Hi CCP4ers,
Need your help, many thanks.
When I was trying to install arp_warp_7.0.1.tar.gz in my CCP4i (6.0.windows
version), it complained as " Failed to unpack and/or read contents of
C:/CcprTemp/arp_warp_7.0.1.tar.gz. This may not be a valid CCP4i package.
Then, I unzipped this file, and f
Dear Crystallographers,
Quasi-off-topic question:
does anybody have a script to download and superimpose automatically some set
of similar structures in the PDB, perhaps as defined by DALI? Preferably this
would be for pymol...
Jacob
***
Jacob Pearson
But Tassos, you and Gerard both should know better (Mark vR already knows,
clearly). THAT is not Dutch diplomacy, because it always starts like this:
No, no, no, you are completely wrong!
Actually, the way I learned about Cicero is better explained with Gaius Julius
Ceasar. There is a tempora
Quite precise occupancy.
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Aaron
Oakley
Sent: Monday, January 12, 2009 4:19 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Ligand binding in multiple conformation
>I had a question about flex
>I had a question about flexibility in ligand binding in an enzyme active site.
>Is it possible for a substrate/product analogue to bind in more than one
>conformation in the active site.
Yes. It is even possible for portions of a ligand to be disordered and not
discernable in electron densit
hi
yes this may happen in some circumstanceshave a look at
J Am Chem Soc. 2008 Oct 15;130(41):13514-5.
> Hi,
>
> I had a question about flexibility in ligand binding in an enzyme active
> site. Is it possible for a substrate/product analogue to bind in more
> than
> one conformation in the
Hi Mariah,
We have had one case of this, with two partially overlapping conformations
of a ligand, which is not yet published.
Model in both ligand conformations. Then edit the PDB to give them the same
Chain ID, but with alternative conformations for each atom, or each one that
is different. Yo
Hi,
I had a question about flexibility in ligand binding in an enzyme active
site. Is it possible for a substrate/product analogue to bind in more than
one conformation in the active site. Since the ligand/enzyme interactions
are very specific I am a little confused about this.
Also which progra
> -Original Message-
> From: marc.schi...@epfl.ch [mailto:marc.schi...@epfl.ch]
> Sent: 12 January 2009 22:35
> To: Ian Tickle
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] structure (factor) amplitude
>
> Ian Tickle wrote:
>
> OK, limiting the vote to people whom I think we can
- Original Message -
From: "Bernhard Rupp"
To:
Sent: Saturday, January 10, 2009 4:09 PM
Subject: [ccp4bb] structure (factor) amplitude
Dear All,
I am getting conflicting comments on the use of
'structure factor amplitude'
vs. just
'structure amplitude'
for |F|.
Is there some 'moder
Ian Tickle wrote:
OK, limiting the vote to people whom I think we can assume know what
vaguely they're talking about, i.e. Acta Cryst. / J. Appl. Cryst.
authors, and using the IUCr search engine we get 553 hits for "structure
amplitude" and 256 for "structure factor amplitude"
But be warned t
On Jan 12, 2009, at 11:09 AM, Ethan Merritt wrote:
"geometrical structure factor" gets 68 hits in the IUCr search engine,
and 2190 GHits (GHits == Google Hits)
To avoid confusion, can we use "gHit" as a google Hit unit? First,
"google" is traditionally spelled with a lowercase "g"[1]. Secon
Dear,
So what is the problem? to be honest with you, I have hardly heard that
someone use hanging drop vapour diffusion to glow 2D crystal because usually
you ll end up have 3D crystal or severe stacking problem.
I guess one of your major problem might be stacking, If this is the
case, you should
My apologies as well about the incomplete James perusal. I was just looking
for either term in the table of contents, and assumed that a similar meaning
would apply to such a similar (identical) term. Perhaps there are some
structures in the PDB, then, that have Jamesian structure amplitudes?
I'll add my 2 calories then. Gerard's new naming carefully avoids the
"Factor" and "Amplitude". The following term should get everybody to
agree:
"FA-free STRUDL".
Example of politically correct use:
"It is good practice to deposit your FA-free STRUDL in the Protein Data
Bank along with the atomic
> PS: I vote for that "structure factor amplitude" be used in text books
> and |F| on cell phones. Student of 2015: "You mean 'abs-F' is really
> pronounced 'structure factor amplitude'? I didn't know that!"
By 2015, it would probably be some less-comprehensible variant of
instant-messenging con
Dear Gerard,
As usual, your contribution is a hard act to follow. However, given
that your actual proposal can be rather indigestible (especially with lots
of cream) we might have to stick with the current options.
What the perusal of James has revealed is that, if we want to respect
> to my knowledge, none of the existing reciprocal-space refinement
> programs is really suitable for low-resolution refinement. In my
For what it's worth, I've had good luck with refmac5D, which
incorporates an SAS target into model refinement (I believe this was has
now been incorporated into th
As suggested by Tassos, what we need now more than ever is some Dutch
diplomacy so that he healing can really begin. Various people have argued for
a shorter term (Brazilians, Pflugrath) and since I'm personally rather partial
to Brazilians I would say we ought to go with that and shave off a fe
Come on, Jim, even now 90% of students don't realize that F
is a phased amplitude, we think of it as a complex number, and that F(obs)
or F(calc) are probably the appropriate |F|.
