Hi Dirk,
When it happens that I reply to a ccp4bb message and that the answer, or
solution I may have (which I think is better or more appropriate)
involves using non-ccp4 programs, I do it off-list. By replying
privately to the person who asked the question.
Fred.
Dirk Kostrewa wrote:
James Stroud wrote:
1. Gee, I thought that it was specified to be case sensitive.
2. Well, someone once told me that it was specified to be
case insensitive but I can't remember who that was.
3. I thought it was specified to be something too but
most programs largely ignore
Salve Claudia,
Glycerol is not the only cryo-protectant that is available. Have you
tried with ethylene glycol for example?
HTH (spero che aiuta),
Fred.
Claudia Scotti wrote:
Dear list,
I'm trying to freeze crystals in cryoconditions containing the following:
0.1 M Sodium acetate pH
Hi Katja,
What I personally do in such a situation is to start to fill the density
by water oxygen atoms, refine a bit (the position plus the isotropic
temperature factors) and then compute a new map. Usually it has cleared
up somewhat, thus allowing you to find out what it really is. This is
Dear John Campbell (not you, the real John Campbell whom I know and who
would never do such a thing as to send SPAM, the other John Campbell),
Thank you very much for your kind offer. May I suggest that you fly to
Haiti immediately and offer these commodities there at once, for free?
They are
somnath mukherjee wrote:
Dear All,
Happy new year!
I have a small query.
I have a substrate bound structure of my protein and I presume that I
want to connect the Sulphur atom of catalytically active Cys151 with
the 1st carbon atom of the substrate.
How can I make it in Coot?
Thanks in
Nothing wrong with that approach in principle. You may want to have a
few cycles of rigid body refinement before classical refinement. Just in
case (but the cell parameters are very very close indeed). And the
starting Rfactors should tell you if there is a problem or not.
Fred.
Jane Bailey
Hi Martyn,
When it comes to micro-dialysis, you could check the following paper:
http://www.jbc.org/content/260/25/13580.full.pdf+html
(freely available, check in particular the appendix for the
micro-dialysis setup that was used, that was for heat-labile enterotoxin)
Fred.
PS I know this
I would try placing waters in the positive difference Fourier peaks
(waters could make hydrogen bonds, if you follow the standard colour
coding for the atoms), refine and see how the density looks like then.
Kadhirvel Saraboji wrote:
Hi all,
In one of my 1.6Ang resolution structure, I came
Hi all,
Like everyone else, I was appalled.
My two cents worth: Nature and Science are not scientific journals in
the strict sense of the term. They are more like magazines (I won't go
all the way to say tabloids), and as such will do anything to publish
what seems to be hot. And will reject
Dear Subbu,
One more thing you can do is to search with an ensemble of structures (4
in your case) for molecular replacement.
Fred.
Narayanan Ramasubbu wrote:
Deal All:
I have a 2.0 A data for a SeMet protein (native crystal not available
yet!) that has 6 Se sites.
The cell comes out to be
Dear bb,
I have received the following information concerning the Warren L.
DeLano memorial fund:
Our estimate is that we're about half-way to our stated goal of
$100,000 to create a permanent endowment
So, with the end-of-the-year season fast approaching, when people tend
to be more
Simon Kolstoe wrote:
Hi,
I have 20 identical monomers in my asu of a 2.5A structure. We have
previously model built all twenty monomers and used strict NCS in the
refinement, however I would like to compare this with the maps
generated by building one monomer into an averaged map and then
Dear ccp4bb,
I learned that there is a prize for the best page made on the
Wikipedia-style encyclopedia of biological macromolecular structures
Proteopedia ( http://www.proteopedia.org ). For pages made before Dec 31
this year. The prize is a 32Gbyte IPod Touch. What I have done myself
(not
Forgot to hit the Reply all button (sorry :-( )
---BeginMessage---
Katja Schleider wrote:
Hi everybody,
sorry for my off-topic question. I got small initial crystals in 200mM
NaSulfat and 20% PEG 3350.
There is no buffer in this condition. How can I optimize these
crystals? Just vary the PEG
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
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.
