Dear Wulf,
I have had a similar experience recently when water treatment in SHELXL
became a nightmare - as you say they
started shifting away even if those were clear water sites. I have not found
a final solution to this but
I was not worried by those where density disappeared - those were the
Dear Rongjin,
In addition to what the others said, I would do the following:
1) check your apo-structure to make sure the putative ligand binding is
not blocked by a crystal contact and also check that there is a channel
leading to the binding site. You may not get hits in your
A few remarks:
I still believe that this is related to the max. likelihood vs.
conjugated gradients and FFT vs. full summation Fourier and bulk
solvent treatment in those programs.
- max. likelihood is a refinement target function, and conjugated
gradients is an optimization method.
- FFT
On Nov 13, 2009, at 1:04 AM, Vellieux Frederic wrote:
Hi James,
Could not understand much. Can you explain?
If anyone out there has a program in circulation/for sale that was
written more than 10 years ago, please change the headers and
recompile it to take advantage of modern
Dear Fred
A really nice video that would be great for giving non-crystallographers
(including colleagues and 1st year students, and perhaps also friends and
family) an overview of what we do. Thank you for pointing it out - and of
course very many thanks to Dominique Sauter for making it. I am
Hi Wulf,
For your waters that move slightly out of the centre of density I think SHELX
FAQ #27 would apply:
Q27: Some Waters are moving away from the centre of density toward the corner
of the density.
What is going on ?
George: We have sometimes seen atoms move to the edge of density in a
Hi, the latest arpwarp via ccp4 6.1.2 GUI on Mac OS X 10.5 something
does
not work, it wants a sequence file which isnt an option in the GUI...
(you put in the coordinates and update them thats all right?) i just
want to improve
the maps if possible. also the model if possible.. flex-warp
Sorry, it's a bugg.
Go back to a mode for autobuilding, turn off sequence docking,then
back to map improvement and it will work.
A.
Sent from my iPhone
On 13 Nov 2009, at 13:23, Tommi Kajander tommi.kajan...@helsinki.fi
wrote:
Hi, the latest arpwarp via ccp4 6.1.2 GUI on Mac OS X
Additional to all other suggestions you can also mix your ligand at
low concentration to lots of low concentrated protein and then
concentrate your protein over time. The advantage, ligands with low
solubility can bind to your protein while you are concentrating it.
And then I would
Dear Rongjin,
In addition to all suggestions, you would also want to check 2007
proceedings of CCP4 study weekends about crystallography of complexes.
http://www.ccp4.ac.uk/ccp4course.php
I also liked following papers that give you so much information about
crystallization of protein-ligand
Dear Colleagues,
In the proper buffer (e.g. PBS) and after sterile filtration
(possibly, also upon addition of 0.02 % NaN3) Fab fragments can be
stored at 4 oC and stay functional over more than a year.
For long term storage they should be shock-frozen in liquid nitrogen
and may be kept at -20
I am currently trying to run CCP4 6.1.2 under RHEL5 (actually
Scientific Linux 5.3) and have run into the apparently-familiar
problem of not having bltwish.
Specifically, while I can download blt-2.4-21.z.el5.i386.rpm from the
EPEL repository, it does not contain bltwish.
I have also tried
... and thanks also to Ines Kahlaoui who pointed it out to you!
On 11 Nov 2009, at 09:44, Vellieux Frederic wrote:
Dear all,
Thought I'd share this with you:
I located this through Ms Ines Kahlaoui, from the Beja Higher Institute of
Biotechnology in Tunisia (Ines has to teach and
mb1pja wrote:
Dear Fred
A really nice video that would be great for giving non-crystallographers
(including colleagues and 1st year students, and perhaps also friends and
family) an overview of what we do. Thank you for pointing it out - and of
course very many thanks to Dominique Sauter for
Did you try here?
ftp://ftp.ccp4.ac.uk/ccp4/6.1.2/extras/
Kevin Anderson wrote:
I am currently trying to run CCP4 6.1.2 under RHEL5 (actually
Scientific Linux 5.3) and have run into the apparently-familiar
problem of not having bltwish.
Specifically, while I can download
I'm not sure which package there you're referring to. I downloaded
the BLT source from http://blt.sourceforge.net . (It seems to finally
be working now; I just had to compile it on a 32-bit machine.)
-Kevin A.
On Fri, Nov 13, 2009 at 10:00 AM, Kevin Cowtan cow...@ysbl.york.ac.uk wrote:
Did
The Linux i386 version works on Fedora and Ubuntu. Not tried RHEL.
ftp://ftp.ccp4.ac.uk/ccp4/6.1.2/extras/Tcl-Tk++-linux-i386.tar.gz
Kevin Anderson wrote:
I'm not sure which package there you're referring to. I downloaded
the BLT source from http://blt.sourceforge.net . (It seems to finally
Hi,
I think the plates are Greiner bio-one plates. We use them on the
nanodrop crystallisation robot at PSB-EMBL (https://htxlab.embl.fr).
Will check with Jean-Luc Ferrer from IBS (if he has not gone home
already, it is late on a Friday...).
