Hi Mark
I think you need to distinguish between the mechanics of the
refinement software on the one hand and the effect on the statistics
on the other. I think you are referring to the former, in other words
in the software the restraints are as you say treated exactly like the
X-ray observations
Sorry for the confusion. It has been solved. Thanks for your help.
Raja
From: S. Shunmugasundararaj
To: CCP4BB@JISCMAIL.AC.UK
Sent: Fri, 9 April, 2010 1:11:27 PM
Subject: Re: [ccp4bb] fink update
I think your xcode is out dated. You can download the lates
You may also want to look at some other structures at similar resolution and
see what the density and interactions for their sulfates look like. E.g., if
you go to HIC-Up, get to the SO4 page and then click on the link to EDS
statistics - http://xray.bmc.uu.se/hicup/SO4/so4_eds_stats.html - it w
Well, I have mac osx 10.5.8 and the latest Xcode available is X11- 2.5.0. To
get the Xcode 3.2.2, do I have to go with OSX 10.6.X? I am wondering if that
might cause problem to run programs already installed in 10.5.X.
Raja
From: S. Shunmugasundararaj
Hi All,
in a paper (which I can't locate now...) which I read recently it was stated
that restraints do not reduce the number of parameters, rather they augment
the number of data points (so strong restraints are like strong data, weak
restraints weak data...). Only strict NCS constraints, where th
You can download the latest download from
"developer.apple.com/technologies/xcode.htm". The latest version is
Xcode 3.2.2 and iPhone SDK 3.2Apr 3, 2010
SSSRaj
http://www.careforlearning.org
Let us make learning a fun to everyone
**
I think your xcode is out dated. You can download the latest one for free by
login into http://connect.apple.com. Its under the "Developer Tools" heading.
SSSRaj
http://www.careforlearning.org
Let us make learning a fun to everyone
**
Hi Ed
It's very difficult to deal theoretically with NCS because, unlike
bond lengths where the uncertainties are known a priori (at least in
principle), with NCS you don't know the uncertainties a priori, if you
see what I mean (rather like unknown unknowns!). In other words the
optimal weights
We have drawings available for both pucks and tools, freely available
for anybody to use:
http://bcsb.als.lbl.gov/wiki/index.php/Automounter#Technical_drawings_and_CAD_models_for_the_pucks_and_automounter_tools
At the moment, crystal positioning is the only supplier possible (they
will have the A
Hi Raja,I assume you are running OS X?I had this same problem since I was running xcode v3.0. The new compiler (the one its complaining about) should be packaged with the xcode on the snow leopard disc, which I believe is the most recent version. I could be wrong, since I haven't yet fixed my own p
Has anyone looked theoretically at how ncs-restraints affect
the expected Rfree/R ratio?
Tickle et al., Acta Cryst. (1998). D54, 547-557
concluded Rfree/R = sqrt(Nobs/(Nobs-Nparam)) .
He suggested that, with restrained refinement of coordinates
plus individual isotropic B-factors, the effective n
Hi,
Sorry for a non-ccp4 question. I hope there is someone who can solve the
problem. I was trying to update fink and I got the following error.
rajadey$ fink update-all
Password:
Information about packages read in 2 seconds.
fink needs help picking an alternative to satisfy a virtual de
Does anyone know the status of Crystal Positioning? They are not
responding to email or phone calls.
Are they the only alternative to the late Peter Boyd?
Deena
Deena Abells Oren, PhD
Manager, Structural Biology Resource Center
Rockefeller University
1230 York Avenue, Box 295
New York, NY 10
Hi Alessandra,
Here is a list of nucleic acid and protein-nucleic acid related tools
(including the ones mentioned by Luca and Maia:
3DNA
http://rutchem.rutgers.edu/~xiangjun/3DNA/
http://w3dna.rutgers.edu/
curves
http://gbio-pbil.ibcp.fr/Curves_plus/Curves+.html
nucplot
http://www.biochem.ucl.a
In the instance where we grew crystals is isopropanol, we found they also
grew in PEG6000. The best crystals grew in isopropanol, so we just
harvested the crystals into a similar PEG6000 solution. I would imagine
that you can get the crystals to grow in something beside isopropanol
especially now
Nat,
A few years ago I had K channel crystals that formed under similar
conditions. I found that using MPD as a cryo-protectant worked best. As
for the evaporation issue, I had a little extra time as I was performing the
mounting in a cold room.
