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 re
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 w
Hi everyone,
Thanks again for the help. As several people suggested, it seems to have
been a fonts package that was needed. I'm not sure if there is a single
particular package that would have solved the problem, but I installed the
following combination:
t1-xfree86-nonfree
ttf-xfree86-nonfree
Hi everyone,
I now meet some problems when trying to solve structure.Space group is P6422,
and Mathews function shows there are 4 molecules in one asymmetry unit.
However, Phenix-autobuild shows only 2 molecules in on one asymmetry unit,
after refinement, Rfree=20%,(resolution is 2.8A). Althou
Dear group,
I have a insertion code question. I used molecular replacement (CCP4,
autoMR) to solve two structures: one is monomer, and another one is
tetramer. The model I used is one chain of a dimer and the model has
insertion code. After molecular replacement and refinement using refmac5
in
Dear Eugene
plz find the merging statics over this link
https://www.dropbox.com/sh/3155bp0c8axo7tx/0P1RWTTD8z?n=21758536
I have tried different subset of images for indexing, only cell edges are
changing very marginal ( < 1 ) but no change in space group.
Dear Manfred
I have collected my dat
This may no longer apply to the current version, but in older versions
of imosflm and mosflm, I needed to install some xfonts to get the
windows to display text properly. These xfonts are also required for
ccp4i to fit the fonts properly into the windows unless you like
tweaking the install. In
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Hi, Phil,
Sorry for the confusion. I did use MR solution/data combination to run
Refmac and I did reindex the data and re-run MR with the reindexed MTZ file
and run refmac. Both gave the above given high Rwork/Rfree values
(0.35/0.41). If I refine the original MTZ native data file with the PDB
Hi everyone,
Thanks for all your responses. I will try working on the fonts when I get
back to my computer and report back when I find a working solution. I'm
using a fresh installation of Ubuntu 13.04 amd64, so hopefully it will be
relevant to other users of newer Ubuntu releases.
Harry, I cou
that should have been
sort -gk5 XDS_ASCII.HKL | more
(I should have tested before posting!)
best,
Kay
On Tue, 25 Jun 2013 09:16:52 +0100, Kay Diederichs
wrote:
...
>b) inspect the outliers in XDS_ASCII.HKL with something like
>sort -nk5 XDS_ASCII.HKL | more
>looking for observations which h
Dear Boaz,
Dear Boaz,
On 06/25/13 14:09, Boaz Shaanan wrote:
Dear Loes,
Thanks for the message. To the best of my recollection (I actually come from
small molecules crystallography) the problems of small molecule
crystallographers when it comes to studying accurate e.d.'s (e.g. bond
densiti
Hi,
I have seen this before. I would also check the screen resolution (size) used
by the terminal to launch the program matches the largest size capable by your
monitor. You can check and change this with the xrandr command. Type man xrandr
for info.
Cheers,
Reginald McNulty
On Jun 25, 2013,
Dear Loes,
Thanks for the message. To the best of my recollection (I actually come from
small molecules crystallography) the problems of small molecule
crystallographers when it comes to studying accurate e.d.'s (e.g. bond
densities and such) have mostly to do with separating the effect of atom
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Dear Boaz,
Indeed, small molecule crystallographers are routinely converting pixels
into I's and can refine structures to very low R-values, but only to a
limited resolution. The Bragg intensities are very strong, and
background scattering stays almost unnoticed. Once they start studying
accu
Hi
As David suggests, this is certainly a problem with fonts - you're getting a
large variant of Courier; the default font in iMosflm is Helvetica, and it
looks like your X-display isn't finding it for some reason.
You should be able to re-size the window by dragging out the bottom right hand
This might be a problem with fonts. On my laptop the menu items use a sans
serif font and that particular window is just wide enough to fit all the
items. The font also looks more attractive and readable than your
screenshot. I'm guessing (from your desktop background!) that you also use
Ubuntu. Un
Hi Peter,
my estimate of the distance between the peaks would be based on bond distances
and about twice that of Dale, but I agree with his general conclusion. Either a
reflection (roughly in the h 0 0 direction) is stronger than it should be
(ice?), or a very strong reflection was considered a
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