Dear All -
We are well into the 2nd round of Warren's Fund now -and the
lucky Winner of the first round is:
Miles Pufall, a post-doc in the UCSF Yamamoto lab. Incidentally,
UCSF is where Warren did his graduate work with Jim Wells, and many
there had very strong ties to him.
The gross of 150
Your format string works for me. It's hard to say what has gone wrong without
seeing how you ran it. Perhaps you could send me the complete log file?
If you choose column type X X-plor Rfree, then it should convert automatically
between the conventions.
HTH
Martyn
-Original Message-
Fr
Hi Michele,
On Tue, Nov 17, 2009 at 10:28:45PM +0100, Michele Lunelli wrote:
> Clemens Vonrhein wrote:
>
> >
> > SCALA (as far as I know) gets its cell dimensions from the so-called
> > batch header (since each image could have a different cell it averages
> > those). So the problem isn't yet vi
Clemens Vonrhein wrote:
>
> SCALA (as far as I know) gets its cell dimensions from the so-called
> batch header (since each image could have a different cell it averages
> those). So the problem isn't yet visible in your output - just do
>
> % mtzdmp CONVERT/F2MTZCOMBAT_peak.mtz -b
>
> and lo
A two-year postdoctoral position, funded by the French National Research
Agency (ANR) is available immediately in the group of Lionel Mourey at the
Institut de Pharmacologie et Biologie Structurale in Toulouse
(http://www.ipbs.fr).
We are seeking a motivated scientist to join a research project on
To all those who are flagellating themselves in public for
leaving the 'h' out of my first name: It's ok, I've been called
a lot worse - no more postings needed.
10 tickets to go for the first drawing!
Cheers, BR
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.u
On Tue, Nov 17, 2009 at 05:48:31PM +0100, Michele Lunelli wrote:
> I am doing SAD phasing with the latest autoSHARP and CCP4 6.1.1 (SCALA
> version 3.3.9). The space
> group is P21 with unit cell dimension 52.67, 28.61 and 105.16. If I give the
> data as unmerged SHELX
> file, it happens that th
I mean "Bernhard". Apologies for the misspelling.
James
On Nov 17, 2009, at 10:30 AM, Bernhard Rupp wrote:
Dear All -
sofar over 90 tickets sold in 3 days. We are getting close
to drawing the first book winner - please keep going!!
http://www.ruppweb.org/Garland/Warren_raffle.htm
Thx, BR
--
Bernard: This is an incredibly generous effort!
Note that there is no easy way to buy multiple tickets without cycling
through payment. The raffle might get more entries if multiple
purchases were easier.
James
On Nov 17, 2009, at 10:30 AM, Bernhard Rupp wrote:
Dear All -
sofar over
On Tue, Nov 17, 2009 at 10:49 AM, Pavel Afonine wrote:
> one of many possible options to do this:
>
> If you have the latest PHENIX installed ( http://www.phenix-online.org/
> download/nightly_builds.cgi), then you can use "Reflection file editor"
> from the main GUI to do what you want.
>
With
Alexandra,
one of many possible options to do this:
If you have the latest PHENIX installed
(http://www.phenix-online.org/download/nightly_builds.cgi), then you can
use "Reflection file editor" from the main GUI to do what you want.
Pavel.
On 11/17/09 9:49 AM, Alexandra Deaconescu wrote:
Dear All -
sofar over 90 tickets sold in 3 days. We are getting close
to drawing the first book winner - please keep going!!
http://www.ruppweb.org/Garland/Warren_raffle.htm
Thx, BR
-
Bernhard Rupp
b...@ruppweb.org
http://www.rupp
Hello:
I am switching from CNS to Refmac for refinement, and given that my FORTRAN
classes were such a long time ago, I am having problems with the conversion.
This is the format I give ccp4 (skipped the first 7 lines)
'(6X,3F5.0,6X,F10.3,6X,F10.3,6X,F9.3/26X,F10.3,6X,F9.0)'
and here is the b
Hi Fred,
you can do all this in PHENIX, using command line or the GUI.
- GUI: from main PHENIX GUI click on "Comprehensive validation", the
rest should be obvious.
- also, all these values are computed and available after any
phenix.refine run using PHENIX GUI.
