Dear All,
I've wonder for a simple problem for a long time, that is: What is the
ideal bond length and angel?
Every lecture or book says this is a criteria from small organic molecules,
but I still donnot know
exactly. Like is bond length point to the peptide bond length? Or many other
bonds?
Dear All,
Thank you for your previous response. I have built a 3-mer oligosaccharides
in the electron density by using coot. I prefer to refine my structure in
CNS due the resolution is only 2.6 Ang. I found there are only topology and
parameter files for carbohydrate in CNS but no linkage file for
With such good data you would expect lower R factors I agree.
I use all the COOT validation tools - Ramachandran, diff map peaks etc
to try to pinpoint errors.
Also anomalous difference maps hoping to verify S positions and check
the sequence fitting.
You could let Arp/Warp rebuild it from t
James,
CCP4mg will allow you select a set of atoms and draw a surface over them
in whatever colour scheme that you choose.
The tutorial explaining this is at
http://www.ysbl.york.ac.uk/~ccp4mg/ccp4mg_help/tutorial/surfaces.html
Cheers
Liz
James Thompson wrote:
Dear CCP4'ers,
Any Window
On 9 Jan 2008, at 10:34, Eleanor Dodson wrote:
Bong angels are probably ideal already!
There is really no such animal as an ideal bondlength or angle -
they depend to some extent on the atomic environment.
Not to a complete extent?
Stuart
Bong angels are probably ideal already!
There is really no such animal as an ideal bondlength or angle - they
depend to some extent on the atomic environment.
There are papers by Engh and Huber who looked at small molecule highly
refined structures to get AVERAGE bond lengths and standard devi
Can you explain the define of the bond length and bond angel--especially
bond angel--here?
i leave the definition of angels (be they ideal or not) to clerics, but if you
want to find out about bonds and angles, AND YOUR SUPERVISOR IS REALLY UNABLE
OR TOO BUSY TO EXPLAIN THESE BASIC CONCEPTS
By the way, I think my bad english embarrassed my meaning. What I want
to say
is which bond length is used as the standard? the C=N or Ca-N or even the
side chains?
Or all of them?Which angel is used to compare, the Ca-C'-N or C'-N-Ca or
others.
At first I suppose the bond length only calc
Dear Prof Gerard:
In fact I have read your Model Validation on-line, and I have to say it
is youe lecture
that made me to think about this problem, though I have used it as a common
stand for
the quality of the model without understand it for a long time.
And the http://en.wikipedia.org/
them today before I post my mail, but unable to access them. For some
reason, wiki is forbiddon here. I really coouldnot find the best answer and
have discussed
i am shocked. i just checked with one of my 25 chinese students here and
indeed even universities in china do not have access to a ba
Hey Gerard,
wikipedia might tell you how to angle for fishes, but I fear it falls
short of teaching you how to fish for angels.
Andreas
Imperial College of Aquatic and Fisheries Sciences London
Gerard DVD Kleywegt wrote:
Can you explain the define of the bond length and bond
angel-
On Wed, 2008-01-09 at 12:47 +0100, Gerard DVD Kleywegt wrote:
> (rhetorical question of the day: just like teaching a person how to fish is
> better than to give them a fish, isn't providing the url to google or
> wikipedia better than providing an answer to a basic question?)
You can read a fe
Simply use a bong for a while, and you will hear the angels sing :)
It's amazing to see how this thread devolved, within two or three
posts, into a discussion about drug abuse and totalitarian political
regimes...
Good way to start the day :)
On Jan 9, 2008, at 8:35 AM, Jim Pflugrath wro
Bong angels are probably ideal already!
Please explain, so that I can teach this to my students. :) Jim
Hi,
Sorry for the non-ccp4 related question.
We are planning to buy a crystallization robot. We looked at the
'Mosquito'. We felt it is good for setting 96 well plates (for screening
the conditions). Though they say that we can use it for 24 well plates
(hanging drop) it didn't seem to be ideal bec
In your generate.inp file that generates the input pdb and mtf files for
cns there is a section called carbohydrate links which you can use to
define the links... see below for an example of a beta link between the
C1 and Asn N and a beta link between O4 and C1 of the next sugar. Then
just make
Hi Yang Li:
Macromolecular crystal refinement programs use ideal bond lengths and angles.
The simplest ones just assume any carbon-carbon single bond (C-C) is the
same as any other, and use one average value, and any carbon-carbon double
bond (C=C) is the same as any other, and use another averag
Douglas Oryx6 or 8. It works well on sitting drop and microbatch in our
division.
Nalam, Madhavi wrote:
Hi,
Sorry for the non-ccp4 related question.