Bob
On Mon, 12 Jan 2009, Jim Pflugrath wrote:
I wonder if the early use of the shortened "structure amplitude" is
On Monday 12 January 2009 10:45:30 Gerard Bricogne wrote:
> Dear Jacob and Jianghai,
>
> The trouble with this "King James version" is that what he calls the
> "structure amplitude" A is the amplitude of the scattered electromagnetic
> wave! If you look at equation (2.3) on p.27, the expressi
Gerard,
You are absolutely right. My apology for the confusion. Keep on
reading, looks like that James called |F| "geometrical structure
factor", which probably is not commonly used anymore.
-- Jianghai
On Jan 12, 2009, at 1:45 PM, Gerard Bricogne wrote:
Dear Jacob and Jianghai,
Mark,
What bothers me about your message is that you already have talked to Rigaku.
Until now we have never been able to create a problem that they could not
diagnose and help me solve from remote. In danger of offending ccp4 readers:
specialized Rigaku experts are a remarkable source for inf
Dear Jacob and Jianghai,
The trouble with this "King James version" is that what he calls the
"structure amplitude" A is the amplitude of the scattered electromagnetic
wave! If you look at equation (2.3) on p.27, the expression for A is first
of all complex (!), and refers for each atom to it
Well according to Google this paper (JCS, 1936) contains the phrase
"magnitudes of the structure amplitude factors (F)":
http://www.google.co.uk/search?hl=en&q=%22magnitudes+of+the+structure+am
plitude+factors%22&btnG=Search&meta= .
It seems that "structure amplitude factor" is what we have now
a
JPK beats me on this one. Here is the quote from R. W. James, "The
Optical Principles of the Diffraction of X-rays".
"We shall call A the 'structure amplitude', a name introduced by
Ewald, to denote the fact that its value depends essentially on the
structure of the group associated with e
Hmmm.
Sacha just threw another wrench into that discourse. Seems we are
also faced with a duality problem here:
Coming from a mathematical point of view treating F as a complex number,
structure factor magnitude or
structure factor modulus
is more logical and more direct.
If you are taki
[King?] James says "structure amplitude."
(1950 ed., Ch II, 1a (p27))
JPK
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.
Dear All,
The deadline for general user proposals for PX beamtime at the ALS is
coming up soon (Jan 15)! At the BCSB, we have 5 beamlines for which you can
apply for beamtime. At the Berkeley Center for Structural Biology
(BCSB) we have recently completed a number of upgrades:
Sector 8: Recent i
On Monday 12 January 2009 02:42:43 Ian Tickle wrote:
> Also I did a 'Google vote' for the two terms. 'Structure amplitude' has
> 11300 hits. 'Structure factor amplitude' has only 4750. So all round I
> would say that 'structure amplitude' wins by a considerable margin.
The field of crystagoogl
Post-doctoral positions in macromolecular crystallography and NMR
spectroscopy at the University of Pittsburgh in the Department of
Structural Biology. There are several postdoctoral positions available
immediately, with opportunities to work in projects related to
Metabolic Membrane Protei
Hello all,
While testing a newly installed ARP/wARP interface (ver. 7.0.1) in ccp4i
(ver. 6.1.0) on Ubuntu (8.10) I noticed that the Fobs and Sigma pull-down
menus are missing from the ARP/wARP Quick Fold window. This is accompanied
by the following error message, which is output in stderr by
Not only in Stout & Jensen but also in Blundell & Johnson 1976, Jan
Drenth's book and many more use "structure amplitude".
I like to think that "structure amplitude" (would not dare to call it
"slang") is the crystallographers short form of "structure factor
amplitude".
Although all of us know
Hi,
Thanks for the suggestion. Here is more info: It is a soluble protein, a
monomer has 3alpha and 3 beta subunits, and exists in solution as a dimer. The
technique is hanging drop, vapor diffusion.? And the? mother liquor is ~ 0.1 mM
cacodylate pH 6.2ish, MgCl2 and PEG 20k.
=v=
-
OK, limiting the vote to people whom I think we can assume know what
vaguely they're talking about, i.e. Acta Cryst. / J. Appl. Cryst.
authors, and using the IUCr search engine we get 553 hits for "structure
amplitude" and 256 for "structure factor amplitude" (quite close to the
ratio for Google so
>
> My preference is also for the full structure factor amplitude. I would have
> said that I'd never seen
> the term structure amplitude used. However, I just looked this up in my old
> Stout & Jensen (1968
> edition - brown cover) and find that (on p. 195) where |F| is introduced they
> def
I wonder if the early use of the shortened "structure amplitude" is
because it was a pain to do any typing, word processing, typesetting, etc
before Gutenberg.
