Hi Robert,
This is very easy with the CCP4 program JLigand. Just start a new ligand
with the sulfur atom, add the phenyl groups, the extra bond and the
hydrogens. Then regularise and save the restraint file.
HTH,
Robbie
-Original Message-
From: CCP4 bulletin board
@ Ian:
Not quite, here's a table giving the complete list of the 3 types:
http://pd.chem.ucl.ac.uk/pdnn/symm3/allsgp.htm
Yes, this Table is known and agrees with what I wrote.
I still do not like, to the point of vehement opposition, the use of
enantiomorphic for the entire 65 because of
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Dear Robert,
this is what I just did:
1) went to en.wikipedia.org and entered your ligands name Dibenzothiophene
2) copied the SMILES string provided for many small molecules in Wikipedia
3) went to http://http://grade.globalphasing.org and paste the
Dear All,
Is there any protocol for preparing a sample from
(cleaning/dissolving) protein crystals for verifying their mass through mass
spectrometry or SDS-PAGE? How many protein crystals are required? Should they
all be from the same well, or can they be from different wells
prodrg should work
Robert ccp4a...@163.com wrote:
Dear all,
How can I get a cif configure for a new ligand. Right now, I want to
use the phenix to refine a complex structure. But I found that I cannot
get the ligand cif file from the CCP4 search. The ligand is
dibenzothiophene. So do you have any
and others..
Wow what a response, seems I started several discussions too.
Good to see the experts views, thanks.
I will try and respond individually but for now a bit background (many
questions asking for details and suggesting similar things done already - glad
to see I've been on the
In principle this is straightforward, but you'll need reasonably-sized
crystals. You'll have to wash them very well in mother liquor (protein buffer
will probably dissolve the crystals). I do at least 3 serial transfers in large
(5-10 ul) drops (with a loop), and for each transfer I move the
Dear All,
I am trying to crystallize a protein with Adenosine. My protein is in 20
mM Tris, 300 mM NaCl and the crystals appear in a condition with 5 percent
PEG8K, 0.1 M Sodium Cacodylate. The protein is incubated with adenosine
for 1/2 hr before setting the drop. The crystals appear right
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Dear Maria,
this is similar to the condition I used for my PhD thesis. I suppose
the following happens:
when you mix the drop the protein crystallises by inverse salting-in
because you dilute the high-salt concentration. This happens
instantaneously
Dear Tim,
you are right that 150mM NaCl is 'stronger' than 2.5% PEG. If you
calculate the relative humidity difference between 150 and 300mM Nacl
you get 99.5 vs 98.9% whereas the difference between 5 and 2.5% P8K is
99.96 vs 99.99% ie virtually nothing. You can calculate these values
here:
After all this discussion, I think that Bernhard can now lay the claim that
these 65 space groups should really just be labelled the Rupp space groups.
At least it is one word.
Jim
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Bernhard Rupp
We are seeking a motivated Software Engineer to join the Protein Data
Bank in Europe team at the European Bioinformatics Institute located on
the Wellcome Trust Genome Campus near Cambridge in the UK.
Together with our international partner organizations, PDBe accepts and
curates depositions
Or space gRupps?
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jim
Pflugrath
Sent: Friday, May 02, 2014 8:36 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Confusion about space group nomenclature
After all this discussion, I think that Bernhard can now lay the claim
Exciting program featuring many highly-esteemed colleagues from all over
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*Early abstract submission deadline May 16th if to be considered for an
oral presentation*,
last possible submission date is July 31th, if to be included in the
Abstract book.
*15th
Hi all,
I'm planning migration from CRT monitor to wall mounted screen with projector
that will support stereo. Mid-range emitter like AE125 for small office (4m by
4m) like mine is sufficient. I'm looking for advise on projector and screen. It
looks like ViewSonic PJD7820HD ($699) with
You guys are enantioqueer.
BR
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Keller, Jacob
Sent: Freitag, 2. Mai 2014 15:43
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Confusion about space group nomenclature
Or space gRupps?
