Dear CCP4 users,
I am currently solving a structure (2.8-2.9 A resolution) of a protein
complexed with a ligand using MR with the apo-form of this protein as
model (resolution of the model is 2.4). After MR-phasing I performed a
regular autobuild run giving me good outputs and thus I refined
Hi Nathan,
While what you observe does sound like a bug I would not like to comment
whether this is right or wrong. However a CCP4 alternative to this which
I find easier to use is pointless -
pointless -c xdsin XDS_ASCII.HKL hklout sorted.mtz
This will give an unmerged MTZ which can be used in
Dear Nathan,
the xds documentation explains:
At present, MERGE=TRUE is enforced by XDSCONV for all output file formats other
than CNS and SHELX.
so this is not a bug but known. Pointless is probably the route to take, as
Graeme suggested.
Regards,
Tim
On Wed, Apr 29, 2015 at 12:47:05AM -0500,
We are working with a multi-domain protein crystallized in SG P6_5 with
one molecule per asymmetric unit. The structure was refined at 2.00 A
resolution with reasonable R-factors but unfortunately the domain we are
most interested in seems to be disordered. Interestingly, the
self-rotation
If you know what residues are likely to be involved, then set their
occupancies to 0.0 (In coot go to Measures - Residue info - edit occ)
then do a few cycles of refinement with that model, and then see if there
is difference density for those residues...
Quicker than an omit map procedure.
Hello,
I would certainly try the usual approaches (map coefficients that are
less sensitive to model-bias, i.e. Sigmaa; OMIT maps - there are several
of these which can be calculated). In addition, you may have a look at
the approach of Liu and Xiong (2014, J. Mol. Biol. 426, 980-993). It is
Dear Aleksandar,
I did use SA-OMIT map feature in Phenix, implemented by Tom Terwilliger.
I would strongly recommend you to use this feature.
Remove the suspicious residues from the pdb and run first SA-omit map in
phenix with default settings, and later with different starting
temperatures.
Make
Hmm - I think these peaks MUST be related to some internal symmetry in the
1200 aa solved structure. Is there some arrangement of helices or other
features which are replicated in another part of the structure?
A phi value of ~ 19 degrees can't be explained by a different related space
group I
Hi Aleks:
Maybe you can try CNS ( Initial refinement by simulated annealing) also. It may
help to get rid of the model bias and takes short time to run.
Xiaodi
Date: Wed, 29 Apr 2015 13:52:53 +0200
From: frederic.velli...@ibs.fr
Subject: Re: [ccp4bb] model bias
To: CCP4BB@JISCMAIL.AC.UK
Sometimes (sadly, not always) the problem with thin plates is that they get
damaged in mounting. If none of the tricks suggested work, you might try
seeing if you get any better data from the existing crystals using those tennis
racket shaped loops that give more support to the thin plate.
Dear All,
thank you all for your suggestions and support. The quick look (by
removing interacting AA and subsequent refinement with and without
little SA) revealed that some AAs are mislocated and indeed seem to be
more directed to the density belonging to the ligand. So, I will try
some of
Dear Bei,
It can sometimes be difficult to tell a real molecular replacement solution
from noise at low resolution.
In addition to Eleanor's excellent advice, you might try to use your
potential derivative data to test the top molrep solutions, even if their
statistics are crappy. Try
Dear Bei,
Since you have multiple HA data sets you can also try using dmmulti, which
can be used to data from one or more crystal forms simultaneously.
Best of luck,
Sridhar
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Phoebe
Rice
Sent:
I recently solved a 4-identical chain protein structure. First I got it from
initial model with NCS, good enough. Then from the initial model I process it
without NCS, quality better than solved with NCS.
Smith
At 2015-04-30 02:07:31, Eleanor Dodson eleanor.dod...@york.ac.uk wrote:
Hi Peer,
I would definitively second Pierre's suggestion to use calculated data to
simulate the self-rotation results.
Do you see any density for the lost domain, or nothing at all?
Could it be that this domain is flipped by 180° in part of the molecules, maybe
due to a proteolytic cleavage?
Hi Peer,
The first thing I would suggest is calculating the self-rotation again but
using the FC from the refined model, for comparaison. Then, if you don't see
the same supplementary peaks, you can try to play with the integration radius
and resolution range. This could give you some hint on
Well - PG P6/mmm (possible SG P6522) will have peaks at kappa = 180 omega
= 90 phi = 0 30 60 etc..
But if there is only one molecule / asymm unit there cant be an extra
2-fold.
How big are the relative domains? Your interesting domain couldnt just be
cleaved off could it?
Eleanor
On 29
Thanks everyone for pointing out Pointless and, in particular, to Tim
Gruene for explaining my failure to RTFM.
Nate
On Wed, Apr 29, 2015 at 3:21 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
Dear Nathan,
the xds documentation explains:
At present, MERGE=TRUE is enforced by XDSCONV for
Zbyszek Otwinowski and Fred Vellieux suggested to run the self-rotation
on Fcalcs. This suggestion solved the problem, since there are similar
peaks on the kappa=180° planes as well. However, I wasn't able to get
rid of those peaks by playing around with resolution and integration
radius. I
I forgot to acknowledge Pierre Legrand for the same suggestion.
-Peer
Zbyszek Otwinowski and Fred Vellieux suggested to run the self-rotation on Fcalcs. This
suggestion solved the problem, since there are similar peaks on the
kappa=180° planes as well. However, I wasn't able to get rid of
Peer, you didn't say which program you are using for this? Polarrfn or
Molrep? Do you get the same results with both programs? Also did you try
sharpening the Fs with Ecalc and/or using all your data? In my experience
sharpening works better with self- than with cross-rotation functions
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