Dear Mike,
strange - I just filed a repair job with labcrew for our old ÄKTA Prime. A
technician was in house (for other reasons) when it stopped working and he
was confident that he can replace our pump (rotary unit, as he called
it)... Well let's hope he really does...
On the other hand,
Dear all,
can anyone tell me how to obtain the B11, B22, B33 values?
After i performed the "anisotropic" refinement of the dataset at 1.6 A using
REFMAC5, i can't read these values from the output PDB. thanks
stephen
--
Dr. Stephen Sin-Yin Chui (徐先賢)
Assistant Professor,
Department of Chemistry
It's not difficult to replace parts of AKTAprime. But the pump may not be
available anymore. It should be cheaper to get a new AKTAprime plus than
getting a service contract for AKTAprime. AKTAprime plus costs just a little
bit over $10,000 for a new one and lasts at least 5 years without a service
try file > search monomer library. Hit search without typing anything. It
will give you what it has.
Jackie Vitali
2011/10/12 Dr. STEPHEN SIN-YIN, CHUI
> Dear All,
>
> For all monomers (3 letter) used in COOT, where can i find the full names
> of the
> whole library? Many thanks
>
> stephen
>
Dear All,
For all monomers (3 letter) used in COOT, where can i find the full names of the
whole library? Many thanks
stephen
--
Dr. Stephen Sin-Yin Chui (徐先賢)
Assistant Professor,
Department of Chemistry,
The University of Hong Kong, Pokfulam Road,
Hong Kong SAR, China.
Tel: 22415814 (Office
At this point I usually chime in with an explanation of why
the Protein Data Bank made some choice or other in the early
days but on the matter of U vs. B I have not information to
contribute.
I can point out the at that time characters were stored in
display code on a CDC 6600 and display code u
Hello,
The more I read this mailing list, the more I feel
the crystallographer is a very special human being:
- he lives in the Fourier space
- when he goes to the Cartesian space, he restricts
himself to a small box that is replicated to the infinity
using symmetry operators and origin shif
Michael,
Unfortunately, I actually don't know who serves these machines apart from GE.
Because you brought up the subject of GE equipment and service, I thought I
would ask the community about the best options for routine crystallographic
scale FPLC.
In my opinion, following the takeover of Ph
Thank you for all your advice.They are all good suggestions!
2011/10/12 王瑞
> Dear Everybody,
>
> I am sorry for a little off-topic. Could anyone tell me how to
> determine a protein, peptide and ligand of a new pdb's b factor? I know
> there are rampage and sfcheck to validate in ccp4, but I
I think the PDB decided to store "B" instead of "U" because unless the
B factor was > 80, there would always be a leading "0." in that
column, and that would just be a pitiful waste of two bytes. At the
time the PDB was created, I understand bytes cost about $100 each!
(But that could be a slight
Indeed that paper does lay out clearly the various definitions, thank you, but
I note that you do explicitly discourage use of B (= 8 pi^2 U), and don't
explain why the factor is 8 rather than 2 (ie why it multiplies (d*/2)^2 rather
than d*^2). I think James Holton's reminder that the definition
Dear Ethan,
Thankyou for the reference, but actually it's the wrong paper and anyway
my only contribution to the 'free lunch algorithm' was to name it (in the
title of the paper by Uson et al., Acta Cryst. (2007) D63, 1069-1074). By
that time the method was already being used in ACORN and by the
On Wednesday, October 12, 2011 01:12:11 pm Edward A. Berry wrote:
> Tim Gruene wrote:
> > -BEGIN PGP SIGNED MESSAGE-
> > Hash: SHA1
> >
> >
> > On 10/11/2011 09:58 PM, Ethan Merritt wrote:
> >> On Tuesday, October 11, 2011 12:33:09 pm Garib N Murshudov wrote:
> >>> In the limit yes. however
This may answer some of your questions or at least give pointers:
Grosse-Kunstleve RW, Adams PD:
On the handling of atomic anisotropic displacement parameters.
Journal of Applied Crystallography 2002, 35, 477-480.
http://cci.lbl.gov/~rwgk/my_papers/iucr/ks0128_reprint.pdf
Pavel
On Wed, Oct 12,
Hello,
2011/10/12 Xiaopeng Hu
> I made a simple script for this, perhaps you can edit it for your case.
> Just save it as baverage.sh, then run it as ./baverage.sh your.pdb.
