Hi Seema,
for python scripting in Coot (and syntax) you may want to refer to the
WIKI:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Python_Scripts
or the manual:
http://www.biop.ox.ac.uk/coot/doc/user-manual.html#Scripting
I meant to complete a more comprehensive man
Hi,
I'm using COOT-0.6 following the manual,but while trying to use
(calculate>scripting>)>python or (calculate>scripting>)>scheme to write any
command (say,set_show_origin_marker 0) it shows
"BL WARNING:: Python syntax error!
(Or you attempted to use an invalid guile command...)
Py
James,
I must admit not (yet) having read the "data processing paper PMID: 20389587"
nor the 88 author paper. Nevertheless, I would like to comment on your remark
"Personally, I was quite impressed by how good the R factors were, all things
considered."
If I am not mistaken, perfectly twinne
Hi Dale,
Thanks for posting this interesting piece of history.
My non-PX initiation into PX was through DEC too. On a summer internship in
1996 after my junior year, I landed up at this
institute which had just received their new DEC ALPHA2000.
My project was to write up a C code (I had rece
The twin fraction for REFMAC was exactly 0.5. The individual crystals were
not twinned (or at least I would be VERY surprised if they were), but they
do belong to the space group P63, and autoindexing will give you one of the
two possible axis conventions at random. So, of the 15445 crystals that
I performed DEN-refinement with CNS using the same data and starting model, and
obtained
similar "twinned" R values and maps. The twin fraction is 0.5.
Axel
On Feb 9, 2011, at 3:29 PM, Jon Schuermann wrote:
> According to the paper, the data was refined in REFMAC in 'twin mode' which,
> I
I observe under some conditions that ctruncate sets some reflections
amplitudes to zero. AFAIU, this should not be happening as even
negative intensities (there are none in this particular dataset) should
produce FP>0 upon truncation.
66 out of ~23000 reflections are zeros after ctruncate is ap
According to the paper, the data was refined in REFMAC in 'twin mode'
which, I believe, calculates the R-factor using a non-conventional
R-factor equation which usually lower than the conventional R-factor. I
believe this is dependent on the twin fraction which wasn't mentioned in
the paper (o
Hi,
I am using CCP4 6.1.13 in Windows 7. It worked fine after installation, but
now stopped running after I moved CCP4-DATABASE to a subdirectory for
consolidation. So I uninstalled the whole program and removed folders
(CCP4-Packages and Ccp4Temp) from C: drive, and then I downloaded it again
and
This was "molecular replacement" from 1jb0, so the phases came from the
model. Probably more properly called "direct refinement" since all we did
was a few cycles of rigid body. Personally, I was quite impressed by how
good the R factors were, all things considered.
-James Holton
MAD Scientist
I have used phaser to successfully solve a structure in P2x2x2x that had
pseudo-translational symmetry. It was unable to correctly choose the space
group, but after running phaser in all 8 possible space groups and inspecting
the best solutions in each the correct solution was clear. Furthermo
Any idea where then phases came from?
BR
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Thomas
Juettemann
Sent: Wednesday, February 09, 2011 12:16 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] First images of proteins and viruses caught with a
molrep can deal with some of the PST cases.
Garib
On 9 Feb 2011, at 22:27, Phil Jeffrey wrote:
> Is there a program that does ? I was under the impression that they were all
> equally good/bad at this, because any solution that agrees with the PTS has
> quite a high score and any solution tha
Is there a program that does ? I was under the impression that they
were all equally good/bad at this, because any solution that agrees with
the PTS has quite a high score and any solution that doesn't has a low
score, irrespective of the correctness of the placement of the molecules.
In one
Just to add to Phil and Eleanor's response...
I would NOT use Phaser for MR with PTS present. It doesn't handle it
correctly yet, since the likelihood targets don't account for PTS.
Others may be able to explain it better.
Its probably not C-centered (as Eleanor mentions) and you should try t
find . -name '*.osc' -or -name '*.img' -type f -size +3000 -print -exec
bzip2 '{}' \;
is a personal favorite, along those lines, with ample opportunities for
customization. (If the above command line wraps, it's all supposed to
be on one line)
Phil Jeffrey
Princeton
On 2/9/11 2:46 PM, Davi
Thank you for clarifying this James. Those details are indeed often
lost/misinterpreted when the paper is discussed in journal club, so
your comment was especially helpful.
Best wishes,
Thomas
On Wed, Feb 9, 2011 at 20:38, James Holton wrote:
>
> As one of the people involved (I'm author #74 ou
On 02/09/11 09:49, Andreas Förster wrote:
Dear all,
I'm trying to create some space on our server and want to compress all
x-ray data files. I'm wondering what extensions I should search for.
mccd and img come to mind easily. What other extensions are commonly used?
