Dear Melanie,
To obtain a reasonable error estimate of R-free you could try to refine your
structure against different sets of reflections. You can force the R-free set
to be the reflections flagged with 1 or 2, etc. instead of 0 (at least in
Refmac) and refine to convergence again. You should
Very easy way is the Swiss-Model server via the alignment mode
Good luck
Rotem
On 4 Mar, 2010, at 0:59, Brett, Thomas wrote:
Dear all:
I am trying to create a homology model of a coiled-coil for use in
molecular replacement. I have a template poly-ala coiled coil that
I like to use, so that
Hello,
My aim is to calculate SIRAS/MIRAS phases using PHENIX. Which should be the
correct column labels and associated "Differences" in the derivative data
one should select to calculate SIRAS phases? I am supplying both native and
derivative data and for the derivative data i am selecting F_HA,
>I am trying to create a homology model of a coiled-coil for use in
molecular >replacement. I have a template poly-ala coiled coil that I like
to use, so that is fine. >I want to thread my sequence onto the helix and am
trying to find a server/easy >program that will do this.
As a starting point
Yuan Cheng wrote:
I am trying to model a S-adenosylmethionine (SAM) molecule into the
active site of a protein using the SAH (exists in the crystal structure)
as the template.
2)Coot: I tried to superpose SAM to SAH in coot. Bot SSM superpose and
LSQ superpose didn't work. when I did SSM supe
I would echo Ethan on this metric being something of a relic and add a bit
more data.
Several years ago I tried to get a practical solution to the questions:
- when is a refinement finished?
- how to detect the correctable abnormalities (errors) in a structure so they
can all be corrected durin
Hi Yuan,
LSQ within Coot works quite well for superimposing similar ligands. Are you
sure you are selecting the appropriate chain IDs and residue numbers in the LSQ
dialog box? It is a rigid body superposition though so it will only get you in
the neighborhood (i.e. the adenine and sugar ring
Dear all:
I am trying to create a homology model of a coiled-coil for use in molecular
replacement. I have a template poly-ala coiled coil that I like to use, so that
is fine. I want to thread my sequence onto the helix and am trying to find a
server/easy program that will do this. I want to use
Hi everyone,
I am trying to model a S-adenosylmethionine (SAM) molecule into the
active site of a protein using the SAH (exists in the crystal structure)
as the template.
What I have already tried but failed so far are
1)Pymol: I loaded the pdbs of SAM and protein-SAH into pymol and copy
S
Hi All,
I have a question regarding developing inhibitor for UTP binding protein.
Since UTP is a common nucleotide substrate for a lot of glycoenzymes
similiar to ATP for kinases, developing potent inhibitor for UTP in vitro
may not seem to be an impossible task, or at least it's technically
feas
Director, Institute for Structural Biology, Virginia Commonwealth University
(VCU).
VCU seeks an outstanding investigator in the field of structural biology to
direct the VCU Institute for Structural Biology and Drug Discovery (ISBDD),
which was established in 1995 as the nidus of structural
Jerry,
One thing you might try is a combination of Endo F1, F3, and possibly
Endo H(might trim a little bit more). This works for me on
glycoproteins expressed in insect cells which show little or no
sensitivity to PNGaseF and EndoH. Depending on the host strain you
are using to express, the sens
Dear Jerry,
First of all, it will be hard to reproduce the conditions with the
glycosylated protein because by its nature, it is heterogeneous. One
thing I would try with the glycosylated protein is a detergent screen,
or if you don't have one, use a few NDSB's. Second, I would try setting
up
On Wed, 2010-03-03 at 08:45 -0800, Greg Warren wrote:
> This is most likely a 3800 problem since the 3800 has 1 DVI and 2 HDMI
> outputs instead of 2 DVI outputs.
Those are DisplayPort, not HDMI.
--
===
All Things Serve the
Dear all,
we have a protein isolated from mouse liver which crystallized in P1. The
amount of protein was very little so we could not get better crystals. The
protein expressed in E.coli did not yield any usable crystals.
We managed to collect data from 2 crystals after annealing at the beamline
I have Nvidia 3D vision running on the Samsung SyncMaster 2233. One note of
caution, for the Quadra FX3800 if you are using dual monitors I haven't found a
way to get TwinView to work with the Nvidia 195.30 beta linux driver. You can
configure for 2 X-screens to drive the two screens as a work
No, and it has nothing to do with the monitor. It's the sync signal
from the nvidia emitter which isn't compatible with nuvision,
crystaleyes, or edimensional goggles.
On Wed, Mar 3, 2010 at 10:22 AM, Brick, Peter wrote:
> A related question:
>
> Can one use the old Crystal Eyes glasses system wi
A related question:
Can one use the old Crystal Eyes glasses system with the new LCD displays? And
if not why not?
Peter B.
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Christian
Rausch
Sent: 03 March 2010 15:51
To: CCP4BB@JISCMAIL.AC.UK
Su
I am using the combination you are asking for with alienware monitor. The
driver I am using is 195.30 beta. It works very well.
Quality is much much better than Zalman and somewhat better than CRTs.
Hope it helps.
Ajit B.
- Original Message -
From: Christian Rausch
Date: Wednesday, Mar
Dear ALL:
Recently we've been trying hard to crystallize a highly glycosylated
protein complex ( 30% percent of carbohydrate in the total 120KD molecular
weight).
IT is a high affinity protein complex. One component can be crystallized in
high salt condition and the other can be crys
Hello,
is someone using Nvidia 3D vision + a compatible 1920x1080 23.5" Desktop
Display e.g.
ACER GD245HQ 120 Hz LCD display
OR
Alienware OptX AW2310 120 Hz LCD display?
Is it running nicely with Linux + Nvidia's Linux driver?
How is the stereo quality compared to Zalman's 3D-LCDs or the old
Is this a cause for concern? FOM's are over 0.5 and Phasing Power is over 2.0.
Thanks
FR
-
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5
I'll update the CCP4 version of the dictionary
(ccp4/lib/data/cif_mm.dic). Thanks for the heads-up.
As you say, the workaround meanwhile is to edit the .cif file to
remove/change any offending lines.
Martyn
On Wed, 2010-03-03 at 11:24 +, Thomas Womack wrote:
> I notice that a fair number of
-
REMINDER: BEAMTIME ON THE ESRF Bio-SAXS BEAMLINE ID14-3
The Bio-SAXS beamline at ID14-3 at the ESRF (
http://www.esrf.fr/UsersAndScience/Experiments/MX/About_our_beamlines/ID14-3
) has now been in operation for over a year.
Robotic sample loading
I notice that a fair number of PDB-deposited sets of structure factors in
sf.cif format (fourteen of them in the March 2 2010 release) contain an
_diffrn.detail line; this comes to my attention because ccp4-6.1.2's cif2mtz
falls over when it encounters such a line and I have to edit the CIF manu
Hi,
You don't say whether you've considered the possibility that the true symmetry
is higher than P61, e.g. P6122. If there's higher symmetry consistent with
your data, then either pointless or xtriage will tell you which space groups to
consider for test refinements. Another good test (if yo
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