Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 86 44
Fax: +33(0) 491 26 67 20
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El 09/10/13 20:04, Navdeep Sidhu escribió:
John Bohannon wrote about his experience writing a computer
Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 86 44
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
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El 10/10/13 03:56
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El 26/06/13 19:46, Kay Diederichs escribió:
Hi Sebastiano,
ok, I think I have the solution, and, hoping it's correct, have put it into
http://strucbio.biologie.uni-konstanz.de
, France
Tel: +33(0) 491 82 55 93
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http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
: +33(0) 491 82 55 93
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mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
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cootbuilddiffs.tgz
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Luminy, 13288 Marseille cedex 9, France
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mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
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et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
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/Miguel-Ortiz-Lombardia
mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
...@afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
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Le 25 mars 2010 à 16:43, Tim Gruene a écrit :
Hello Rebecca,
this is merely a guess, but I think, it should work.
As you calculate the electrostatic surface potential in pymol, it uses apbs.
apbs, if I remember correctly creates an intermediate PDB-file where the
B-factor column is
Le 26 déc. 2009 à 09:51, Anastassis Perrakis a écrit :
Dear all,
A couple of people have pointed out problems when installing the ARP/wARP
CCP4i GUI over 64-bit fink installations
of CCP4, in Mac OSX 10.6 Snow Leopard. Although I am not confident we
understand the problem 100%, it
/tasks and the task
is not there.
Best regards,
Miguel
Le 26 déc. 2009 à 13:51, Miguel Ortiz Lombardia a écrit :
Le 26 déc. 2009 à 09:51, Anastassis Perrakis a écrit :
Dear all,
A couple of people have pointed out problems when installing the ARP/wARP
CCP4i GUI over 64-bit fink
installation for this workaround to
work. You have to source /sw/bin/init.sh.
Best,
Mark
On 12/26/09 6:51 AM, Miguel Ortiz Lombardia wrote:
Le 26 déc. 2009 à 09:51, Anastassis Perrakis a écrit :
Dear all,
A couple of people have pointed out problems when installing the ARP
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
Le 15 nov. 09 à 12:54, Kjeldgaard Morten a écrit :
On 14/11/2009, at 20.17, Miguel Ortiz Lombardia wrote:
Le 14 nov. 09 à 19:15, Kjeldgaard Morten a écrit :
On 14/11/2009, at 18.55, Ronald E Stenkamp wrote:
The rumblings here at the Univ. of Washington among the
computational modelers
Le 14 nov. 09 à 10:53, Frederic VELLIEUX a écrit :
Dear Bulletin Board,
The following URL's may help people to understand crystallography
(this was also pointed out to me by Ines Kahlaoui last night, I am
so grateful to her):
http://videolectures.net/mit3091f04_sadoway_lec14/ (for the
Le 14 nov. 09 à 19:15, Kjeldgaard Morten a écrit :
On 14/11/2009, at 18.55, Ronald E Stenkamp wrote:
The rumblings here at the Univ. of Washington among the
computational modelers is that some of their current models might
be more representative of protein structures in solution than are
Le 11 nov. 09 à 13:16, Matthias Zebisch a écrit :
Dear bb!
What is the optimal wavelength for Sulfur SAD phasing?
Is it 1.9A or should one go below that to reduce absorption/damage.
Also, would the same wavelength be appropriate to maximize anomalous
scattering to position chlorides, calcium,
Le 11 nov. 09 à 14:26, Jürgen Bosch a écrit :
Dear CCP4 community,
(hijacking the thread)
I so far failed to get a sulfur SAD phased structure and I blamed it
on the low symmetry space group C2 plus weakish diffraction if you
don't want to overexpose your crystal and be able to collect
Dear all,
I cannot get imosflm refining any cell, the program simply stalls: all
you have is the little E at the top right rotating, but no messages,
no errors, no crashes. 'Abort' doesn't have any effect either, nor it
has the sequence 'Pause'-'Continue'.
I have this problem with:
OS:
Le 30 sept. 09 à 17:27, Graeme Winter a écrit :
Dear Miguel,
You may find that replacing the ipmosflm binary with the one from
Harry's web page may be more reliable - typically these sorts of
things come down to gfortran or g77 being a little keen in
optimization.
