On Fri, 13 Jul 2007, john kryst wrote:
> Hi all !!!
>
>Is it possible to fix one domain and search for the second one in
> phaser !!! What are the keywords to use.
> I have a protein with two domains. It i give both the domains together or as
> two ensembles it is not finding the solutio
Hi all !!!
Is it possible to fix one domain and search for the second one in
phaser !!! What are the keywords to use.
I have a protein with two domains. It i give both the domains together or as
two ensembles it is not finding the solution. If i give only one domain it
is giving the soluti
Frank and everybody else ... I must apologize because the CrystalClear
Reciprocal Space Viewer (click on the icon in the toolbar) uses a refln
list file and does not convert pixel values in images to an undistorted
view of reciprocal space.
Jim
On Thu, 12 Jul 2007, Frank von Delft wrote:
Re
NSLS-II USER WORKSHOP - Last day to register
https://www.bnl.gov/nsls2meeting
We would like to invite all members of the community to participate in
the NSLS-II user workshop hosted by Brookhaven National Laboratory on
July 17-18th. Following general sessions on the 17th several specific
Life Sci
1) Rfree in the first cycle seem to be more apparent than actual. You
need to check you free reflection conversion. It may turn out that you
have more reflections for free than for working R.
2) You may need to use tighter restraints. For example by changing
weight matrix value to smaller numb
Dear Sir or madam,
I have some questions about refmac5.
I am new to Refmac. I optimized the structure with CNS (Rwork: 23%, Rfree:
25%).
Cell :71.48071.480 151.81390.00090.00090.000
Space group p43212
resolution 100 1.97
protein contain 350 amino acids.
Nmol/asym: 1
nu
--
Cheryl A. Kerfeld Ph.D.
Education/Structural Genomics
DOE Joint Genome Institute
2800 Mitchell Drive
Walnut Creek, CA 94598
(925) 296-5691
[EMAIL PROTECTED]
postdoc2_ck.doc
Description: MS-Word document
I am often receiving only responses to the original queries posted on CCP4BB
but not the original
query itself. They are not going to my spam box either.
Has anyone else noticed the same?
Thanks.
Raji
-Included Message--
>Many thanks to good people who have responded
>to my mes
What about CrystalClear from Rigaku?
-Original Message-
From: Peter Zwart <[EMAIL PROTECTED]>
Date: Thu, 12 Jul 2007 08:55:04
To:CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Program to 'visualize' the reciprocal space ?
> I don't think that there is a program available to do what
I don't think that there is a program available to do what you want, but
What about APEX2 from Bruker?
P
Hi Sergei,
I don't think that there is a program available to do what you want, but
I think that the tools are there for you to make one. The biggest
challenge you will have is keeping the mathematics straight!
So, if you start off with something like the DiffractionImage library,
this will help
Many thanks to good people who have responded
to my message! Apparently I have to apologize for not formulating
my question clearly enough. Here is more explanation.
According to Ewald construction, diffraction images
collected by oscillation method correspond to thin 'curved' slices of the
recip
Dear All,
We at CCP4 look forward to seeing you at this year's ACA in Salt Lake
City.
Please drop by the CCP4 booth, #110, to learn about the latest
developments in the suite, and have your queries answered (or at
least forwarded onto someone who might know the answer.
CCP4 staff will b
John Pak wrote:
Hi all, I was hoping to receive some guidance on the following subject.
I'm refining a structure using REFMAC that shows all the symptoms of
radiation damage. Namely partially broken disulphide bonds and
decarboxylated Asp/Glu residues. I have an idea of how to handle the
pa
Yes there is a way to do something anyway.
Is your metal only linked to protein or are there extra atoms as part of
the metal?
If there is protein lins you need to make a LINK record in your PDB and
provide a dictionary description of your expected geometry.
If you have more details I can b
Is this a SHELX data set where the FreeR is flagged as -1?
There seems to be a variety of methods ..
But if you read in the FreeR flag from SHELX and ask to have a FreeRflag
output the convert -t o - mtz script under Reflection data utilities
will output the SHELX value
Eleanor
Leonard Tho
msd pisa does that
eleanor
[EMAIL PROTECTED] wrote:
Dear all,
I’m wondering anyone can recommend some programs or servers to
evaluate protein-protein contacts. I’m currently have a homogeneous
tetramer. However, the protein exists as a dimer in solution. I’m
thinking where to cut the line
Hello,
if anybody else needs the .cif file correctly describing a 2`-deoxyuridine its
bonds to the adjacent nucleotides in a DNA strand for Refmac :
in the attachment you can find the file I kindly received at my question.
Best regards,
Kristina
Ud_cif.doc
Description: MS-Word document
2007/7/12, Gebhard Schertler <[EMAIL PROTECTED]>:
I have obtained some promising X-tals in 2M Ammonium Nitrate. I am now looking
for freezing
conditions. Has anybody had experience in successfully freezing X-tals under
similar conditions
? What was the best cryo-protectant and which concent
I have obtained some promising X-tals in 2M Ammonium Nitrate. I am
now looking for freezing conditions. Has anybody had experience in
successfully freezing X-tals under similar conditions ? What was the
best cryo-protectant and which concentration was optimal ?
---
Look at http://www.ccp4.ac.uk/dist/html/twinning.html for introduction..
Eleanor
Li Sheng wrote:
> Hi, Dear All,
>
> How could I know whether a crystal was twin or not from it's
> diffraction data?
> Thanx in advance.
>
>
>
>
> Sincerely,
> Li
> 07-08-2007
This sort of information is summarised on the MSDpisa site
http://www.ebi.ac.uk/msd/
Eleanor
U Sam wrote:
In this connection I like to know how symmetry (in degrees and
translation) is calculated between two or more molecules in the
asymmetric unit (A.U.).
Suppose if I download a PDB then I
Coot (and SSM) should give matrix - euler and polar angles! Paul? Eugene?
But if you do the superposition with lsqkab (superpose molecules - match
residues) then that gives all 3 ways.
Or use ROTMAT which converts everything to everything else.. ( rather
clumsy though..)
Eleanor
Jiamu D
There is a lot of confusion about this!
You can call it R3:H ( indexed with a=b and gamma = 120)
This is also called H 3 in the PDB deposition and the CCP4 symmetry
libraries.
(But for the CCP4 library - it checks the axes and angles to decide
whether this is using the H ( or hexagonal) convent
To add additional capacity to our protein crystallography unit we are
looking for a Senior Research Scientist, PhD in Protein Biochemistry or
similar.
Senior Protein Crystallographer
The protein crystallographer will have the project responsibility for all
steps upstream of the purified protei
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