- command line: type "phenix
It's hard to know exactly what is going on without the files. I suspect
some problem in converting shelx files to mtz.
The very latest Pointless (from 1.4.1, now 1.4.4) will convert ShelX
input files, and work better
(from our ftp site
ftp://ftp,mrc-lmb.cam.ac/uk/pub/pre/pointless-1.4.4.linux
I am doing SAD phasing with the latest autoSHARP and CCP4 6.1.1 (SCALA version
3.3.9). The space
group is P21 with unit cell dimension 52.67, 28.61 and 105.16. If I give the
data as unmerged SHELX
file, it happens that the third cell dimension become identical to the first
when the data are
mer
Eleanor Dodson wrote:
First you must be on the same origin
There are various ways to get there - brute force method is to
calculate phases from both models, combine them, and use the
reflection utility phase match to move one to the other by an
appropriate origin shift...
Then
Use the GUI m
First you must be on the same origin
There are various ways to get there - brute force method is to calculate
phases from both models, combine them, and use the reflection utility
phase match to move one to the other by an appropriate origin shift...
Then
Use the GUI map correlation.
It will
Kevin Cowtan wrote:
For residue by residue:
Map and Mask utilities/Map correlation
Thanks Kevin, indeed this second option was what I was looking for. And
thanks for the other suggestions too. Unfortunately, I do not know all
CCP4i programs by heart :-(
Fred.
For a global CC:
Reflaction Data utilities/Phase comparison
For residue by residue:
Map and Mask utilities/Map correlation
Note that the global CC will not be the average of the residue by
residue, since it also correlates over solvent, etc.
Kevin
Vellieux Frederic wrote:
Dear all,
I am
How about overlapmap in ccp4?
Thanks
Abhinav
Stanford Synchrotron Radiation Lightsource
Joint Center for Structural Genomics
Mail Stop 99
Phone: (650) 926-2992
Fax: (650) 926-3292
Vellieux Frederic wrote:
Dear all,
I am writing because I have a question that concerns coot or ccp4
(
Dear all,
I am writing because I have a question that concerns coot or ccp4 (don't
know which one). I have 2 maps and one model. One of the map is an
experimental map that has not seen one inch of a model, the second map
is generated after refinement of a molecular replacement model. Same
mol
Le 17 nov. 09 à 12:40, Morten Kjeldgaard a écrit :
Tim Gruene wrote:
Yes, but models that can be validated against experimental data.
The
defining characteristics of computational models is that they (A)
are 100% dependent on the algortihm, (B) can't be validated at
all.
Cheers,
Morten
This discussion seems to have moved a very long way from the original
topic, and hence the reported "Subject", could this be continued as a
new thread please ?
Thanks
Andrew
On 17 Nov 2009, at 11:40, Morten Kjeldgaard wrote:
Tim Gruene wrote:
Yes, but models that can be validated again
Tim Gruene wrote:
Yes, but models that can be validated against experimental data. The
defining characteristics of computational models is that they (A)
are 100% dependent on the algortihm, (B) can't be validated at all.
Cheers,
Morten
>>> Sorry, they can be validated
I would say that any prediction that can be derived from a model and
confirmed is a validation of the model and the model remains valid until
replaced by a better one. The sun was orbiting the earth until evidence
became too contradictorily for this model. Until then it was a good model
- bette
>> Sorry, they can be validated to some extend using biochemical data!
>You are joking, right?
Perhaps a distinction has to be made between model validation and making
useful predictions from the model. Something like
Model Validation - testing model against data. In case of protein
crystallograp
On 17/11/2009, at 08.10, mesters wrote:
Yes, but models that can be validated against experimental data.
The defining characteristics of computational models is that they
(A) are 100% dependent on the algortihm, (B) can't be validated at
all.
Cheers,
Morten
Sorry, they can be validated t
Hi everybody
I need some advice about a good book on membrane protein crystallization.
Thanks in advance
Marta
Dr. Marta Martínez Júlvez
Departamento de Bioquímica y Biología Molecular y Celular
Facultad de Ciencias
Universidad de Zaragoza
Pedro Cerbuna 12
50009-Zaragoza
Spain
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