From: CCP4 bulletin board
I actually meant enantioweird.
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Keller, Jacob
Sent: Freitag, 2. Mai 2014 15:43
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Confusion about space group nomenclature
Or space gRupps?
From: CCP4 bulletin board
Hi Maria -
I think you already have a likely answer, but here's another one which I
have observed many times:
Temperature differences. If your crystallization plate is moved from
one temperature to another (lab vs. crystal incubator), or even if it's
left on the bench but the lab
Dear all,
It is nice to see this rather high-brow thread end with some verbal
humour, but I think the subject might deserve a better treatment than it has
received. Three-dimensional crystallographic space groups were classified by
3 different people as far back as the 19th century, and
Dear all,
Thank all of you for helping me. And my problem is solved.
Robert.
In my program documentation I usually call these 65 the Sohnke space
groups, as defined by the IUCr:
http://reference.iucr.org/dictionary/Sohnke_groups
George
On 05/02/2014 02:35 PM, Jim Pflugrath wrote:
After all this discussion, I think that Bernhard can now lay the claim
that these 65
I agree with George. Sohnke is only six letters and it's been used for a long
time to label these groups. Ron
On Fri, 2 May 2014, George Sheldrick wrote:
In my program documentation I usually call these 65 the Sohnke space groups,
as defined by the IUCr:
Dear George
My student class would not find that IUCr dictionary definition helpful. What
they do find helpful is to state that they cannot contain an inversion or a
mirror.
To honour Sohnke is one thing but is it really necessary as a label? You're
from Huddersfield I am from Wakefield ie
It well-known in the mathematics community to refer to these as Sohnke groups,
or even Jordan-Sohnke groups. Camille Jordan identified them in 1868-1869, and
L. A. Sohnke in 1879. William Barlow derived all 230 space groups by adding
reflection operations to Sohnke's 65 groups in 1894-1989.
Dear John,
What is wrong with honouring Sohnke by using his name for something
that he first saw a point in defining, and in investigating the properties
resulting from that definition? Why insist that we should instead replace
his name by an adjective or a circumlocution? What would we say
Bernhard et al,
@ Jens:
I think the precise and correct term applicable to the 65 should
be pro-chiral spacegroups. They are not chiral by themselves, but
addition of something /allows/ for the creation of a chiral object
(i.e. the crystal).
For a moment I though we have it…. but
Dear Jens,
I hope I can make a couple more remarks, and then I will keep quiet.
The first is that your suggestion that we do use Sohncke's name in
relation to these groups may still leave the impression that, as John put it
earlier, this name is just a label. This is where I want
Dear Gerard
I am duly reprimanded .
You are quite correct .
Have a good weekend
John
Prof John R Helliwell DSc
On 2 May 2014, at 18:16, Gerard Bricogne g...@globalphasing.com wrote:
Dear John,
What is wrong with honouring Sohnke by using his name for something
that he first saw a
Fellows,
my apologies for having sparked that space war.
I wish to interject than in my earlier postings to this thread
to Howard I did give credit to the '65 sons of Sohnke' (albeit sans c).
If we honor him, we ought to spell him right.
http://reference.iucr.org/dictionary/Sohnke_groups
Sohnke
namely chirality-preserving.
enantiostatic ;-) ?
BR
Bernhard
On 2 May 2014 21:51, Bernhard Rupp hofkristall...@gmail.com wrote:
Nonetheless, this does not necessarily discredit my quest for a
descriptive adjective, and the
absence of such after this lively engagement might indicate that the
question was not quite as
illegitimate as it might
Bernhard is giving me too much credit. I just told him I'd seen someone's name
associated with the 65 space groups, but that's the only information I
provided. Ron
On Fri, 2 May 2014, Bernhard Rupp wrote:
Fellows,
my apologies for having sparked that space war.
I wish to interject than in
I'm watching the periphery of this, having just taught something about The
Sixty-Five Space Groups a few days ago, but my impression is that you guys have
too much time on your hands. If you'd like something really interesting (and
perhaps useful) to spend your time on, let us know. We'll put
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