Fred.
Narayanan Ramasubbu wrote:
mb1pja wrote:
Vellieux Frederic wrote:
Hi,
I think the plates are Greiner bio-one plates. We use them on the
nanodrop crystallisation robot at PSB-EMBL (https://htxlab.embl.fr).
Will check with Jean-Luc Ferrer from IBS (if he has not gone home
already, it is late on a Friday...).
Fred.
And the plates
Narayanan Ramasubbu a écrit :
mb1pja wrote:
Dear Fred
A really nice video that would be great for giving
non-crystallographers (including colleagues and 1st year students, and
perhaps also friends and family) an overview of what we do. Thank you
for pointing it out - and of course very many
Thank you Dr. Sauter for making such an awesome movie. I am sure it will
be very valuable for teaching as well as for showing the general public
what we do. Definitely try to have the DVD ready for Christmas shopping...
Best regards,
christian
claude sauter wrote:
Narayanan Ramasubbu a écrit :
Dear all,
I have heard (really heard, nothing seen in print so far) about a
computer program called Biomatx (I think). Computer program that might
be used to search for structural motifs in amino acid sequences (here
might is in between quotes because I haven't seen anything in print, and
a
How about Laskowsky et al.
http://nar.oxfordjournals.org/cgi/reprint/33/suppl_2/W89?ijkey=0EJWHewQp1zaEeJkeytype=ref
http://www.ebi.ac.uk/thornton-srv/databases/ProFunc/
Jürgen
On Nov 13, 2009, at 12:39 PM, Vellieux Frederic wrote:
Dear all,
I have heard (really heard, nothing seen in print
I see.
While we're on the subject, I notice that imosflm has a convenient
environment variable for specifying the location of wish. Is there a
similar means of specifying the location of bltwish for ccp4, or am I
obliged to dump it in /usr/bin ?
-Kevin A.
On Fri, Nov 13, 2009 at 10:18 AM,
Just thought this will be of interest to all.
Subbu
---BeginMessage---
Narayanan Ramasubbu wrote:
Vellieux Frederic wrote:
Narayanan Ramasubbu wrote:
Hi:
Could someone point out the name and where to get these
crystallization plates used in the video?
By the way, this is a wonderful video.
Just one precision concerning the QIAGEN EasyXtal crystallisation plates:
there are 2 types,
one with white O rings (these were shown on the video) where there is
evaporation through the O ring as in greased hanging drop plates,
and one with black O rings, where there is far less evaporation
While we're on the subject, I notice that imosflm has a convenient
environment variable for specifying the location of wish. Is there a
similar means of specifying the location of bltwish for ccp4, or am I
obliged to dump it in /usr/bin ?
CCCP4I_TCLTK in include/ccp4.setup-[bash|csh].
On Fri, Nov 13, 2009 at 01:26:27PM -0600, Kevin Anderson wrote:
While we're on the subject, I notice that imosflm has a convenient
environment variable for specifying the location of wish. Is there a
similar means of specifying the location of bltwish for ccp4, or am I
obliged to dump it in
Howdy folks
I'm having an infuriating problem with an mtz file and sftools. I'm
sure this is an easy fix. Here's the situation: phaser gave me an
mtz and pdb file with bad cell information. It's I213, but the cell
is listed as
168.981 168.981 168.982
i.e. NOT cubic - this creates an error
Hi Matt
The problem may be that SFTOOLS is changing the wrong cell, because
different cells may be associated with dataset identifiers in the file.
You can convert the file to ASCII using mtztona4, edit all the cells you
see (DCELL and CELL) and convert back to MTZ using na4tomtz.
Cheers
-- Ian
Dear All,
About a year ago I made a short demo video, only intended to illustrate how
robotics
figure in drug target crystallography. It is biased and somewhat out of date
of course, but shows some nice crystal growth, harvesting and data
collection.
Material credits are at the end.
You may be able to open mtz files in a primitive text editor such as
nano (I just did). It's a little awkward, as there are no line breaks.
MTZ header is in the end of the file and it is plain text, so should be
easy to edit manually - just make sure you don't introduce extra space.
There are
On Nov 11, 2009, at 1:44 AM, Vellieux Frederic wrote:
but also shows what we crystallographers have known for a long time, since
the first colour ES graphics workstations in fact, that the electron are blue
That is the color of electrons dissolved in liquid ammonia (thus allowing the
viewer
Dear All,
following the twinning threads as well as the refmac manual it is
not quite clear to me yet whether refmac finds the twin operator and
fraction, detwins the data, and refines against those detwinned data,
or refines against the original twinned data like (I believe) phenix and
shelxl.
Dear All,
I received this from Bernhard Rupp. I thought that the bb should be consulted.
The only (small) thing I could do is to post this video on my Facebook profile
with a link to the Warren DeLano Memorial web site.
Fred.
Message du 13/11/09 23:44
De : Bernhard Rupp
A : 'Frederic
It is also the color of F-centers (electron holes) in crystals such as
Fluorite CaF2
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
William G. Scott
Sent: Friday, November 13, 2009 1:47 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] video
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