I very much agree - refinement will tell you if the high-res data make
sense. Another very good test is the Wilson plot - it should look
straight and reasonable. Inflated I/sigI values will not escape a
strange appearance such as the WIlson plot flattening out at higher
resolution. I
On Thu, 22 Apr 2010 10:13:40 -0700, tirumal ch_tiru...@yahoo.com wrote:
If you have a poor density (which I guess, generally is the case for large
glycoprotein structures) you have to depend on trial and error strategy to
get the right NAG conformation. I don't know how other refinement
I'd worry a bit. If the data are strong and the R factor is that bad you may
have got your space group wrong (pseudo, not crystallographic 4 fold?)
Pete Artymiuk
On 22 Apr 2010, at 18:22, Frank von Delft wrote:
Yeah, stop worrying! Your I/sdI is all that matters.
phx
On 22/04/2010
Dear Rashmi,
The original standard for microbatch crystallisation is paraffin oil (from
Sigma or elsewhere). Drops set under paraffin oil lose almost no water, so it
works like a well-sealed batch experiment, in other words you need to have your
conditions right and you do get crystals.
An aspect that is sometimes overlooked is that the need to avoid mini
freeze-thaw cycles does not only call for a quick, snap-freeze process for
samples (in thin-walled PCR tube and not too large volume; 50-100 ul I'd
recommend), but - in turn - also for quick thawing: I prefer holding the PCR
Sounds like good advice - I suppose that since pure water un-freezes last, you
could have protein concentration inhomogeneities? So in areas where the protein
concentration is raised it could start to feel like crashing out.
All the best
Martyn
Martyn Symmons
Cambridge
- Original
Hello,
we are using the latex phenix version (1.6.1) on PCs with Debain Stable or
Testing. After starting a refinement job, the following error message shows up:
snip 8 --
A Python error was detected. This is probably a bug; click OK to send a bug
report to the PHENIX
On Fri, Apr 23, 2010 at 01:12:36PM +0200, Tim Gruene wrote:
Hello,
we are using the latex phenix version (1.6.1) on PCs with Debain Stable or
Sorry, I meant 'latest' version, in case this causes confusion...
Testing. After starting a refinement job, the following error message shows
up:
An alternative could be to disolve your cholesterol in methanol or maybe in
50% methanol, then add it directly to the drop. Does your protein tolerate
10-20% methanol? Then you can add the methanol-cholesterol solution you
your hanging drops directly and mix fast. The methanol is volatile and will
Dear all,
I just got a MacBookPro.
I have two questions:
How to get the keyboard shortcuts in coot or pymol up, e.g. altF to
open the file dialog.
and
whenever I connect a zalman 220 (stereo ready) monitor to the mac using
a miniDisplayPort to DVI
adapter, the monitor is not recognized and so
Hello,
I am trying to use Buccaneer to improve the model of a protein/DNA complex
which I solved recently. However, my initial attempt failed because the
program deleted the DNA chains and rebuilt protein chains in their density.
Is there a way to specify that the expected outcome should contain
Yes, this can be done, but you need buccaneer 1.4, which I haven't
released yet. We've seen significant benefits to preserving the heavy
atoms through to the refinement, although the code has been written so
that it can preserve DNA or any other know structure features as well.
I'll try and
I'm using a MacbookPro with a Zalman monitor with a DVI to DVI connector (an
older MBP with a DVI port), and it works fine with no problems - not much help
to you though
and altF works for me
Phil
On 23 Apr 2010, at 14:37, Joachim Reichelt wrote:
Dear all,
I just got a MacBookPro.
I
On Fri, Apr 23, 2010 at 4:12 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
we are using the latex phenix version (1.6.1) on PCs with Debain Stable or
Testing. After starting a refinement job, the following error message shows
up:
Tim: please report these errors to either
Biobar version 2.0.1 is now available.
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EMBL-EBI's Protein Data Bank in Europe (PDBe; pdbe.org).
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Very much appreciable.
thanks
S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany.
On Fri, Apr 23, 2010 at 4:50 PM, Jawahar Swaminathan jawa...@ebi.ac.ukwrote:
Biobar version 2.0.1 is now available.