>
Here is another option:
phenix.pdbtools model_statistics=true model.pdb
or
phenix.model_vs_data model.pdb data.hkl
w
Tim Gruene wrote:
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On 10/11/2011 09:58 PM, Ethan Merritt wrote:
On Tuesday, October 11, 2011 12:33:09 pm Garib N Murshudov wrote:
In the limit yes. however limit is when we do not have solution, i.e. when model errors are very large. In
the limit
Dear all,
We have an AktaPrime and GE Lifesciences stop servicing these instruments
because they are getting old. Does anyone know of a third party company
that gives contracts to maintain these instruments? Thank you.
Mike Colaneri
Hi, all
I don't know how to make a geometric and energetic statistics for 20 NMR
solution structures calculated by CNS program.
How to calculate r.m.s. deviations from idealized geometry; and how to
calculate bond, angle, improper, vdw, NOE, cdih, and total energy?
The pdb output files by C
Hi Phil
My understanding is that when the B factor was devised it was believed
that it wouldn't represent any physical reality and was initially at
least widely regarded as a "garbage dump" for errors. So it made no
difference whether or not it was related to the natural length in
reciprocal spac
Hi,
as Tim pointed out Rsym, I/sigma, Redundancy could not be obtained from a pdb,
but you find it in the ouptut of SCALA, XSCALE, or similar scaling programs. I
use Moleman2 from the Uppsala Software Factory to get the B values out of my
pdb. F.e. "Bf St Type" provide B-Factors for every compon
I made a simple script for this, perhaps you can edit it for your case.
Just save it as baverage.sh, then run it as ./baverage.sh your.pdb.
#!/bin/bash
echo "--"
grep '^ATOM' $1|cut -b61-66|cat |awk '{sum+=$1} END { print " Protein
Average B =",sum/NR;print
Not sure if this is helpful Phil, but SCALEIT output includes various
definitions taken from the Willis and Prior book.
But then there is the problem of converting the amplitude B factors to
real space..
I attach my anisotropy notes..
It doesnt address the ? of sensible conventions!!
E
On 10
I've been struggling a bit to understand the definition of B-factors,
particularly anisotropic Bs, and I think I've finally more-or-less got my head
around the various definitions of B, U, beta etc, but one thing puzzles me.
It seems to me that the natural measure of length in reciprocal space i
On 12/10/11 12:53, 王瑞 wrote:
> Dear Everybody,
>
> I am sorry for a little off-topic. Could anyone tell me how to
> determine a protein, peptide and ligand of a new pdb's b factor? I
> know there are rampage and sfcheck to validate in ccp4, but I only
> found a overall b factor in their result.
>
>
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Dear ,
A PDB file is a coordinate file. The quantities you mention, Rsym,
I/sigI, and Redundancy are quantities calculated from the measured data
and can therefore not be determined from a PDB file.
The PDB file also contains the B-factor, so in orde
Dear Everybody,
I am sorry for a little off-topic. Could anyone tell me how to determine
a protein, peptide and ligand of a new pdb's b factor? I know there are
rampage and sfcheck to validate in ccp4, but I only found a overall b factor
in their result. By the way, are there a software to det
We wish to recruit a Research Associate to work with Professor Xiaodong Zhang’s
research team in the Division of Molecular Biosciences, Centre for Structural
Biology, at the South Kensington Campus of Imperial College London. This
project is led by Prof. Xiaodong Zhang
(http://www3.imperial.ac.
If you have two pdb files - one for each ha solution, you can use
csymmatch -pdbin-ref soln1.pdb -pdbin soln2.pdb -origin-hand
-connetivity-radius 1
Eleanor
On 10/11/2011 10:58 PM, George M. Sheldrick wrote:
There are 4 possible origins in I222. There is a simple but inelegant way to
check.
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On 10/11/2011 09:58 PM, Ethan Merritt wrote:
> On Tuesday, October 11, 2011 12:33:09 pm Garib N Murshudov wrote:
>> In the limit yes. however limit is when we do not have solution, i.e. when
>> model errors are very large. In the limit map coefficie
Here we are I presume only worried about strong reflections lost behind
an ice ring. At least that is where the discussion began.
Isnt the best approach t this problem to use integration software which
attempts to give a measurement, albeit with a high error estimate?
The discussion has stra
On Wed, Oct 12, 2011 at 1:35 AM, James Holton wrote:
> My list has 8 different allowed
> shifts for I222, but I assume this is because the 0,0,1/2 shift is
> part of a symmetry operator. I guess it is a matter of semantics as
> to wether or not that is an "allowed shift"?
>
> James, the (0,0,1/2
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