To recap it turns out that the element symbol does supersede the atom and
residue name which seems to provide a sneaky workaround to the unrecognized
ligand issue in PISA.
However this information does come with the disclaimer that it does not
replace electrostatic calculations such as CHARMM or A
Hi Rashmi,
The concentration of your stock solution will depend on how you plan to mix
your screen conditions. It's not really that important as long as: 1.)
Glutathione stays soluble, and 2.) You can make your condition with the desired
glutathione concentration. If your glutathione is reduced
Hi all,
I have a ligand-corresponding density which I cannot identify:
http://s1194.photobucket.com/albums/aa376/dziuba22/?action=view¤t=coot1.png
Here is the story. I collected a couple of datasets, three of them belong
to methylated protein and one to non-methylated. The protein is putative
ch
Jacob,
Roger is correct, this concept does refer to the Pearson HSAB theory. To
summarize: This theory is applicable outside of inorganic chemistry as well,
but it is extremely useful for explaining coordination chemistry of
metal-ligand complexes. The theory states that "hard" acids interact w
can mosflm handle a dataset defined by images with correct but unequal
oscillation angles in the image headers?
-Bryan
If I recall correctly this refers to the Pearson (?) hard/soft acid base
theory. It's been a long time since inorganic chemistry.
Cheers, Roger Rowlett
On Feb 24, 2011 1:39 PM, "Jacob Keller"
wrote:
> I have heard "hard" and "soft" many times now about O's and N's--to
> what property of those lig
Based on Peter's suggestion: yes: the SUMO protease does an efficient job
for removal of the tag.
Lucigen (www.lucigen.com) does sell new generation of cloning vectors (IPTG
and Rhamnose inducible) with SUMO tag as well as SUMO protease included in
their kit. The novel Expressioneering Technology
I have heard "hard" and "soft" many times now about O's and N's--to
what property of those ligands does this metaphor refer?
JPK
On Thu, Feb 24, 2011 at 12:47 PM, Jeffrey D Brodin wrote:
> Alex,
>
> I modeled in the bis-tris with the tertiary amine and and his imidazole
> coordinating axially an
Amgen has an opening in Protein Biochemistry. Experience in the purification
of ion channels and/or G-protein coupled receptors for crystallography would be
a plus.
Please apply via the Amgen website with 8235BR code.
https://sjobs.brassring.com/1033/asp/tg/cim_jobdetail.asp?jobId=771243&Partner
Alex,
I modeled in the bis-tris with the tertiary amine and and his
imidazole coordinating axially and the four oxygens coordinating in
the equatorial plane. However, it's hard for me to tell from your
images if there are two His coordinating? Either way, that crescent
shape could easily
Dear Alex,
Sorry yes I was focussing on the crescent density, since I imagined
the metal atom assignment was secure. SInce Zn and Fe are now
mentioned you would need to consider a tuned Xray wavelength anomalous
experiment to be sure it is nickel, although the circumstatial
evidence looks promising
I haven't used it personally, but I've heard some people engineering a his SUMO
tag on to the protein and then use SUMO protease to cleave it off. The protease
apparently makes very clean cuts and no extra residues are left.
Best of luck,
Peter
Hi,
Slightly deviating from the original thread perhaps: I am having
trouble with recent releases of Ubuntu on my Toshiba Satellite laptop,
mainly associated with ACPI. The internet is awash with discussions on
how to fix the problems with ACPI (fan speed, screen brightness etc).
None of the solu
Hi -- thank you for all your help. The majority opinion seems to be a
metal for the sphere (Ni from the Ni-affinity column, which (Joe
Patel, correct) was used during purification, but Zn and Fe were also
mentioned), and either water molecules, bis-tris or some other small
molecule forming
Hi Maher,
(...) how to calculate the map correlation coefficient using Overlapamp *or
> any other program*?
>
in addition to suggested options:
- This will give you map CC calculated per residue or per atom (depending on
resolution of the data):
phenix.model_vs_data model.pdb data.hkl --compreh
Hello Dave,
> 1. For my stereo preferences, i used to be an active stereo nut - but I
> have switched over to passive - and will never go back. It's cheaper to
> maintain (even with expensive monitors), easier to load operating
> systems (you don't need nvidia drivers - you don't even need a
An additional information would be to calculate an anomalous difference
map: at typical synchrotron wavelenght of ~1 A, Ni would have ~2
electrons f'', whereas Cl would have only ~0.2 electrons f''. So, a
strong anomalous difference density peak would be more consistent with
Ni than with Cl.
Ho
I'm voting with Roger this time.
If I were you I would model a nickel in there (unless you have a better
candidate)
if it is right, the distances to the His should be like seen in a SOD active
site.
Then you can model the bonds and waters. You may need partial occupancy on
the metal.
Reminds me o
This looks suspiciously like a metal ion with 3
or more resolved water ligands. It's hard to tell from the
images provided, but it looks like the metal could be close to
octahedral, with 2 His and 3 water ligands well-defined. The
estimated metal-nitrogen bond distance
Hi,
Slightly deviating from the original thread perhaps: I am having
trouble with recent releases of Ubuntu on my Toshiba Satellite laptop,
mainly associated with ACPI. The internet is awash with discussions on
how to fix the problems with ACPI (fan speed, screen brightness etc).
None of the solut
Dear Alex
I take it this density effect is in each of the four molecules?
I wonder if the crescent is a series termination effect, although relatively
rare in our field. If so what might have caused it? Do you have (radial) gaps
in your data set eg due to heavy ice rings?
Best wishes,
John
Prof
Dear David,
I did not read all answer already there, but if you add the line
blacklist nouveau
to a file like /etc/modprobe.d/blacklist.conf
the nouveau kernel module should not get loaded upon booting the machine and
installing the nvidia drivers then work straight away.
I'd say with some basic
cphasematch will do it in reciprocal space and give you a variety of
statistics, including F- and E-map correlation.
Go to reflection data utilities/phase comparison.
Maher Alayyoubi wrote:
Hi Everybody, I am a new user on the ccp4 bulletin, I have a question on
how to calculate the map correl
Hi Alex,
Was it purified via a Ni2+ resin? Is the protein oligomeric in
solution? Could it have stripped an ion out during purification and
brought it all the way through to crystallisation?
Have you tried refining a Ni2+ in the location?
JP
--
Hi Phil,
Depending on the characteristics of the c-terminal region of interest, you
might try a carboxypeptidase. These enzymes cleave residues from the c-terminus
and stop at various motifs, depending on the specific enzyme. There are several
available commercially, each having a slightly diff
Hi Everybody, I am a new user on the ccp4 bulletin, I have a question on how
to calculate the map correlation coefficient using Overlapamp or any other
program?
Thank You,
Maher
Hi all,
Thank you all very much for your insightful help on this matter. Just a
quick summary of what I have learned about this:
1. For my stereo preferences, i used to be an active stereo nut - but I
have switched over to passive - and will never go back. It's cheaper to
maintain (even w
Hi All,
I've got data that go to only about 3.2 A and they're anisotropic, i.e. better
along c but worse along a and b. Heard that density sharpening may give
improvements.
I searched the BB for relevant info. It seems that Truncate has been modified
years ago to allow sharpening. Is it done
Another vote for Ubuntu.
I have to say that a Live CD version is not a good test of this excellent Linux
distro. We have 3 identical PCs. On two of these the latest version of 10.10
64bit live cd loads to a blank (completely black) screen. Google: "blank screen
ubuntu live cd" - thankfully ther
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