You can do it without having to do an assay at high temperature, because the
substrate stability would also change at higher temperature. What you could
do is the following:
1. Use a PCR machine to heat the enzyme, and then cool it down.
2. Keep one fraction at 4C / RT separately.
3. Do the
Hi Peter,
Both BeF3(-) and AlF4(-) need to be made fresh, or used from frozen. It
should not be stored at room temperature. While using, you may wish to keep
it on ice. If you are using Vanadate, that should be fresh (Methods in
Enzymology).
Also kindly note that unlike AlF4(-), which is a
Hi Sandeep, if someone sends one, kindly share the references.
In general, Ca2+ could have more Asp, Asn kind of coordination and distorted
pentagonal bipyramidal geometry with waters (about 2.5A), Cd can also have
S- since it is softer, I guess Co might have N/O/S (i.e all three with
paired
Dear BBusers,
Could you point me to a few classic reviews on enzyme engineering? In
particular:
a) pH, thermal pressure stability
b) de novo design
c) increasing low temperature activity
Regards,
Partha
What if the negative results contradict some recent papers in big journals?
Would the PI risk his / her contacts connections? Of course for the PhD
student or postdoc, it matters a lot to get it 'published'..
On Mon, Jul 11, 2011 at 4:27 PM, Bosch, Juergen jubo...@jhsph.edu wrote:
Hello,
From experimental crystallography kinetics background, I have
arrived at a situation where I need to model certain membrane related
phenomena and correlate it to experimental (metabolonomic) data. In
particular, I am looking for mathematical expressions and derivations
for:
a) Change of
Dear all,
Apologies for a off topic question. I could not think of a better
place to ask this.
Suppose, we have four enzymes turning over five molecules, either in
the living cell, or in fresh mammalian cell lyset. The molecules could
be as simple as ATP, GTP, NADP, GSH etc. Now, one can add a
Hi Jason,
Instead of doing rigid body refinement of each residue, you may
consider rigid.inp of CNS or an equivalent strategy in Phenix which
will do SA, rigid body and B factor refinement, followed by either
composite omit (CNS) or 'prime switch' of phenix (rather resolve) to
fix the side
Dear BBusers,
I initially did not want to post this in the BB. With all due respect,
could we use the word open source for those programs where the
latest build or source code are available to the community?
Regards, Partha
Hi Shankar,
Another fascinating example might be Dscam (Down Syndrome cell adhesion
molecule) with multiple Ig like domains and Fibronectin type III domains.
Different splice isoforms are expressed in different nerves, and it serves
as a recognition module, same repels, different ones attract.
Hi Jonathan,
This is purely a chemistry guess, but if you have a PEG400 derived compound
like:
(HO)-CH2-CH2-O-CH2-CHO,
i.e, part oxidised, then the CHO might form a N,O acetal ring with the free
amine and side chain. Five membered ring formation is kinetically
favourable, though the chemistry
Hi,
Sorry to sound stupid, could someone explain what does refmac do if one
chooses mixed (bref MIXED) or overall (bref OVER) B factor refinement in
the context of TLS refinement?
Is it something like: Isotropic for the main chain and/or waters and
anisotropic for the side chain?
Regards,
For Linux, there is also a program called Bibus, which works with either
MS office or open office.. it is like endnote, just a little less..
It is in the Fedora repo, possibly also Ubuntu..
On Mon, May 4, 2009 at 10:48 PM, Donnie Berkholz dberkh...@gentoo.orgwrote:
On 14:02 Mon 04 May ,
Cygwin has problems with Vista.. you need to run it as administrator.. works
fine with XP though. Moreover, Cygwin is not very well supported anymore, as
the developer works for Red Hat now. If it is just the X, there are other
free programs.. XMing is quite good.
You can indeed install Ubuntu
Hi,
I am running a 64 bit Fedora 10 machine and having problems with coot, if i
say
ldd coot-real
linux-gate.so.1 = (0x5000)
libguilegtk-2.0.so.0 = not found
libgthread-2.0.so.0 = /lib/libgthread-2.0.so.0 (0x00df8000)
librt.so.1 = /lib/librt.so.1 (0x005f)
libguile.so.17
Just to add couple of things to what Artem said..
If it is something similar to a mammalian kinase or malaria protein for
example,
1. Recodonizaton can change expression from near zero to substantial
amounts, however,
a) ideally, it needs to be recodonized separately for each target expression
Hi,
Sorry for the off topic question. It seems that for some of the new
laptops that have more than 2 GB RAM and Nvidia 9 series, graphics is
a serious problem. I have tried recompiling the graphics driver with
kernel headers etc., no success. Was wondering if someone knows a fix,
such as
Chris,
Try this:
sudo apt-get install envyng
sudo apt-get install envyng-gtk
fire the envyng-gtk interface from the command line or menu and see if
it finds a solution..