Scott
Pegan S, Arrabit C, Zhou W, Kwiatkowski W,
Yes, oil is great, but you have to be careful to choose an oil in which
the alcohol is not soluble, or the oil will suck it out of your drop,
(just like air). This is particularly annoying with detergents, which
are almost all soluble in oil. I've always thought that maybe some
synthetic moto
I have wondered if placing a layer of oil over the drop would help
solve the problem of the crystals moving around. Haven't tried it,
but don't people harvest from a microbatch tray by dragging the loop
and crystal through oil?
Nat
On Fri, Apr 9, 2010 at 11:21 AM, James Holton wrote:
> Yes, iso
I know two programs;
3DNA by Lu and curves by Lavery and Sklenar. 3DNA is easier to use, it
can also make input for the Curves.
Maia
Alessandra Pesce wrote:
Dear All,
I am looking for available programs and/or websites able to check the
structure of DNA in DNA-protein complexes. I need to
Yes, isopropanol is a cryoprotectant, and a relatively good one. So are
the other alcohols. It was even popular in the "olden days" when we
would typically set up drops that were 5-10 microliters in volume
(each!). These take a while (minutes) to evaporate, giving you enough
working time to
On Thu, 2010-04-08 at 23:26 +0100, Daniel Bonsor wrote:
> both the Rfactor and Rfree get stuck at 30% and 36%
according to
http://xray.bmc.uu.se/gerard/supmat/rfree2000/plotter.html
these are higher than expected. With that said, R/Rfree should not be a
fetish, and your model may be fine (i.e. a
It is also possible that mother liquor prevents binding (although often
in such cases you would see some precipitant component in the active
site.
I would generally bet on need for conformational change. And you expect
to see the product complex, right?
Ed.
On Fri, 2010-04-09 at 11:15 +0200, Pa
Working with isopropanol at room temperature and in a well ventialted
environment is a nightmare. Everything moves around wildly until all the
isopropanol has evaporated. Simply leaving the plate in the cold room for a
couple of hours or overnight, and then doing all the mounting in the cold
room a
Paul,
couple things come to mind:
-make sure your substrate is actually a binder and not an (unspecific)
inhibitor (ITC, Thermofluor, Biacore)
-soak longer and at higher concentration. (3mM concentration from 100mM
stock in DMSO for a week or more)
-Is there evidence that your protein needs to
Dear Chris,
I recall from many years ago that we had a screening hit in high
isopropanol, which started boiling violently when we opened the well. We
"solved" the problem by using another precipitant but I would also be
interested in tricks how to handle high isopropanol.
Best regards,
Herman
Dear Bulletin Board,
I am trying to soak substrate into crystals of an enzyme, but so far I
can't see the substrate in the structure. Does anyone knows a program
to ensure that the entrance to the central cavity is accessibly? I
mean based on the whole crystal. I already checked the crystal packin
Hi Chris,
Isopropanol can act as a cryoprotectant. Can't say whether 25% are enough. It
dependes also if there are other ingredients that can help to get cryo
conditions (e.g. salts, PEGs, glycerol). Maybe you want to check the mother
liquor if there will be any ice ring formation after freezin
Dear all,
I have a protein which crystallizes in 25% isopropanol, at pH4.5.
Does anyone have experience freezing crystals grown in such a condition?
What cryoprotectants should I try?
Can isopropanol itself act as a cryoprotectant?
Any suggestions on how to deal with isopropanol evaporation dur
Ciao Alessandra,
A couple of pointers:
http://gbio-pbil.ibcp.fr/Curves_plus/Curves+.html
http://rutchem.rutgers.edu/~xiangjun/3DNA/
HTH,
Luca
Luca Jovine, Ph.D.
Group Leader & EMBO Young Investigator
Karolinska I
Dear All,
I am looking for available programs and/or websites able to check the
structure of DNA in DNA-protein complexes. I need to evaluate the DNA
bending, its backbone distortion, the alteration of the base pairing, and
its interaction with the protein. The aim is to compare in easy and quick
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