We are planning to buy a crystallization robot. We looked at the
'Mosquito'. We felt it is good for setting 96 well plates (for screening
the condi
We chose the Phoenix crystallization robot because:
It has no expensive consumables (tips) intrinsic to the machine. This
was also a big item for us because we worry about being able to run the
machine for more than 3 years. Would the tips for our 2008 machine be
available in 2014?
It is easy to
Hi Lisa,
is the Phoenix capable of setting up hanging drops? For me that is one of the
big plusses of the Mosquito. Are there any other robots out there capable of
doing hanging drops?
Cheers, Bert
Bert van den Berg
University of Massachusetts Medical School
Program in Molecular Medicine
Bi
Dear All,
I am very sorry to involve you into such insignificance discussion, I
have reached agreement
with Prof Gerard, please stop talking about things beyond science, thanks!
I read a book today, which said "A refined model should exhibit rms
deviations of no more
than 0.02A for bond
It doesn't have a cover slip flipper.
We only do sitting drops with our robot- even large volumes (2 ul
drops).
We don't have the space to store the volume of linbro plates that would
be generated by a robot.
Also, 24 well linbro plates use a lot of well solution- making them very
expensive fo
Looking at the mosquito, it doesn't have any cover-slip handling
robotics, either. So it's the same thing- rearrange the dispense
location and flip the cover- which is either a glass plate or mylar or
a tape seal.
--
Lisa Nagy
University of Alabama-Birmingham
[EMAIL PROTECTED]
Dear Yang Li:
Happy New Year to you, too, (ahead of Feb. 7th).
You certainly owe us no apology; the reverse may not be true.
Your question is an important one, as is what you have written below.
I'm not certain I have a completely satisfactory answer.
The reason is that ideal bond lengths may
Sorry, that should have read
"because the value is established by social consensus, it is thus NOT
guaranteed to be perfectly accurate, ..."
In other words, one can imagine some source of systematic error in
establishing an ideal bond length. For example, the crystal packing
environment of small
The mosquito has special (albeit fairly pricey at $13 each) plastic sheets that
allow setup of hanging drops in a 96-well format. It can also do multiple drops
per well. As far as I know this is a capability unique to the Mosquito but I
may be wrong.
Bert van den Berg
University of Massachuset
The latest Acta D shows the "social consensus" is sometimes lacking even (or
especially) among very experienced and able crystallographers.
Experimental determination of optimal root-mean-square deviations of
macromolecular bond lengths and angles from their restrained ideal values
Ian J. Tic
For some current thoughts on bond length and bond angle deviations you may
want to look at the following paper:
... but that would be rather a waste of your time (sorry!). if you're only
going to read one paper about this subject this year, make it iain tickle's!
http://journals.iucr.org/
The phoenix can dispense multiple drops per well. You can easily
program dispensing on the deck wherever, whatever and whenever, as long
as it fits in the plate holder . It can handle at least the 1536 pitch
(4 x 384), so if you specify the quadrant of the 384 well cell it will
dispense there. Your
Check out the letters in the Dec 2007 edition of Acta D. There is
lively discussion even among the experts (and while I recall no
mention of angels in this discussion, there IS a reference to Winnie
the Pooh).
Acta Cryst. (2007). D63, 1274-1281
Acta Cryst. (2007). D63, 1282-1283
Some pe
"tables 1" is formally correct but awkward. "table 1s" is confusing. I
would suggest that we treat "table 1" like sheep and make the plural the
same as the singular. If you don't approve of revising the English
language, then a valid way to avoid the need for a plural is to say "each
table 1"
For some current thoughts on bond length and bond angle deviations you may want
to look at the following paper:
Acta Cryst. (2007). D63, 611-620
Stereochemical restraints revisited: how accurate are refinement targets and
how much should protein structures be allowed to deviate from them?
M.
Hi Madhavi
In conjunction with a 96-syringe hydra for filling reservoirs, we have been
using two Genomic Solutions 8-tip "Cartesian" systems (Called HoneybeeX8 now I
believe) for the past 6 years and have been generally very happy with them.
They require a bit of looking after in terms of clean
Hi William & others,
Indeed, phenix.refine uses cross-validation to optimise the scaling of the
X-ray & B-factor weights. All I did was demonstrate that you can do
essentially the same thing as phenix.refine but using Refmac instead. I don't
claim to have done anything new, except I modified
I would only like to iterate a small comment I posted before:
Should the cell parameters be inaccurate, optimization of weights by
cross-validation (getting the best Rfree) will result in 'higher' RMSD.
It is easy to think about it: if in a cell is measured to be 1%
larger than in reality, al
All,
Just a quick correction on the latest price of the plastic sheets. The
new ones cost $5.00, so the overall cost will be much cheaper.
Thanks
Balaji
On Jan 9, 2008, at 11:59 AM, Van Den Berg, Bert wrote:
The mosquito has special (albeit fairly pricey at $13 each) plastic
sheets that a
Dear All,
Does anyone have a python routine that can be used to calculate the
moment of inertia matrix and principal axes of a selection of atoms?
