echo “keyword1 arguments\nkeyword2 arguments\n etc. \nEND” | peakmax MAPIN
myfile.ccp4 XYZOUT myfiles_omit_atom.pdb
should work as well
Thierry
From: CCP4 bulletin board On Behalf Of Philip D. Jeffrey
Sent: Tuesday, June 8, 2021 2:16 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Problem wi
Public
If the large “blob” sits on a 2-fold crystallographic axis then its occupancy
is ½.
So one possible interpretation is:
* A cation present on the 2-fold axis, occupancy 0.5
* Waters next to the cation position, also with occupancy 0.5, even if they
are not on the 2-fold: the wate
Proprietary
Commenting on Patrick’s message:
(snip) might also consider that PEGs are notorious for impurities of various
types; perhaps the Fluka reagent has less of an impurity that is particularly
vexing for your specific
protein.
Of course, I suppose it might have more of a particular impur
We’ve had issues with the adsorbent material inside a dewar peeling out as
small particles but they were white in color. Not sure it’s the same.
If the dewar is defective the stuff will ultimately find its way to and gum up
the goniohead motors, so it’s important to address this.
Thierry
From:
Jim wrote:
"technically, not in Phenix either. The real-space refinement in Phenix simply
picks peaks in the density and then pulls nearby atoms toward them. . Like a
black hole gobbling up nearby planets (snip)"
Do you have a reference to support this assertion?
"It took me a while to realize
It’s with much sadness that I learn of Ward’s passing.
To add to Bob’s message: Ward was elected as Chair of the IMCA’s supervisory
Board. He lead us through some difficult decisions, and always with a great
sense of humor
Thierry
> On Jul 18, 2020, at 7:36 AM, Sweet, Robert
> <27e0eb9d2
It may be worth trying rigid body-refinement of the solution, using two rigid
bodies, one per monomer, if you haven’t tried already. Then perform positional
refinement.
When refining with the original sequence, first remember that R/Rfree are bound
to be and stay high with at most 25% homology.
Thank you for making the 7.1 source available !
For those interested, http://www.ccp4.ac.uk/download/index.php#os=src
Thierry
From: CCP4 bulletin board On Behalf Of Fischmann,
Thierry
Sent: Monday, May 4, 2020 3:26 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] CCP4 source code
EXTERNAL
Hello,
This question is addressed to the CCP4 staff, but the answer may be of general
interest:
Do you have a projection for when the 7.1 source code will be available? Is
there a way to access the source code for 7.0 in the mean time?
Of course it is understood that the source code availabili
Also if you have Chimera installed:
http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-December/006999.html
Thierry
From: CCP4 bulletin board On Behalf Of Eleanor Dodson
Sent: Wednesday, April 1, 2020 9:00 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Change map handedness
EXTERNAL EMA
We should demand that the wwpdb discards all entries that do not satisfy the
“the criteria of I/SigI > 5 and Rmerge <50%” good practical reference” 😊 .
That’s probably a majority of them. And of course all associated pubs should be
retracted, to be consistent with the referee’s attitude of refus
It is with a heavy heart that I pass along these news. Tom Steitz passed away
yesterday afternoon.
Thierry
Notice: This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth,
New Jersey, USA 07033), and/or its affiliates Di
It does happen that “beautiful” crystals have no diffraction. Here is an
example :
https://www.sciencedirect.com/science/article/pii/0022283691906078
In my experience, crystals are fairly stable. But not always: crystals of human
endothelial nitric oxide synthase or inducible nitric oxide syntha
A position for a X-ray macromolecular crystallographer at the Senior Scientist
level has been advertised by Merck, Sharp & Dohme (MSD). We are seeking a
scientist with extensive experience in all steps of protein crystallization and
structure determination. The candidate must be able to work wit
Here is another observation regarding the subject of which rms value is more
sensible to review a structure.
The purpose of the calculation described below was to determine the optimum e-
density value for rejecting waters.
The principle of the test was very simple : waters were added using th
The information about of the cleavage site can be used in two ways : possibly
identify the protease - as it has already been suggested - or introduce a
mutation at the cleavage site which would prevent clipping from occurring.
The caveat of introducing a mutation is that there is always the poss
Elaborating on Phoebe's answer, the question to ask is : "is the structure good
enough to support the conclusions reached in the paper" ?
That is, quoting the abstract : "an unusual overall architecture that allows it
to adopt a conformation that appears to facilitate pairwise cooperative binding
- Regarding very low or very large unit cell after indexing in HKL2000 :
This behavior can be triggered by having either too many reflections (too many
increases the chance that some are artefacts which are going to misled the
indexing), or too few, respectively.
Editing the peak search results
***********
On Apr 8, 2015, at 10:52 AM, "Fischmann, Thierry"
mailto:thierry.fischm...@merck.com>> wrote:
Some counter-arguments to Michael :
There is an "outside force doing the work": macromolecule crystallization
Some counter-arguments to Michael :
There is an "outside force doing the work": macromolecule crystallization
except rare exceptions is driven by competition for water molecules between the
macromolecule and the precipitant. The exceptions are crystallization against
low salt buffer, in which c
One can use the strings command to show the header:
strings myimage.cbf
Thierry
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
herman.schreu...@sanofi.com
Sent: Monday, December 01, 2014 7:40 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] AW: how
There is no "magic bullet", but the following may help:
- Crystal growth at various temperatures
- Additive screen (such as Hampton Research screen)
- Detergent screen
- Micro-seeding
- Looking for another crystal form, with the option of using a
c
Colin wrote:
> Can anyone suggest other sources of error which would be mitigated by having
> different paths through the crystal. I don't think radiation damage
> (mentioned by several people) is one.
