Hi,
>(1) Does the DNA density I saw in the cases where I use models with DNA for
>MR/rigid body fitting only reflect model bias?
If your DNA density is becoming poor as your refine, it is quite likely that
the initial DNA density you are observing after MR is model bias due to
inclusion of
Dear all,
I've been working on a series of DNA-protein complex structures. In my
recently acquired data sets, I got almost no density for DNA if I do
molecular replacement or rigid body fitting with the protein structure,
although I am 100% sure I have DNA in the structure by indepenent means. If
Hi Ray,
I've got a similar concern and contacted SIGMA for advice. I got the following
response:
"We test routinely solubility in water (100 mg/ml). A clear to slightly hazy
light yellow solution is yielded.
This material is 80-90% pure when prepared, but is very unstable. As much as
10% puri
I solved a structure in the presence of SAM, which is the same as SAH but
with a donor methyl group, and saw clear density for SAH, and not SAM, so it
seems that the SAM was either spontaneously de-methylated in solution, or
the protein which bound the SAM spontaneously demethylated it. In any c
Hi all,
I am in the process of obtaining crystals in complex with
s-adenosylhomocysteine but this compound doesn't dissolve in normal
pH. The final concentration needs to be in mM range so the stock
ideally needs to be at least 50mM. I know SAH is quite soluble in DMSO
but is there anyway to get i
Forwarded from bionet.xtallography
--dvd
-- Forwarded message --
Date: Mon, 05 Nov 2007 16:22:11 -0800
From: "[EMAIL PROTECTED]" <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
Newsgroups: bionet.xtallography
Subject: [Protein-crystallography] November 2007 issue of the IUCr Computing
Hi Ian
What system are you running on? I might be able to provide you with
something that works if it's Linux.
And, are you also missing $CBIN/ccp4mapwish?
There is an issue with mapslicer when compiling, if the tclconfig.sh and
tkconfig.sh files are missing (which seems to be the case when
You need to update to CCP4 6.0.2, these items are now recognised.
We try to keep up with the latest cif definitions, but there is a lag.
The documentation for cif2mtz lists the column labels recognised. These are
only labels, so if the worst comes to the worst, you can edit these
in the cif file t
Dear Bjoern,
this is a problem with several newer mmcif files in the PDB. There
are many items in the cif-file which are not in the CCP4 library.
This is a bit annoying when you want to convert large numbers
of mmcifs to mtzs for whatever reason, but I guess the only
solution is to wait until the
Hi,
I also have problems running cif2mtz using ccp4i (5.99) interface with several
mmCIF files downloaded from the pdb (e.g., 2pip, ) on my linux box.
Problems with the _refln.pdbx_F_plus etc cards it seems:
Files without anomalous data work.
--snip from log file:
Line 58:data name "_refl
Hi,
I just installed Leopard, using a clean install (no upgrade), and here
are a few reflections on it so far.
Installation goes very smoothly, clean install on ~40 minutes on my
MacBook 2 Ghz (~30 minutes for an upgrade on an iMac 2.4 GHz).
Fink installation of 0.27.8 via bootstrapping goes
Hi,
I compiled refmac5/ ccp4 libraries with the intel fortran compiler and the
aforementioned problems did not occur anymore.
So it looks like the gcc 4.2.1 that comes with SuSE 10.3 is broken
(again...), which is also what somebody from our group pointed me out to.
Tim
--
Tim Gruene
Insti
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