Good job they did'nt dead heat otherwise it would have been Trumpton. Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://www.springer.com/978-1-4641-3954-7
- Forwarded Message -
From: Ian Tickle
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, 9 November 201
Can anyone suggest a method/program for analysing conserved waters between two
related protein structures? Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://www.springer.com/978-1-4614-3954-7
http://portal.limon.gen.tr/gm/itfhmazeeuauqaqvqmzusuu.html
Rex Palmer
11/23/2013 2:52:00 AM
Good evening http://www.simonebaldini.com/wgyj.html
Does anyone have a nice graphic of type X collagen?
Thanks in advance.
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
We have two refined protein structures of similar proteins. There are
differences in the amino acid sequences however and also in the bound waters
and ligands.
Does anyone know of a program which we could use in order to quantify the
structural differences associated with these factors?
Rex
I have developed a problem with CCP4MG on my pc.
I get the message "python.exe has stopped working".
I have tried recompiling the program to no avail.Any ideas please.
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
I have developed a problem with CCP4MG on my pc.
I get the message "python.exe has stopped working".
I have tried recompiling the program to no avail.
Any ideas please.
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
What is render.exe in COOT?
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
r 2012) is exactly 100 years since
W L Bragg presented his first paper to the Cambridge Philosophical Society and
thus begun the field of X-ray Crystallography."
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
__
Does anyone know why the ligand alpha lactose in COOT has at least one sugar
ring that is not fully symmetrical. The CCDC deposited alpha lactose molecule
has both rings perfectly symmetrical chairs.
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010
I would like to specify a target atom in a pdb file and then isolate all atoms
within a given distance of the target. The selected atoms are then to be placed
in a new pdb file.
Any suggestions please.
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010
Does anyone know if the alpha lactose molecule LBT coordinates are in the Coot
library. If so how can they be accessed?
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
Dear CCP4'ers
With the occurrence of more and more high resolution protein structures does
anyone know at present how many such structures have been successfully refined
anisotropicall?
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
Can anyone please tell me how to extract the pdb for a ligand, eg alpha
lactose, from the COOT library, prior to fitting into difference density.
Thanks in advance.
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
I have been presented with the problem of locating protein data for a structure
which was refined here ten years ago with the CNS program.
Unfortunately I have never used this program so do not know what type of files
I am looking for (or how many files).
Any suggestions please
Rex Palmer
http
Does anyone know how to change a two column format .pdf file into plain one
page at a time format.
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
Is there an easy way to make two .hkl files into one continuous file?
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
Dear CCP4BB
Does anyone know how to convert a .pdf file into a meaningful Word file.
Any suggestions will be greatly appreciated. The pdf file has numerous figures
and tables.
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
The standard notation is 21 axis parallel to [100]?
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
From: James Stroud
To: CCP4BB@JISCMAIL.AC.UK
Sent: Thursday, 14 June 2012, 20:06
Subject: [ccp4bb
Can anyone recommend a program that will search a crystal structure for CH---N,
CH---O and CH---C
contacts by applying space group symmetry and lattice translations.
I also need the geometry and symmetry operations in each case to be output.
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff
I am looking for a program that will display weak CH---N bonds.
The programs I know about only display classical hydrogen bonds such as OH---N
etc.
Any suggestions please?
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
Does anyone have an up-to-date account of protein structure anlysis from
powders?
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
Just enquiring on the off chance that someone has/knows of a teaching video
demonstrating the setting up of hanging and/or sitting drops for
crystallisation.
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
Dear CCP4'ers
Can anyone help with the following problem:
How do we install CCP4I on an imac.
As yet we have had no success only error messages concerning working
directories etc.
Thanks in advance
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalme
collection ie
because smaller crystals can be used.
Any help will be greatly appreciated.
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
peaks generated.
If the keyword RMS is present, then the peak threshold is PEAK * RMS density,
otherwise PEAK is the absolute threshold in the scaled map.
Question: RMS density of what and what is the formula used?
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalme
Once waters have been located and refined is there a program that analyses
their positions
in terms of solvation shells?
Can the results be compared easily with those from related known
protein structures?
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010
individually?
I want to inspect the individual binding sites.
Thanks
Rex Palmer
Birkbeck College
HETATM 3993 C1 GAL B 265 -3.839 64.712 -19.974 1.00 66.90 C
HETATM 3994 C2 GAL B 265 -4.291 64.321 -18.565 1.00 65.48 C
HETATM 3995 C3 GAL B 265 -4.084 62.837
irst warning message
above.
We
also tried running Refmac but get similar problems when trying to create a
project directory.
Can anyone please advise?
Thank you,
David
Lisgarten and Rex Palmer.
Canterbury Christ Church University
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff
with both alpha and beta forms of lactose in
the dictionary?
Rex Palmer
Birkbeck College
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
diamond tipped drill do the same job?
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
Does anyone know how to select an atom and rotate the image about this point in
Rasmol?
Rex Palmer
Birkeck College
Does anyone have a good quality reproducible Bruker AXS (XPREP/RLATT) simulated
precession record for a book chapter (it will be fully acknowledged!).
Rex Palmer
Birkbeck College
We have purchased a 5mg commercial sample of a protein we want to crystallize.
On arrival it transpired that the sample had been lyophilized.
Does anyone know if this is likely to give problems and if so what can/should
be done about it?
Thanks in advance
Rex Palmer
Birkbeck College
Dear All
What is the best program to use for comparing two protein structures which are
very similar both structurally and wrt aa sequence? ie to get the rms
deviations both generally and in selected regions.
