It isn't that your space group is wrong, but are you sure that your mtz file
has that space group in its header?
MR will test all possible alternatives - in this case P3121 or P3221 - but
won't change the symmetry information in the input mtz.
You need to do that with a utility like
mtzutils
Hi
Yes i did check my MTZ file header. It shows p3221. For the same reason i
reprocessed the data again in both p3221, p3121 and p321. Except for p3221
none of the other space groups fit the model. The packing looks good and
the map shows side chains very clearly. When i add the respective side
1) Check free R flag. It may be related with free flag being 1 instead of 0. If
it is the case then you can use newer version of refmac:
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/
or from ccp4 v 6.3
2) Try arp/warp
Garib
On 19 Jul 2012, at 18:29, Deepthi wrote:
Hi
Yes i did check my
Hi all
I am working with a small mutant protein which is 56 amino acids long. The
crystal diffracted at 1.4A0 and the space group is p3221. I did molecular
replacement using Phenix software with all the data (1.4A0) and got a
solution. Phenix did auto building with waters and R-free was 0.3123.
Hi there,
Not much information provided. How was the initial model refined ?
Phenix ? It could be a problem with the Refmac refinement protocol
(difficult to say with so little information) if you switched from
Phenix to Refmac.
How certain are you 1 - of the space group; 2 - that the
Thank You so much . I am trying to process the data again in all space
groups possible for primitive hexagonal and try refinement again. And i
didn't use Phenix after i got the MR solution. Probably refining the
mutated model again would give some more information.
Thank You once again.
How about trying some ARP/WARP?
JPK
On Wed, Jul 18, 2012 at 11:54 AM, Pavel Afonine pafon...@gmail.com wrote:
What happens if you do a round of refinement in phenix.refine after you
have done the mutations? Note: Phenix Autobuild is a tool to build your
model, not refine it (though it does
Can you check space group in your mtz and pdb? I have seen this happening when
they disagree.
It is annoying and I would like it to be sorted out. If you want you can send
your data and I can try to sort it out.
Garib
On 18 Jul 2012, at 17:50, Deepthi wrote:
I tried opening the model with