Le 30 sept. 09 à 22:07, Christopher Law a écrit :
I am just wondering if anyone else is getting just a little bit peeved
that the BB is now primarily being used as a jobs board?
--
Dr. Christopher J. Law,
Queen's University Belfast
Hi Christopher,
Well, I quote from the CCP4 web site:
Dear all,
I'm trying to scale a dataset where 100 frames in the middle (25
degrees) are quite bad so I would like to exclude them. Because the
angular range is too wide I can only do that by creating two runs. So
far, so good. The problem is that even if my input contains these five
Thanks to all who answered!
Removing RUN 1 reference did the trick
Another idea was to simply:
EXCLUDE batch 551 to 650
but then, smoothed scaling is not possible (to wide a gap )
Best regards,
Miguel
2009/7/3 Miguel Ortiz Lombardia miguel.ortiz-lombar...@afmb.univ-mrs.fr
:
Dear all
Hi,
If you were trying to re-run a job created with ccp4 6.1.0 or earlier,
this is a known bug. Have a look at:
http://www.ccp4.ac.uk/problems.php#6.1.1-programs
If that is the case, there is a new refmac.tcl file that solves that
problem.
Best,
Miguel
Le 16 mai 09 à 12:42, Kay
Dear all,
Not a CCP4 question.
We seem unable to process with XDS a set of images collected at ESRF
ID23-1.
Images can be open and processed by other software (adxv, mosflm...)
They have appropriate read permissions and so has the directory where
we run XDS. We use the latest XDS
Hi Ronnie and others,
Le 27 mars 09 à 15:02, Ronnie Berntsson a écrit :
This might be a bit too obvious, but have you checked that the path
to the images is correct? The path written in the input files
generated on the beamline reflects where the images were located in
the file tree
Hi,
I mostly agree with Artem, except on one point:
As long as people publish most of the details necessary to reproduce
the
materials (protein samples and crystals) used in structure
determination -
the crystals may be reproduced 'by persons skilled in the art'.
There is no
need to even
Hi Pavel,
Thanks, it is clear now.
I have a last concern, though. Does phenix impose minimal values to
the refined ADPs? I guess it does not, for I have found nothing like
that in the documentation. But, if it does so, are they imposed to the
individual B-factors or the B-overall is also
Dear all,
While searching for some definition of rotations angles I have bumped
into this very disagreeable indeed discovery: google adds now a step
if you want to go to places _they_ consider as potentially dangerous.
You can proceed that have to copy and paste the address yourself or
The same is true for IUCr, Nature, Science, EMBO (!), Wiley, and
ScienceDirect websites, among many others... including google.com!
Hope it's a (short-lived) bug.
Pedro
The bug is for them to decide what we have or have not to consider as
a threat and to force us to change our websites
Hi Tassos,
I very much like Homolmapper:
http://www.mcb.ucdavis.edu/faculty-labs/lagarias/homolmapper_home/homolmapper%20web%20page.htm
You can map several conserved properties onto your structures, not
just plain sequence.
Best,
Miguel
Le 29 janv. 09 à 22:25, Anastassis Perrakis a
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Hi Jenny and Iain,
But my understanding is that Iain's procedure gives the rmsds of the
_aligned_ C-alphas, whereas Jenny actually seems to be more interested
in those that she excludes from the alignment. I may be wrong, but in
these cases, I use
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Excellent!
Thank you Gerard,
Miguel
Gerard DVD Kleywegt escribió:
But my understanding is that Iain's procedure gives the rmsds of the
_aligned_ C-alphas, whereas Jenny actually seems to be more interested
in those that she excludes from the
to an Expert switch in Preferences.
As developers, we also have to think about long-term maintainability.
Options, in particular little-used options, can soon become out-of-date.
m
On Thu, 2007-05-10 at 12:41 +0200, Miguel Ortiz Lombardia wrote:
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Dear ccp4bbers,
I agree with Dirk. I have also noticed that much due to the way X-ray
crystallography is evolving, a lot of students/early-postdocs find
themselves doing crystallography in labs without a tradition in
crystallography, even without
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Hi Andrew,
Can you get cDNA from human cell lines? Perhaps one of your colleagues
can provide you with a few microliters. You can amplify from there all
the genes you need (provided they are transcribed in that cell line;
therefore, better use cDNA
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