Rex Palmer
Birkbeck College
This is much better than Coronation Steet!
http://blog.the-scientist.com/2011/04/11/multipole-wigglers/
Rex Palmer
Birkbeck College
below:
http://clicks.aweber.com/y/ct/?l=7vf_V&m=1adA9w4Zgg1yh1&b=_szL3OnaO1I3NyRX06YTVA
Rex Palmer
Birkbeck College
MAR describe their latest Image Plate as a CCD. Their early Image Plate designs
were described as barium halide phosphor doped with Eu2+. Does anyone know why
they have kept the name Image Plate when everyone else calls it a CCD?
Rex Palmer
Birkbeck College
Does anyone have an email address for Hide Niwa who was at Birkbeck in the
1990's and went to work back in Japan as a protein crystallographer? The
earthquake is rather worrying.
Rex Palmer
Birkbeck College
Thanks to all for your prompt, detailed and useful answers.
I thought you would all be watching the rugby this afternoon!
Rex
Is MOSFILM 6.2.6 the latest version?
Rex Palmer
Birkbeck College
Does anyone still use CNS ?
Do we expect Rfree from CNS for example to be different from the value given by
Refmac at the end of the refinement?
Rex Palmer
Birkbeck College
--- On Wed, 9/2/11, geoffrey kamau wrote:
From: geoffrey kamau
Subject: RE: Preliminary studies
To: rex.pal...@btinternet.com
Date: Wednesday, 9 February, 2011, 9:03
Dear Dr. Rex Palmer,
Thanks for the message.
Yes, we have been using X-ray diffraction cameras, particularly with respect
Just out of curiosity does any one still use, or know of anyone else who still
uses X-ray photography to screen cell parameters and data quality prior to data
collection, for either macromolecular or small molecule studies?
Rex Palmer
Birkbeck College
What programs are available for processing Laue data to produce an intensity
data set?
Are explanatory notes or publications available?
Rex Palmer
Birkbeck College
Does anyone know of a statistical breakdown of successful protein structure
determinations in terms of the method used?
Rex Palmer
Birkbeck College
- Forwarded Message
From: Dean Palmer
To: Rex Palmer
Sent: Thursday, 16 December, 2010 12:08:20
Subject: FW: Virus alert
From: amanda.po...@uk.henkel.com [amanda.po...@uk.henkel.com]
Sent: 16 December 2010 10:20
To: dpal...@bucksgfl.org.uk
Does anyone know if it is possible to transform the continuous (compacted) pdf
format ino the older version where each atom occupies a single line (and vice
versa).
Rex Palmer
Birkbeck College
Can anyone please recommend a UK protein sequencing service. Our protein is
dimeric with reported molecuar weight of about 85kDa.Our funds are somewhat
limited.
Thanks in advance.
Rex Palmer
Birkbeck College, London
RexPalmer2010.homestead.com
ARGUSLAB and export as a .pdb file (there's
nothing else to do in ARGUSLAB but it is useful for minimizing and producing
various surface types eg ESP).
3. You can test the .pdb file with RASMOL and or DISCOVERY STUDIO VISUALIZER
(both also free downloads and good for making nice pictures).
Rex P
Can anyone reccomend a free download program that will calculate the energy of
a protein/ligand complex? The ligand has been modelled in.
Thanks
Rex Palmer
Birkeck College
Dear CCP4 users
The Shelx lst file includes the entry:
Most Disagreeable Reflections (* if suppressed or used for Rfree)
and includes 50 hkl's with
h k lFo^2 Fc^2 Delta(F^2)/esd Fc/Fc(max) Resolution(A)
Is there a corresponding or similar facility in CCP4?
Rex P
Does anyone know of a program that will mutate a given base in the pdb of a DNA
structure?
Many thanks in advance.
Rex Palmer
Birkbeck College, London
can be done with eg
Quanta but do not have access to this program. Does anyone know of a
downloadable program that we could use instead?
Rex Palmer
Birkbeck College, London
In Refmac: Does anyone know if lactose should be designated as one component
(Lat) or two components (Gal and Glc)?
Rex Palmer
Birkbeck College
chair and would this
necessarily be a valid move? ie why can't the conformation deviate from the
norm?
Rex Palmer
Birkbeck College
Can anyone supply information on the use of the following in ccp4:
1. Bulk-solvent correction
2. Refinement of individual isotropic B-factors
3. Refinement of an anisotropic overall thermal parameter
Rex Palmer
Birkbeck College, London
Our protein includes several glycerols which have been added to the pdb file.
We understand that any required (geometric or other) restraints have to be
specified to Refmac in the refinement library. Can someone please provide the
instructions for how to include these specifications?
Rex
Does anyone know of the existence of a structure for a voltage gated Na (not K)
channel?
Rex Palmer
Birkbeck College, London
If you measure a set of diffraction data without any particular restraints and
it turns out, say at a given theta max, to be only 80% complete, what does this
imply?
Rex Palmer
Birkbeck College
Does anyone know of a program designed to both store information on functional
motifs in proteins, as described in the literature, and to retrieve such motifs
within a given protein sequence?
Rex Palmer
Birkbeck College
Does anyone have a dvd depicting protein crystallization including setting up
microplates and hanging/sitting drops that would be suitable for teaching
purposes?
Rex Palmer
Birkbeck College
What seems to be a possible sulphate has been identified in our electron
density.
What steps could/should be taken to confirm or consolidate this assignment that
would satisfy referees?
Rex Palmer
Birkbeck College
Is there a preferred type of density map to use with Coote for identifying
waters?
Rex Palmer
Birkbeck College
Is there software that will extract a protein sequence in either 3 letter or
single letter code from a given pdb file?
Rex Palmer
Birkbeck College
I want to pick a bond or series of bonds in RASMOL and display with wireframe
or sticks.
Any ideas please?
Rex Palmer
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