, but it appears that Phaser doesn't accept .pdb file for a MR with
partial solution routine? Thank you, Jacob
# [No title given]
SPACEGROUP P 21 21 21
SOLU SET RFZ=3.7 TFZ=8.2 PAK=0 LLG=78 RFZ=3.7 TFZ=16.0 PAK=0 LLG=248
TFZ==17.2 RFZ=3.7 TFZ=17.8 PAK=0 LLG=463 TFZ==19.7 RFZ=2.9 TFZ=23.0 PAK=0
LLG=765 TFZ==23.2 RFZ=2.8 TFZ=28.6 PAK=0 LLG=1201 TFZ==30.0 RFZ=3.9 TFZ=23.1
PAK=0 LLG=1537 TFZ==24.3 RFZ=2.6 TFZ=19.5 PAK=1 LLG=2096 TFZ==32.1 RFZ=3.0
TFZ=5.1 PAK=1 LLG=1945 TFZ==7.0
SOLU 6DIM ENSE ensemble1 EULER 333.533 143.979 14.880 FRAC -0.30547 0.22985
-0.12420 BFAC 0.0
SOLU 6DIM ENSE ensemble1 EULER 287.095 31.031 200.132 FRAC -0.01202 0.48107
-0.12591 BFAC 0.0
SOLU 6DIM ENSE ensemble1 EULER 220.563 33.756 203.275 FRAC -0.33196 0.18927
-0.27514 BFAC 0.0
SOLU 6DIM ENSE ensemble1 EULER 125.978 23.511 167.527 FRAC 0.36411 -0.45096
-0.17121 BFAC 0.0
SOLU 6DIM ENSE ensemble1 EULER 148.925 162.593 356.498 FRAC -0.41711
-0.09462 -0.07282 BFAC 0.0
SOLU 6DIM ENSE ensemble1 EULER 323.033 34.903 192.073 FRAC -0.53201 -0.04754
-0.02533 BFAC 0.0
SOLU 6DIM ENSE ensemble1 EULER 113.904 157.019 345.596 FRAC 0.09892 -0.60041
-0.17986 BFAC 0.0
SOLU 6DIM ENSE ensemble1 EULER 79.967 95.631 1.727 FRAC -0.41239 0.07915
-0.05760 BFAC 0.0