Thanks.
Andreas
/bin
Dear All,
I would like to point your attention to:
*Max F. Perutz International PhD Program Vienna 2011*
The Max F. Perutz Laboratories is inviting applications from talented
students all over the world for our graduate program. The institute is
located at the Vienna Biocenter Campus - a maj
As one of the people involved (I'm author #74 out of 88 on PMID
21293373), I can tell you that about half of the three million snapshots
were blank, but we wanted to be honest about the number that were
collected, as well as the "minimum" number that were needed to get a
useful data set. The b
Dear Andreas,
I had the same problem frequently and wrote a little python-script for
compressing our images on our server. It might help you and you can
easily modify the extension for which the script should search for...
Best Regards,
Georg
-- code starts below
#!/usr/bin/pytho
By "That's" I presume Bob means "the 0.01% bandwidth figure is" approximately
the intrinsic bandwidth of a Si (111) monochromator.
The 0.1% bandwidth in the title of the email is the standard bandwidth often
used to define the output of synchrotron sources.
When defining flux within a certain
http://www.nanowerk.com/news/newsid=20045.php
http://home.slac.stanford.edu/pressreleases/2011/20110202.htm
I think it is pretty exciting, although they only take the few
datasets that conform to their
existing model:
"The team combined 10,000 of the three million snapshots they took to
come up
Dear all,
Thanks for your hearty responses. Below is a summary for the
information I received. Again, I really appreciate all the help.
Best regards,
Junyu
1. Yale University, University of Utah, and Wake Forest University are
three that have core facilities which perform N-terminal seque
That's approximately the bandwidth of a Si (111) monochromator.
On Wed, 9 Feb 2011, Andre Luis Berteli Ambrosio wrote:
Dear ccp4bb,
I sometimes find the flux of x-ray sources reported in units of “photons/s/0.1%
bandwidth”
instead of simply “photons/s”.
Where does the “1/0.1% bandwidth”
Dear Jacob,
Regarding your second question, I stumbled across a relevant article on
Wikipedia recently: en.wikipedia.org/wiki/Megahertz_myth
Cheers,
David.
On 9 Feb 2011 13:53, "Jacob Keller" wrote:
> I love hearing these types of stories, which have a few effects on me:
>
> -Admiration of those
Harry Powell had the most comprehensive answer, giving me the extensions
that are used in mosflm:
.img .mar* (i.e. .mar1600, .mar2300, etc) .mccd .osc .SFRM .sfrm .image
.ipf .cbf
In addition, finding files larger than a certain cutoff might do the
trick too - especially if the objective is
On Tuesday, February 08, 2011 11:47:04 pm Dale Tronrud wrote:
> I see in the news that Ken Olsen has died. Although he was
> not a crystallographer I think we should stop for a moment to
> remember the profound impact the company that this man founded
> had on our field.
>
> My first expe
Dear Wataru
check out the following entry on the CCP4-wiki on 'sticky crystals' which we
compiled based on feeback from many crystallographers:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Sticky_crystals
Best regards
Savvas
Savvas Savvides
Unit for Structural Biology @ L-P
Hi Wataru,
Have you tried Mitegen's polymer MicroTools? These tools have tips made
from soft, flexible microfabricated polymer films and are specifically
designed for this type of application.
There is more information about them here (
http://mitegen.com/products/microtools/microtools.shtml
And before anyone else points out the mistake
Flux in magnetism is the magnetic field (e.g. no. of lines) over a
defined area.
Some similarity to photons/sec over a defined area for x-ray sources
Well I think this is right.
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC
.ipf if you have files from (old) image plate detectors.
clement
> Dear all,
>
> I'm trying to create some space on our server and want to compress all
> x-ray data files. I'm wondering what extensions I should search for.
> mccd and img come to mind easily. What other extensions are commonly
>
Hi Wataru,
I second Bill's suggestion. Additionally, you might want to migrate to a
sitting drop setup and use the vacuum grease with that. It worked for me.
Happy Fishing,
Chris
--
Christopher L. Colbert, Ph.D.
Assistant Professor
Department of Chemistry and Biochemistry
North Dakota State U
Cool the coverslip on the opposite side of the crystal with a chip of dry
ice. Do not freeze the drop. I learned this from Gary Gilliland. Also I
wonder if you can simply move the whole tray into a cooler temperature?
You can imagine that the thermal expansion coefficient of the glass
cover
I think that this CRO can help you:
Proteos
4717 Campus Drive
Kalamazoo, Michigan 49008
269.372.3423
http://www.proteos.net
Good luck!
