Dear all,
From the definition of CCP4
(http://www.ccp4.ac.uk/html/rotationmatrices.html), the polar angle (ϕ,
ω, κ) can be visualised as rotation ϕ about Z, rotation ω about the new
Y, rotation κ about the new Z. It seems the same as the ZXZ convention
of eulerian angle definition. What's
Hi,
I added some explanation for the XSCALE output to the XDSwiki at
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Xdsconv#explanation_of_typical_output
.
hope this helps,
Kay
The polar angles ϕ, ω define the direction of an axis about which a rotation by
angle κ occurs, i.e. a single rotation around a defined axis. This is different
from Eulerian angles which define 3 successive rotations around principal axes
On 27 Mar 2014, at 06:11, Qixu Cai caiq...@gmail.com
Dear CCP4
Does anyone know how to remove the maltose binding
protein after cleavage from the target protein; I have tried gel filtration and
ion exchange but with no luck, my protein is interacting with the MBP even
after complete cleavage. I would be grateful for any help or suggestions
Best
Dear Mark
Thank you for yor reply, and yes I have tried adding it to the maltose resin
after cleavage but the MBP runs through with my protein, I have also tried 1M
NaCl but with no luck and I also apply detergent after cleavage to the dialysis
buffer because I usually dialyze after cleavage ,
Dear All,
I have newly obtained pdb model for my protein where the waters are not
numbered according to the chain they belong to. I generated symmetry
related molecules for some chains but the waters are together. I would
appreciate suggesstions if there is a way out to get symmetry related water
This is a helpful introductory paper on the topic:
http://journals.iucr.org/d/issues/2001/10/00/ba5006/ba5006.pdf
-- David
On 27 March 2014 06:11, Qixu Cai caiq...@gmail.com wrote:
Dear all,
From the definition of CCP4 (http://www.ccp4.ac.uk/html/
rotationmatrices.html), the polar angle
The figures 4 and 5 in Chapter 11 BMC also help to visualize the difference
http://www.ruppweb.org/garland/gallery/Ch11/pages/Biomolecular_Crystallography_Fig_11-04_PART2.htm
http://www.ruppweb.org/garland/gallery/Ch11/pages/Biomolecular_Crystallography_Fig_11-05.htm
Best, BR
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Dear Qixu Cai,
maybe the confusion is due to that your quote seems incomplete.
According to the html-side the 'visualisation' includes two
back-rotations in addition to what you copied here, so there is at
least one difference to the visualisation of
Dear CCP4
Thank you for all your suggestions
Best Regards
Rana
I'm after suggestions as to where the best place(s) for obtaining info on
latest equipment - advances in techniques etc. Oh, for protein crystallisation
and screening ahead of data collection!
cheers
Dean
Dear Rana,
Did your protein come out from the void volume of gel filtration column? In my
case, I have expressed a soluble aggregated protein which always like to
interact with MBP.
Kind regards,
Wenhe
On 27 Mar, 2014, at 6:26 pm, rana ibd rna19792...@yahoo.com wrote:
Dear CCP4
Does
Rana,
It is hard to answer you question without more details (MW and pI of your
target protein). MBP binds very well to amylose resins and is usually quite
easily bound to anion exchange resins. Did you just run a standard ion
exchange protocol or try different pH regimes?
However, you did
Hi,
I am trying to solve the structure of a membrane protein. The protein has 12
helices and I have a good molecular replacement model that seems to work for
about half of the structure. I used chainsaw to convert the amino acid residues
to that of my protein sequence, and the density fits the
I am also trying to merge data from multiple crystals that I collected from. I
have tried to reindex the data in CCP4 after indexing in iimosflm, and then put
these .mtz files through sortmtz before scala, but I keep getting an error in
sort mtz:
From ccp4_lwbat: warning: attempt to add new
I can index my data through imosflm with no problems, but when I try to scale
using aimless, the program will not run if I also run truncate (or old
truncate). Here is the error message I get below. Could anyone elaborate on
what this means? Thanks.
P.S. I can take the scaled .mtz file from
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Dear Jarrod,
try pointless and aimless to merge the data, this should get rid of
this error message. Otherwise you would have to renumber the batches,
which might be tedious and also unnecessary since pointless has been
around.
Best,
Tim
On
On 27 March 2014 14:23, Jarrod Mousa jmo...@ufl.edu wrote:
Using I/sigI 3 with completeness above 0.85, the estimated useful
Resolution Range of this data is 17.964A to 8.982A
Hi, I would imagine that the message above has something to do with it.
Cheers
-- Ian
Hi,
You may also try BLEND to choose the optimal data sets before scaling
and merging
Foadi J, Aller P, Alguel Y, Cameron A, Axford D, Owen RL, Armour W,
Waterman DG, Iwata S Evans G (2013) Clustering procedures for the
optimal selection of data sets from multiple crystals in
Hi Dean:
Why not check out this excellent book:
Bergfors, T., Editor. Protein Crystallization: Second Edition. 2009.
International University Line, La Jolla, California, 500 pp.
http://xray.bmc.uu.se/terese/buybook.html
By the way, the 1st edition has some extra information that's
Hi Jarrod,
I think these 5 helices are either slightly misplaced, or somewhat disordered.
How does the main-chain density look like? Do you see a discrete main-chain, or
is the main-chain blurred and does the helix look like a blurred cylinder? If
the main-chain is clear, I would take off all
According to the html-side the 'visualisation' includes two
back-rotations in addition to what you copied here, so there is at
least one difference to the visualisation of the Eulerian angles.
Right- it says:
This can also be visualised as
rotation ϕ about Z,
rotation ω about the new Y,
Hello All,
I am appealing to the community as I don't seem to be able to find through
Google what I am looking for, and I just don't have the ability to look through
every structure in the PDB to find this.
I have what I think is an interesting case: a two domain protein structure with
a
Hi Tom,
For acidic side-chains, these kind of interactions are described by Maria
Flocco and Sherry Mowbray in:
Strange bedfellows: interactions between acidic side-chains in proteins. J.
Mol. Biol. (1995) 254, 96-105.
Best regards,
Martin
On Mar 28, 2014, at 12:11 AM, Tom Peat
Two Arg side chains stack next to each other in ferritin and in GST (see, for
example, Arg-59 and its symmetry mate in 3F33). I expect there are other
examples, but these two come readily to mind.
Cheers,
Pat
On 27 Mar 2014, at 7:11 PM, Tom Peat wrote:
Hello All,
I am appealing to the
Tom,
I would think the case can be made for sharing a proton (one ionised and one
not) in either case but more so for acidic residues. See HIV protease Asp-Asp
as a well-established example
Hope this helps
J
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]
Hello Joel,
I like the example of HIV protease, but in this case these Asp residues are
found in the active site of the protein, and unless there is substrate (or
inhibitor) in the active site, these would be solvent exposed (unless I'm
looking at the wrong pair of Asp residues). In the
Tom,
How about Magalhaes et al., J. Protein Chem., Vol. 13, p 195?
Chad
From: Tom Peat tom.p...@csiro.au
To: CCP4BB@JISCMAIL.AC.UK
Sent: Thursday, March 27, 2014 8:09 PM
Subject: Re: [ccp4bb] question on charge charge interactions
Hello Joel,
I like
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