Suggestion : any source of error which does not obey the crystal symmetries
will benefit from
You may also get some insights from TLS refinement.
Regards
Thierry
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roger
Rowlett
Sent: Monday, April 29, 2013 12:27 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Poor electron density in some of the chains in an
asymmet
Structures of a protein-ligand complex are often determined without the need of
running a molecular replacement program: a difference Fourier is generated to
locate the ligand, usually after a few rounds of rigid bodies and / or atom
positional refinement..
They may account for many of the 19,0
Ed,
Are the numerical results the same ? Not likely that there is a problem. But if
you haven't done it already it is worth checking by running the tests provided
with the suite. Aggressive optimization can be a source of bugs.
Best regards
Thierry
-Original Message-
From: CCP4 bulleti
Collect small slices of data (instead of a complete data set) on several
crystals then merge the data together to get a full data set.
The slices of must be small enough so that the damage to the S-NO group is
still very limited on each slice. You may have to play with beam attenuation a
bit, de
It will also look in the directory where you start HKL2000.
Thierry
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dmitry
Rodionov
Sent: Tuesday, November 13, 2012 11:13 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] hkl2000 install
I believ
Just a comment
- Your space group is almost certainly P31 2 1. Your scaling statistics
results point to this - if your true space group was P31,
then your statistics would be noticeably (even dramatically) worse in
the higher symmetry space group.
I've seen a "dramatic" counter-example to thi
I concur with Mike
- If the paper reproduces at least in part a result already published,
then the precedent(s) should be referenced (even if the experimental approach
is different)
- If the paper discusses a previous experimental result or inference
from the results of anot
http://www.thermoscientific.com/ecomm/servlet/productsdetail_11152___13721198_-1
Is this what you're looking for?
Thierry
> Hello all,
>
> Could someone please advise me on where to purchase Mercury Phenylglyoxal
> from?
>
> Many thanks,
> Vijay
>
>
> V
Dipankar,
Herman's message describes the most common case, by far. In addition to his
excellent post there are 4 other possibilities which I can think of of why, in
general, the e- density may be missing for part of a ligand:
- the compound solution are never 100% pure. One impurity may be the c
Oops, you meant catalytic residue. Check the following:
Harris TK & Turner GJ Structural basis of pertubed pKa values of catalytic
groups in enzyme active sites IUBMB life, 53 85-98 (Feb 2002)
Thierry
From: Fischmann, Thierry
Sent: Tuesday, February 07, 201
Check this review, for instance:
Pace, C. et al. Protein Ionizable Groups: pK values and Their Contribution to
Protein Stability and Solubility. J. Biol Chem. 284, 13285-13289 (May 15,
2009)
Thierry
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] O
Dianfan
Some kinases have such conformation in non-activated apo form that the ATP
binding site is partially obstructed. Soaking an ATP analog may then have 3
outcomes: 1) successfully open up the binding site without damage to the
crystal, 2) fail to open up the active site and the compound ca
That's a good question ! Here is my take on it:
We are talking of say 5% PEG 2K weight per weight. So 5% PEG 2K and 5% PEG 20K
contains ~ the same weight of polymer per liter of solution, and therefore the
~ same molarity of the ethylene oxide motif. Hence neglecting the effect of the
ends of t
Yes, and if they don't reappear it may be worth moving the trail to an
incubator set at a slightly different temperature than "room temperature". You
may have to try both lower or higher temperatures if you have no idea how the
temperature may have changed (it's the temperature of the room when
Dear Zbyszek
Wouldn't ripples be the results of calculating maps with truncated
Fourier summations (unavoidably), and, consequently, be more obvious
around a sharp feature such as an heavy atom metal center?
The mathematic basis can be found here:
http://en.wikipedia.org/wiki/Gibbs_phenomenon
Wi
Here is another example of a tetramer with neither 222 or 4 fold
symmetry:
http://www.ncbi.nlm.nih.gov/pubmed/7792597
Thierry
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Vellieux Frederic
Sent: Thursday, July 29, 2010 03:35 AM
To: CCP4BB@JISCM
The results from compressing a diffraction image must vary quite a bit on a
case by case basis.
I looked into it a long time ago using images from a few datasets from 2
different projects. Compress was quite faster than gzip or bzip2 in these
tests. It also delivered the less compression. gzip
Marie-Hélène,
If you haven't done so I suggest trying the very simple precautions described
in this paper:
An improved protocol for rapid freezing of protein samples for long-term
storage.
Deng J. et al.
Acta Cryst. (2004). D60, 203-204
Has worked very well for me in a similar case.
Good luck
T
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
presence of PEG.
Thierry
From: Patrick Loll [mailto:[EMAIL PROTECTED]
Sent: Monday, December 01, 2008 05:59 PM
To: Fischmann, Thierry
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] O/T: can a protein which dimerizes in solution
crystallize as a monomer?
depends on the crystallization
Dear fellow crystallographers,
This is a question which is not CCP4-related.
Is anybody aware of a protein which is known to be a dimer in solution
(say by SEC), and yet crystallizes as a monomer? Wouldn't the high
concentration in the crystallization drop further favor dimerization?
In
Loss of a zinc at a dimer interface, triggered by formation of a disulfide
bridge across the interface has already been observed for nitric oxide
synthase. The 1st reported structure had the disulfide bridge:
http://www.sciencemag.org/cgi/content/abstract/279/5359/2121
But 2 other groups indepen
I've been able to build and run hbplus / ligplot and thought that others
may be interested in the experience. Ligplot is not part of the ccp4
suite, but it is very widely used among structural biologists. Therefore
this may be of interest to some of you.
1- Compilation is performed with the follow
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