Biobar is a powerful browsing and searching
On Fri, Apr 23, 2010 at 07:20:15AM -0700, Nathaniel Echols wrote:
On Fri, Apr 23, 2010 at 4:12 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
we are using the latex phenix version (1.6.1) on PCs with Debain Stable or
Testing. After starting a refinement job, the following error message
On 4/23/10 8:14 AM, Tim Gruene wrote:
On Fri, Apr 23, 2010 at 07:20:15AM -0700, Nathaniel Echols wrote:
On Fri, Apr 23, 2010 at 4:12 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
we are using the latex phenix version (1.6.1) on PCs with Debain Stable or
Testing. After starting a
Yeah, send your Zalman vendor a nice email and let them exchange your DVI
adapter. Had that problem too - alternatively you can scavenge one DVI adapter
from another computer and test it. I wouldn't be surprised if it works, that's
how I figured it out.
Jürgen
On Apr 23, 2010, at 9:37 AM,
On Fri, Apr 23, 2010 at 08:23:30AM -0700, Pavel Afonine wrote:
On 4/23/10 8:14 AM, Tim Gruene wrote:
On Fri, Apr 23, 2010 at 07:20:15AM -0700, Nathaniel Echols wrote:
On Fri, Apr 23, 2010 at 4:12 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de
wrote:
we are using the latex phenix
Hi Everyone,
I have a question about the crystallization condition. Currently the
condition I use contains 0.2M lithium sulfate. However, the ligand
there seems to compete the site where sulfate binds in the active
site. Are there any good substitute to replace the Lithium sulfate in
my
Hi all,
I will greatly appreciate your help for the following:
I am getting an error of not having TER card at the end of chain
during precheck of PDB deposition. Hence, I would like to add TER card
at the end of chain in my PDB file. Adding TER card manually is not
problem but how to add Atom
I would test several hypotheses. You have a multitude of salts to choose
from. Test them all.
Let me ask you this: What anions can you test? What's already on your
shelf of chemicals? What did you test already?
Jim
_
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On
You can do it with any text editor. From
$CCP4/html/pdbformat.html#part1ter:
Cols. 1-3Record name TER
7-11Serial number
18-20 Residue name
21-27 Sequence identifier
So you copy the serial number, residue name and sequence identifier from the
very line which
You may be using output reflection data from the previous cycle of
refinement for the next session. After twin refinement output Fobs
(confusingly) may be detwinned. You can try to use original reflection
data file (e.g. after scala/truncate/freerflag) and for refinement
and it may
And another (not so) minor point: Defferences between R/Rfree with
twin on and off suggest that there is strong correlation between twin
and NCS. For this cases better dealt with if you use twin refinement
with sufficiently strong NCS restraints. In new refmac (www.ysbl.york.ac.uk/refmac/
Hari,
What twin tests have you run? Results? If your data really is
P43212 and you drop to P212121 you will still have the additional
two-fold operator in your data. An operator is a mathematical operator,
which could be crystallographic or twin.
I never refine a structure with twin
In a nutshell
=
Is there a way to make solve/resolve behave reasonably if the data
is twinned? Is there a recommended alternative path to clean up and
maybe even auto-trace a map with 4-fold NCS but twinned data?
Maybe Pirate/Buccaneer?
In detail
=
I'm fighting
I hope Kevin will respond soon. I think he has done (or is planning to
do) to twinning and ncs in his pipeline of model building.
I think something like that may already be in new ARP/wARP (Victor and
Tasos will correct me if I am wrong)
regards
Garib
On 23 Apr 2010, at 23:16, Ethan Merritt
I am getting in habit of writing double emails.
I would say that refmac overestimates at early stages and truncate
underestimates (it is just an intuition, not based on theoretical or
empriical results)
Garib
On 23 Apr 2010, at 23:16, Ethan Merritt wrote:
In a nutshell
=
Hello Garib,
I was using the ouput from a refmac run for the next round and using what I
thought were the original fobs .
So I guess as you said at each round I was using the de-twinned result from
the previous round.
I will repeat these refinements with the original scala output mtz to get a
I think your procedure is good with current technology. At early
stages twin refinement may give misleading results.
An intuitive resoning for low R factor would be: Twin is summation of
intensities. As you sum intensities two things happen: 1) distribution
of intensities become more
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