Dear All,
Thanks so much for all of you who spent time answering my questions. These
are all really great suggestions. I'll follow up with your suggestions and
see how it works out with my case.
Thanks again,
Eric
On 7/31/07, Eric Liu <[EMAIL PROTECTED]> wrote:
>
> Hi All,
> I would like to
Hi Eric,
If your Phaser results show a high Z-score (> 8) AND high LLG AND your solution
packs without clashes AND refines (even though starting R/Rfree is high) AND
reproduces density for the model portion AND produces some Fo-Fc density for
the missing portion, most probably your solution is
Hello,
I have been trying to do restrained refinement on a dataset I integrated and
scaled in HKL2000, then converted to a .mtz file using both scalepack2mtz and
sftools. After molecular replacement in Phaser, the rigid body refinement in
Refmac5 works, but when I later attempt a restrained re
Hi All,
I would like to get some help from here for a data set I recently worked on.
I have been working on a new kinase data set which does not have a close
homolog. The data was collected to 2.1A resolution in space group P212121
however the difference between a and b is only 0.5A. If I index th
Post-doc: EM Model Refinement Methods Development; Portland, OR.
A post-doctoral position is available immediately involving development of
software for the refinement of atomic models against electron microscopy
reconstructions. Research goals include parameterizations, optimization
algorithms,
Dear all,
Thank you so much for your valuable thoughts.
The problem is gone after I used rotation matrix instead of O matrix. Now
DM is running fine. Thanks.
Best regards,
Joe
-- Forwarded message --
From: Stein, ND (Norman) <[EMAIL PROTECTED]>
Date: Jul 31, 2007 8:13
Tommi,
I have found that TEXTAL is very good at tracing maps of less than
stellar quality. It is optimized for low resolution maps, which is
where, in my experience, RESOLVE has difficulty. Is is available as a
stand-alone program or as part of the PHENIX package.
See
Gopal, K., McKee, E., Romo
You could try buccaneer to build an initial model, followed by ARP/wARP
to complete the model. I've see some good results on maps in the
2.5-3.5A range with buccaneer, but model completion is still not so good
(although it gets better with each new release).
http://www.ysbl.york.ac.uk/~cowtan/
Hi,
I completely agree with Tassos: I do like ARP/wARP.
... not being involved with ARP/wARP makes this a objective 'objective
opinion'?
Since you mention that you would like to do this iteratively with
phasing it might also be important in what context you want to do the
automatic building. Sin
...sorry but the "quickfold2 didnt work that well
for me... ;(
resolve does deliver some main chain to get an idea
that i have one domain clearly there but different vs
of resolve e.g 2.06 and newest vs give very different
results... i dont care about side chains right now..
what is a not so goo
On Jul 31, 2007, at 15:24, Tommi Kajander wrote:
Hi,
i would be interested in hearing about people's preferences on
programs
for doign auto-tracing of protein chains (with not so great maps),
I do like ARP/wARP (objective opinion).
so far
my feeling has been nothing is at least much bette
Would you like to submit your structure to our server? We predict metal
binding sites from the coordinates, recognizing that it is difficult to
locate metals (especially low electrons) in low resolution maps. The
server address is:
sunserver.cdfd.org.in:8080/protease/PAR_3D
It is publis
Hi,
i would be interested in hearing about people's preferences on programs
for doign auto-tracing of protein chains (with not so great maps), so far
my feeling has been nothing is at least much better than resolve in doing
this. but i was wondering if people would care to share examples on cases
Hi,
I am currently working on a 3A map and am wondering how to tell a sodium ion
from other ions or water on this map. Any tips?
Thanks,
Brenda
Engineer (fixed term contract for 2 years)
Responsible for setting up and developing a protein production and
crystallisation facility
Environment
The Structural Enzymology and Biochemistry Laboratory (LEBS) is part
of the Gif sur Yvette CNRS campus, 40mn from Paris by local train.
Usin
Hi
Is DNAse essential in your protocol? Maybe it's better to not add DNAse if
you are worried about its presence. If you really need to brake DNA, using
sonication may be enough.
Michel
2007/7/31, Dima Klenchin <[EMAIL PROTECTED]>:
>
> >I have small crystals of protein DNA complex. I am worried
BS"D
Dear All,
The sleeping REFMAC problem I reported a couple of weeks ago, was
tracked down to a problem that many of you suggested: NFS mounted
scratch directory (CCP4_SCR). I also knew about this, and in the
ccp4.setup file, this scratch directory is defined as /tmp/$USER.
Turns
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