Dear Rain,
Insertion codes are still a sore point for many CCP4 programs and one of the
reasons I prefer Buster over Refmac. Refmac5 does not remove insertion codes so
I suspect the problem was with autoMR. The easiest is to superimpose your
search model with insertion codes onto the pdb file
I think pdbset from CCP4 can renumber a PDB and hence get rid of the
uggly insertion codes.
On 06/26/2013 03:33 PM, herman.schreu...@sanofi.com wrote:
Dear Rain,
Insertion codes are still a sore point for many CCP4 programs and one of
the reasons I prefer Buster over Refmac. Refmac5 does not
Dear Francois,
I also prefer not to use insertion codes. However, for certain protein families
(serine proteases, antibodies), vast amounts of literature exist using amino
acid numbering schemes with insertion codes. By creating a new numbering scheme
without insertion codes, one would create
Dear Jiang Yan,
The Matthews function is based on an average protein crystal with 50% solvent.
However, crystals do exist with as little as 25% solvent or as much as 75%
solvent, so if your structure refines to an Rfree of 20%, your structure is
solved and you have a crystal with a high
The Matthews function is based on an average protein crystal with 50%
solvent.
Not sure what that a 'Matthews function' exactly would be - and that an
assumption of 50 solvent
content is made anywhere in the Vm calculation is new to me. The only
defensible
prior that goes into the
Hi Dwayne,
Please send me a copy of your stack traces.
I have just release PiMS4.4. I would like to review the errors that have
affected you before building a release of xtalPiMS.
Regards,
Chris Morris
From: McCully, Dwayne (NIH/NIAMS) [C]
dmccu...@mail.nih.govmailto:dmccu...@mail.nih.gov
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Dear Jiang Yan,
how many reflections to you have in the free-set. At P6422 with a
resolution of 2.8 you may have only a few hundred and thus not get a
reliable Rfree value. Its low value may be due to overfitting.
What does the cyrstal packing look
Hi
I've just installed a Plain vanilla copy of Ubuntu 13.0.4 (aka
rastafarian reefer or somesuch) with iMosflm 1.0.7 and CCP4 6.3.0
and found that Roger's suggestions were all that was needed (but I
did log out and in again to use them) -
sudo apt-get install ttf-mscorefonts-installer #
you may have only a few hundred and thus not get a reliable Rfree value.
The estimate for the error in R free as a function of the number of
reflections is as follows:
Brunger initially estimated^35 that the uncertainty in R-free is
proportional to
(Nref )^-1/2, which is reasonable to assume
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Sure, but in P6422 with 2.8A I'd say that 5% of reflections are more
likely near 40-50 than 'a few hundreds' if the cell too small. And
most people simply flag 5% of their reflections without checking how
many these really are. Splitting these up into
Hi Kay, hi all,
sorry to bother again, but I was wondering if people is experiencing the same
problem I am.
With the nice new XDS graphical interface, I cannot manage to have the show
frame with predicted spots script to work.
It looks like all the steps are performed correctly, but then
Hi Sebastiano,
sorry, I don't see immediately what's wrong. The console seems to show the XDS
output of an INTEGRATE job that only looked at a single (judging from the small
number of reflections ...) frame (number 10, I'd guess; you could check this if
you scroll up a bit). Could you please
Hi Sebastiano,
Yes, you have to put the xds-viewer executable in your PATH. In the Mac
and assuming /usr/local/bin is in your PATH:
cd /usr/local/bin
ln -s
/Applications/Sci/Struct/XDS-Viewer.app/Contents/MacOS/xds-viewer-bin .
Cheers,
Miguel Ortiz Lombardía
Architecture et Fonction des
Hmm,
My XDS-Viewer.app installation is not in a standard place, more likely
you need:
cd /usr/local/bin
ln -s /Applications/XDS-Viewer.app/Contents/MacOS/xds-viewer-bin .
Cheers,
Miguel Ortiz Lombardía
Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille
Hi Bernhard,
The formula from Tickly applies to the weighted/generalized/Hamilton free
R-factor. From k-fold cross validation tests we observed that the 'regular'
R-free has a standard deviation of R-free*(Nref )^-1/2
Cheers,
Robbie
-Original Message-
From: CCP4 bulletin board
Hello Everyone
I have two data sets, from the same crystal form (space group P32) of the same
protein, collected at 100 K at SSRL, about 2.2 A resolution, that refining to R
= 0.14, Rf = 0.26 (refmac/TLS). This is a molecular replacement solution, from
a model with about 40% homology (after
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Dear Sue,
if you made your rmsd (bonds) 20-30 times smaller I would agree they
were not too loose. 0.14A is pretty high. So two suggestions:
a) check the molprobity report of your PDB if its geometry is sane
b) check the CC plot of one data set
HI Sue,
Can you give rmsZ for the bond and angles (from the Refmac output)? I never
could figure these rmsd values out...
I'm guessing that the restraint are too loose, or at least not optimal.
Perhaps, they went overboard with the TLS as well (sometimes fewer TLS goups
give much better R and
Yep, sorry that is the link I actually made, I wrote it too hastily, my bad.
Miguel Ortiz Lombardía
Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax:
Hi All,
I have done a few searches of the archive and googled a few times but not found
what I am looking for.
Could someone point me in the direction of a supplier of the X-ray sensitive
paper I have used in the past to confirm beam position on a home source. I am
specifically after this
Hi Joe -
This is what I've used in the past. It's film, not paper, but needs no
developer and is instant-readout. I think the find a distributor link
should help you obtain it.
http://www.ashland.com/products/gafchromic-radiology-films
- Matt
On 6/26/13 3:51 PM, Patel, Joe wrote:
Hi
We are trying to get SAD phases using a Ta6Br12 cluster using phaser.
Sites were found with ShelxD and we have set the ha.pdb in the form:
ATOM 1 TX HAT 1 24.569 195.940 54.912 1.00 20.00
TX
and we define the scatterer in phaser.inp with:
SCATTERING TYPE TX FP = -25.31 FDP =
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