Dear colleagues,
Thank you for your suggestions. I was able to do the refinement of the
sulfates and tartaric acid in phenix by changing the occupancies to 0.33 and
0.5,
It appears to me (from the log file and from graphics afterwards) that the
program automatically turns off the interaction wit
Dear all,
Recently I deposited a structure to PDB. However, I was told
>> The R value of SF check are different from your reported value.
>>
>> R work in SF check = 0.2859
>> your reported R work = 0.1474
>> Also there are no R free flags in your sending files, but you reported R
>> fre
Dear ALL;
Firstly I'd like to thank folks for the various suggestions to handle the
degradation of MBP fusion protein.
According to these suggestions, I have tried shortening the linker between
MBP and target protein.
We can get decent yield of the full-length protein now.
We
Dear All;
We just got some crystals from 35% (v/v) Dioxane. We are going to collect
some data soon.
Does anyone have the experience with the cryoprotectant in this condition?
Thanks a lot,
Jerry McCully
Hi,
I have helices that I did rigid body refinement with Phaser (after phased
rotation and phased translation in Molrep). I compare FOM output by Phaser to
the FOM computed by sigmaA using the Phaser refined coordinates and found that
FOM from Phaser is only about half (~0.25) of FOM from Sigma
SSBOND actually predicts pairs of residues that, if mutated to
cysteine, can form a stable disulfide but does so on first principles,
not with a database of preferred conformations. (The server is at
http://129.128.24.248/forms/ssbond.html)
In this case the 2.7 Angstrom S-S distance is clearly
Bart Hazes wrote a program (and published as well, Hazes & Dijkstra perhaps)
called SSBOND I think. I cannot remember exactly what the computer program
does, but it certainly has a data base of "possible" disulphide bond
conformers. Hence I would myself certainly check your second didulphide to
Hi All,
I have engineered intra-molecular disulfide bond in my protein
monomer. The protein functions as a homodimer.
In crystal structure, there is clean electron density for the S-S
bond in one monomer (bond length 2.2A), but there seems to be
slightly messy density for the same in th
I know I'm late to the game, but for anyone who needs a supported version of
libg2c.so for running old code then you need to install gcc-3.4. From the
following site go to the jaunty link. You then need to install the
gcc-3.4-base and the lib32g2c0 runtime library.
https://launchpad.net/ubuntu/+so
On the scalepack download site there are multiple versions of the
latest version.
drwxrwxr-x 20 root presiden 4096 Jun 2 12:27 archive
drwxr-xr-x 4 iwonapresiden 4096 Jul 17 2008 ver_098.698s
drwxr-xr-x 2 iwonapresiden 4096 Apr 3 2009 ver_098.699SM
drwxr-xr-x 3 iwonap
We are still waiting for proofs, so it might be a few weeks before its
published. If anyone is interested, please email me requesting a preview
version.
Paula
PS: Francois, we did cite and used your work as starting point.
On 20 October 2010 10:39, francois@cbs.cnrs.fr wrote:
> Hi Paula
>
On Wed, Oct 20, 2010 at 10:13:09AM +, Leiman Petr wrote:
> Dear Ed,
>
> This libg2c:
> http://dl.dropbox.com/u/3579334/libg2c.tgz
> works with older scalepack versions requiring it. It is a 32 bit library and
> should run on 64 bit and 32 bit systems.
>
> I have not tried the 699m version of
Dear Ed,
This libg2c:
http://dl.dropbox.com/u/3579334/libg2c.tgz
works with older scalepack versions requiring it. It is a 32 bit library and
should run on 64 bit and 32 bit systems.
I have not tried the 699m version of HKL2000, but 699a and 699k2 segfault on my
standard 64 bit Ubuntu (10.04.1)
Dear Edward,
the latest version of HKL2000 does not require libg2c.so anymore:
t...@shelx8:/usr/local/bin$ ldd scalepack
linux-gate.so.1 => (0xf7744000)
libm.so.6 => /lib32/libm.so.6 (0xf7702000)
libcrypt.so.1 => /lib32/libcrypt.so.1 (0xf76d)
libc.so.6 => /lib3
On 10/19/2010 12:39 AM, Jyotica Batra wrote:
Hi All
I have a dataset at 1.9A, spacegroup-P212121 (unit cell: 37.7, 39.52, 231.72,
90, 90, 90),
I used MR phaser and got a structure solution with LLG= 320 (1copy/a.u) .
During refinement, the R-free (50%) and R-factors (42%) never go down.
I hav
Dear Sudhir,
You don not need to deposit these logfiles themselves, and only need to fill in
the fields in the web-mask of the PDB-desposition procedure with the appropriate
statistics you should find in these files.
Tim
On Wed, Oct 20, 2010 at 10:09:07AM +0530, Sudhir Kumar wrote:
> dear all,
>
Hi,
For questions relating to a specific package (if it is in rpm format, I
don't know what the Uuntu installation software uses as packages), you
can use the rpm search web site http://rpm.pbone.net/ (in addition to
http://www.rpmfind.net/ , can't search in rpmfind.net at the moment, it
says
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