HTH, Partha
On Wed, Jan 7, 2009 at 10:49 AM, Chris Ulens
chris.ul...@med.kuleuven.be wrote:
Hi,
I'm trying to install a
Hi Charu,
Indonesia is one option, system independent but you need Java for that.
http://xray.bmc.uu.se/dennis/
Cheers, Partha
On Mon, Nov 10, 2008 at 6:53 PM, Charu Chaudhry [EMAIL PROTECTED] wrote:
Hello,
Does anyone know of a program that can automatically generate a folding
pattern
Since we learn a lot from this BB, here is a new view.. ;)
-- Forwarded message --
From: Rajan Pillai [EMAIL PROTECTED]
Date: Mon, Sep 8, 2008 at 6:46 PM
Subject: Re: [ccp4bb] Ratio of Number of Reflections to Number of
restrained Parameters
To: Partha Chakrabarti [EMAIL
Hi
Sorry for a mixed up question about two great software.
Has anybody tried to use Resolve after sharp / autosharp? i.e.,
escaping the Solomon step other than handedness determination and
doing the density modification ( maybe NCS / building) directly with
the sharp output? If so, I would
Hi
While building from scratch in Coot (3A resolution), if I can supply
NCS operators in CCP4 format, is it possible to display NCS related
molecules in the same way as crystallographic symmetry related ones?
External scheme script is fine if that is the way..
(I worked out the operators using
what happens if you type:
env | grep SYMINFO
Does it show the path? Either Solve or CCP4?
On Tue, Jul 8, 2008 at 10:15 AM, Petr Kolenko [EMAIL PROTECTED] wrote:
Unfortunately, it also failed:
Failed to find spacegroup in SYMINFO!
MTZTONA4: Fatal error in ccp4spg_register_by_symops
Does
One question is, why do you want to fix that and from what literature
are you expecting the values?
BeF3- is often a ground state analogue for GTP binding proteins for
example.. and the depending on the coordination state, the bond angle
and length might change a bit I would have thought.. for
Hi,
Is it possible to cut out a spherical map around a heavy atom site
directly without having to make bones or building something? I want to
place that in a larger P1 cell and use that for phased molecular
replacement (Phaser / Molrep).. can someone point me how to do that?
Regards, Partha
Or, make sure that you don't post it on Monday, some people, sometimes
are in very bad mood on Mondays, I am not going to explain why.. :P
On Mon, May 12, 2008 at 5:57 PM, Yong, Wei [EMAIL PROTECTED] wrote:
Sorry that I missed a letter. I wanted to extract mRNA from pig liver. Thank
you,
I had similar problem with Mosflm due to odd combination of Suse and
AMD-64. Copied those files from a different installation, everything
runs just fine.. would agree with James.. lol..
On Mon, May 5, 2008 at 8:32 PM, Chris Waddling [EMAIL PROTECTED] wrote:
Basically, the newest version of
Hi,
Apologies for the off topic question. I am curious if the CNS/Explore
language is a derivative of Lisp. In that case, how does it invoke
C/Fortran routines? There seems to be something called Lush which
does it inline and supports GPL/maths libraries..
Cheers, Partha
Hi,
Just a newbie question:
Could someone explain what might have gone wrong in this case? I guess
the structure factors should not change anyway! I am a bit confused
because I have used solve resolve several times for experimental
phasing, never had such a problem, on the other hand, have not
Hi Melody,
There was a nice discussion in this year's ccp4 study weekend. In
general, one needs to consider several factors.. If you were at 3A, or
low symmetry, you would of course try to get the maximum out of it, on
the other hand, there are requirements for experimental phasing.. in
general,
[EMAIL PROTECTED] wrote:
well, redundancy for the highest shell is 4.8, I/sigma is 3, Rmerge for
overall is 0.08 for highest shell is 0.336. I/sigma and Rmerge don't seem
quite nice...
thanks.
On Mon, Mar 17, 2008 at 11:51 AM, Partha Chakrabarti [EMAIL PROTECTED]
wrote:
Hi Melody
One point which I don't understand is how can someone compare the two
different programs when they don't use the same numbers for
xray:geometry terms? Taking the default settings for a given
resolution might not be enough.. !
On Tue, Mar 4, 2008 at 7:58 PM, Savvas Savvides
[EMAIL PROTECTED]
Hi Andrea,
We have seen examples where it can make a dramatic difference, no
expression even with codon plus strains, but really good expression
with the daughter constructs as already pointed out. It is
particularly true for parasite proteins where the percentage of AT is
higher than bacteria.
Hiya,
I used shelex C/D/E on a SAD data, and wanted to refile the positions in
MLPHARE before going for AddSOLVE. Confused with the output of two shelex
files.
shelx1.pdb file says
CRYST1 50.050 65.520 105.180 90.00 90.00 90.00
SCALE1 0.019980 0.00 0.000.0
Hi,
The assumption is hard to understand. We are thankful to the community who
are developing the great programs (and teaching), and with limited
experience, I think it is good to have choices. So, thanks also to people
who provide such scripts.
If we have to convert file formats, then whats
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