Bryan
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Junyu Xiao
Sent: Tuesday, February 08, 2011 2:52 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject:
Andre
I should have replaced flux in my email by photons/sec to be clear (or
at least a bit clearer). Flux in magnetism is the strength of the
magnetic field per unit area so it is confusing to use the term in the
way I did. Different fields use the same term for different purposes.
Techn
.osc
2011/2/9 Andreas Förster :
> Dear all,
>
> I'm trying to create some space on our server and want to compress all x-ray
> data files. I'm wondering what extensions I should search for. mccd and img
> come to mind easily. What other extensions are commonly used?
>
> Thanks.
>
>
> Andreas
>
>
Dear all,
I'm trying to create some space on our server and want to compress all
x-ray data files. I'm wondering what extensions I should search for.
mccd and img come to mind easily. What other extensions are commonly used?
Thanks.
Andreas
--
Andreas Förster, Research Associat
Andre
The 0.1% bandwidth is a standard for flux/mrad/bandwidth or brightness
(flux/mrad^2/mm^2/bandwidth) from the synchrotron source. It is an
emittance rather than an acceptance. A typical perfect crystal
monochromator might take (i.e. accept) a tenth of this. However,
dependent on the range of
Hi Jacob,
On Wed, 9 Feb 2011, Jacob Keller wrote:
Regarding the last point, does anybody have a good response to the
Moore's law conundrum that some programs which will take, say, ten
years to run now will take only ~1 year to run 8 years from now,
making it futile to run the program now? Maybe
Dear Andre
For a continuum wavelength band source this unit is needed. A monochromator of
a given type then extracts it's rocking curves worth of bandpass. Or in Laue
diffraction a wide band is selected with eg a mirror cut off at short
wavelengths and a filter or transmission mirror at long wav
I love hearing these types of stories, which have a few effects on me:
-Admiration of those who worked with so little to produce so much
-Thankfulness for the resources we have now
-Excitement for the forthcoming technogies
-Despair about using current technologies, knowing they will be
supplanted
Hi Everyone,
Merck Research Laboratories has an opening for a summer intern in the
Structural Chemistry (X-ray crystallography) groups located in either
Kenilworth, NJ or West Point, PA. The idea is to have someone
comfortable with programming and mathematics to explore some
computational ideas t
The Agilent Technologies' X-ray Diffraction department, located in Yarnton near
Oxford, is looking for an Application Scientist to join a small team of
highly-skilled chemical and macromolecular crystallographers.
Your principle activities within the team will include macromolecular X-ray
data
Dear ccp4bb,
I sometimes find the flux of x-ray sources reported in units of "photons/s/0.1%
bandwidth" instead of simply "photons/s".
Where does the "1/0.1% bandwidth" unit come from? I have also seen other
percentages like 0.01% bw or 0.02% bw...
Is it simply defining some degree of acceptanc
Dear all,
is there a short cut to define an entire chain as one group in the rigid body
refinement of refmac, or do I have to explicitly name the starting and ending
residues - that's a little tedious with several domains, and using a wild card
would come very handy.
Cheers, Tim
--
--
Tim Gruen
--- On Wed, 9/2/11, geoffrey kamau wrote:
From: geoffrey kamau
Subject: RE: Preliminary studies
To: rex.pal...@btinternet.com
Date: Wednesday, 9 February, 2011, 9:03
Dear Dr. Rex Palmer,
Thanks for the message.
Yes, we have been using X-ray diffraction cameras, particularly with respect t
At times DEC we innovative in ways that no hardware company
today even comes close. But I guess innovation and commercial
success do not go hand in hand. OK, this is abridged from
Wikipedia, but much of it is true...
Digital supported/developed the ANSI standards, especially the
ASCII and mult
Dear all,
I would like to draw your attention to the following protein
crystallization and characterization course we are offering:
2nd Advanced Protein Characterisation and Crystallisation Course: May
2.- 6. 2011
The Biocenter Finland Protein crystallisation unit is again organising
an
Yees - a translation of 0.5 along x means you must consider SGs P212121
and P2 21 21 since the absences will be present (at least at low
resolution) with either SG.
I dont know how good Phenix would be at distinguishing between z=0.233
and z=0.25
However even if the exact peak is at z0.25, i
Dear Daniel,
You can get it here as well...
University of Pittsburgh
Department of Biological Sciences
Fifth and Ruskin Aves
Clapp Hall 301
Pittsburgh PA 15260
email: hem...@pitt.edu
ph: 412.624.0106
or
Jack Presley
Laboratory Manager
UC Davis
Molecular Structure Facility
http://msf.ucdavis.edu
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