But soon crystallographers will be solving all their structures on their
cell phones and also just text messaging manuscripts to edito
Hi All,
Sorry for a non CCP4 querry.
I am using CNS for composite omit map calculations. the structure is having
a ligand for which parameter and topology files have been generated using
PRODRG server. however while running composite_omit_map.inp i m getting the
following torsion topology error
My preference is also for the full structure factor amplitude. I
would have said that I'd never seen the term structure amplitude used.
However, I just looked this up in my old Stout & Jensen (1968 edition
- brown cover) and find that (on p. 195) where |F| is introduced they
define it as:
On Mon, 2009-01-12 at 10:42 +, Ian Tickle wrote:
> I was taught 'structure amplitude' - makes perfect sense to me! Why
> does 'structure amplitude' make any less sense than 'structure factor'?
>
> It also clearly made sense to Phil Coppens, a crystallographer of
> considerable repute, see ITC
THE UNIVERSITY OF LIVERPOOL
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POSTDOCTORAL RESEARCHER
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You will join the Molecular Biophysics Group
(www.biophysics.liv.ac.uk) to work on a BBSRC-supported project on
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The pro
Dear Tassos,
just to add some pepper to the conversation,
I am obliged to say that "Chichero" (as it's typed) in modern (as well
as in old) italian would be pronounced in exactly the same way as
greek "Kikero" ...
Does it help, or make more confusion ???
:-)
alE
PS. I am also for Stru
> Also I did a 'Google vote' for the two terms. 'Structure amplitude' has
> 11300 hits. 'Structure factor amplitude' has only 4750. So all round I
> would say that 'structure amplitude' wins by a considerable margin.
Results of another Google vote:
"Earth is flat":
55,
This chain reminds me of another discussion we had during dinner at
Grenoble in the late '90s.
The topic of the argument was how to pronounce the name 'Cicero'.
Namely, my Italian friend (Gino C) was claiming it should be
pronounced like in modern Italian, 'Chichero',
while I was claiming that
We've been able to run months with an old Xstream 2000 system, so that
shouldn't be the problem. Unlike Frank, we haven't had problems with water
in the nitrogen from a nitrogen generator.
If Frank is correct, that it's water, then either the molecular sieves
need to be replaced, or there is ice b
Hi Gerard & Marc
My answer was my interpretation of Bernhard's original question "what
*is* the currently accepted name of the object whose description is
'structure factor amplitude' ?", and was based both on authoritative
precedent, i.e. ITC Vol. B, and on frequency of current usage, i.e.
Google
Ian Tickle wrote:
I think there's a confusion here between the name of an object (what you
call it) and its description (i.e. its properties). The name of the
object is "structure amplitude" and it's description is "amplitude of
the structure factor", or if you prefer the shortened form "structu
Hi,
If you have ice on the crystal (loop) but no blockages of the cryostream
itself (and this seems to be what you're saying), it is unlikely to be a
problem with the LN2 (although I only have experience with Oxford
Crystreams, but I imagine this also applies to X-streams).
Our main problems
Hi Mark
We had a LOT of pain with icing, and it really comes down to one thing:
water in the gN2. And don't expect to measure some other way whether
you have it, because your X-stream (or Cobra) is the most sensitive
water meter there is.
In our case, the symptom was the X-stream (and late
Dear Ian,
My reply to this question will be less literate and less democratic
than yours. In spite of the nice Alice quote, I remain in favour of trying
to use compound names whose internal structure is, as much as possible,
"isomorphic" to the composition of meanings they refer to (even thou
Dear Ian,
many thanks for this clarification - I have to think about this,
though ;-)
Best regards,
Dirk.
Am 12.01.2009 um 12:09 schrieb Ian Tickle:
I think there's a confusion here between the name of an object (what
you
call it) and its description (i.e. its properties). The name of
I think there's a confusion here between the name of an object (what you
call it) and its description (i.e. its properties). The name of the
object is "structure amplitude" and it's description is "amplitude of
the structure factor", or if you prefer the shortened form "structure
factor amplitude"
Apologies for this slightly off topic question:
I am having a great deal of trouble with my X-Stream 2000 cryostream system and
I wondered if other users have similar problems.
I've replaced almost all components (new GAST compressors, helium recharges,
filters, etc., etc.) in the last coup
... despite these informations, I still prefer "structure factor
amplitude", because it is the amplitude of the "structure factor" ...
Best regards,
Dirk.
Am 12.01.2009 um 11:42 schrieb Ian Tickle:
I was taught 'structure amplitude' - makes perfect sense to me! Why
does 'structure amplitud
I was taught 'structure amplitude' - makes perfect sense to me! Why
does 'structure amplitude' make any less sense than 'structure factor'?
It also clearly made sense to Phil Coppens, a crystallographer of
considerable repute, see ITC Vol. B (2nd Ed.), sect 1.2., p.10: 'The
Structure Factor'. To
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