Thanks! and all the best,
--Buz
On Jan 9, 2008, at 5:30 AM, Gerard DVD Kleywegt wrote:
them today before I post my mail, but unable to access them. For
some reason, wiki is forbiddon here. I really coouldnot find the
best answer and have discussed
i am shocked. i just checked with one of my 25 chinese students here
and i
Be care, you insolence might get someone sent disappear.
is the chinese secret service editing my incoming mail already, or are you
merely using a microsoft grammar checker?
--dvd
**
Gerard J. Kleywegt
Dear all
I have a sulfate ion sitting on a 2-fold axis. Should I put in pdb file
one S atom with occu=0.5 and two O atoms with occu=1, or should
I put one S and four O atoms all with occu=0.5?
Thanks for your inputs.
Jie
The Gilson crystallisation robots (horrible machines: no longer
available) were specific for hanging drops - other robots can set them
up (using the Mosquito sheets or equivalent), but the flipping will have
to be done by hand. The Douglas Instrument machines can basically
pipette onto anything yo
Dear All,
I have got large and nice crystals in a condition that contains 40% glycerol, 75 mM DL-Malic Acid pH7.0, and that's it! No precipitant?! No buffer?! I'm so comfused. As far as from the product website, the Malic Acid has no buffering function. I don't know whether it's a precipitant. The
Dear Jinjin:
Malic acid, a diprotic acid, has a pKa of about 3.4 for the first dissociation
and a second at about 5.1. So it is best as a buffer within a pH range of about
2.4 to 6.1, and it at its best around best in the range of 3.4 to 5.1. If the
pH of your solution is indeed 7, then it is
Hi Jie,
Depending on your resolution, you may be forced use to use S(0.5) and
4x(0.5) in order to restrain the SO4 to stay tetrahedral in refinement.
Cheers,
Charlie
Jie Liu wrote:
> Dear all
>
> I have a sulfate ion sitting on a 2-fold axis. Should I put in pdb file
> one S atom with occu=0.5 a
In my understanding, unbiased electron density map usually refers to the Fo-Fc
map.But I have seen in some papers sentences like that "The initial, unbiased
2FoFc map is contoured at".I was a bit confused since I was told by my
instructor that the 2Fo-Fc was usually biased.
Can anyone clear up
Dear Jie,
It also depends on whether you believe the SO4 sits
with its internal two-fold along the crystal's two-fold
axis. If it does you should probably have a 0.5 occ
sulfur and two 1.0 occ oxygen atoms. If the symmetry
is not obeyed you will have to have four 0.5 occ oxygen
atoms.
Be
The map will be biased by whatever model is used to generate the phases.
If a heavy atom phasing method was used (MIR, MAD, etc) then at least you
do not have model bias.
A sigma-A weighted 2Fo-Fc map strives to have minimal bias, as does an
EDEN map with phase perturbation. However, minimally b
On Jan 9, 2008, at 11:56 AM, Buz Barstow wrote:
Does anyone have a python routine that can be used to calculate the
moment
of inertia matrix and principal axes of a selection of atoms?
I compulsively write python code sometimes--its that fun of a
language...
If you can get the x, y, z, a
A 2Fo-Fc map is simply an Fc map with two times the Fo-Fc map added
to it. ( Fc + 2(Fo-Fc) = Fc + 2Fo - 2Fc = 2Fo - Fc ) The phase comes
from the Fc's. The basic formulation is biased toward the model used
to calculate the Fc's. You did, after all, start with a pure Fc map!
Various tech
Could anybody also advise about an imaging system for automatic
inspection of crystallization plates?
Is there a newsgroup dedicated to crystallization robotics?
> Hi,
> Sorry for the non-ccp4 related question.
> We are planning to buy a crystallization robot. We looked at the
> 'Mosquito'. We
Hi,
Heavy atoms can be unpredictable. There are rules of thumb regarding their
use but these rules are frequently bent and broken.
Which heavy atom derivatives have you tried, and at what (approximately)
concentrations and exposure times? Does your protein have residues that
*can* react wit
The CrysCam manufactured by Art Robbins is quite versatile at
a very competitive price-performance ratio. They also do quick
custom mods if you have special tasks, and they always provide
a demo.
http://www.artrobbinsinstruments.com/cryscam.html
Best regards, BR
-Original Message-
F
Thank you for your help. I have make my CNS work on the structure refine
successfully.
Best Regards.
On Jan 10, 2008 4:51 AM, Li Zhijie <[EMAIL PROTECTED]> wrote:
> Hi Jiamu,
>
> I think the glycoside linkages are specified in the generate.inp file.
> The text I list in the end of this email is
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