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
sure it will prove very popular.
bet wishes
Pete
(Pete Artymiuk)
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
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
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
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 locates videos on the
internet, which she then downloads and uses for teaching). Ines located
this jewel:
Matthias Zebisch wrote:
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, sulfate in already phased
Miguel Ortiz Lombardia wrote:
Of course, as Fred said, the precission of the measurements is
extremely important for sulfur-SAD phasing.
What I was really meaning is the combination of i) accuracy and ii)
sufficient redundancy. Not too much, in your case, as you rightly say in
your mail.
Dear subscribers,
I was having a small problem with a program (compiled with gfortran)
that gave me run time errors when writing to a direct access file.
Fortran runtime error: Record number not allowed for sequential access
data transfer. And I could not figure out why.
So I wrote a
Well, I did hear from the gfortran people... Immediately after I sent my
message to the bb.
So sorry about the post (the error had never occurred on all previous
compilers).
Fred.
---BeginMessage---
On Mon, Nov 02, 2009 at 05:58:09PM +0100, Vellieux Frederic wrote:
Dear gfortran developers
I can suggest 2 things:
look for the work by Janet Thornton et alteri, they have analysed loops
(and classified them) in protein structures so that they might have
loop modelling tools;
also Gert Vriend's program WHATIF might have something along those
lines... I think the program still
Hi Fabien,
Quinoprotein methanol dehydrogenase was supposed to contain only one
subunit when it was discovered.
Then 3D structure determination indicated the presence of a second,
small subunit.
See Nunn, Day Anthony, Biochem J. 1989 June 15; 260(3): 857–862.
Perhaps this is relevant.
Hi Yuan,
I think you cannot merge the 2 data sets if the space group is indeed
P21. If you have systematic extinctions along the b* axis both on the
data set with b=87.085 and with b=79.857 then the crystals are simply
different.
Fred.
Yuan Cheng wrote:
The problem is one dataset has cell
You can do it easily in coot:
display your objects.
Then display the symmetry (draw, cell symmetry) with a large enough
radius.
Then File: save symmetry coordinates, click on one atom of one of the
equivalent copies you're interested in.
You have to repeat the process several times. It
Michael Rossmann and colleagues did some work on the binding of
fragments of cofactors to dogfish lactate dehydrogenase. In the 70's I
think. Can be found on google scholar. Perhaps that's what you are
after? Can't find the reference right now (it's in one of my drawers but
I don't know which
Dear Sylvia,
The discrepancy is only 8% and that is acceptable (you may be able to
get the Rfree lower by changing the refinement program for the ultimate
rounds of refinement, or by using TLS refinement if you don't do that
already --- you don't mention what refinement program you are
To properly omit reflections from the Rfree calculations can be done
using reciprocal space masks as implemented in the program WEIGHTS from
the DEMON/ANGEL program suite (Vellieux, Hunt, Roy Read [1995], J.
Appl. Cryst. 28, 347-351). I don't have the time to do it. But people
are welcome to
Hi there,
Would there be a kind soul that could pass this message on to cnsbb? I
am registered with e-mail address velli...@ibs.fr but the e-mail address
has changed to frederic.velli...@ibs.fr 12 months ago perhaps. I am not
very good at all these e-mail diffusion lists and cannot see how to
Hi Paul,
I am now running Coot (latest stable version from yesterday,
coot-0.6-pre-1-revision-2415) this time on another molecule (a 12-mer
with many many atoms in the asymmetric unit, like a small virus, that
was refined with CNS) and this time I have no problems real-space
refining. I
Paul Emsley wrote:
Hmm... I have not heard of such a thing before.
There must be something with the coordinate file.
That would be my guess too. From what you sent (I didn't see the
results of you trying to refine something), it has the symptoms of the
residue names not matching anything
restraints. Restarting coot
from scratch helped, though. I've never seen this happen before. I don't
think it has anything to do with refmac because I do refinement in phenix.
Katya
On Fri, Oct 16, 2009 at 5:28 AM, Vellieux Frederic frederic.velli...@ibs.fr
wrote:
Paul Emsley wrote:
Hmm... I
Dear all,
I just installed on my box the latest binary for coot. Just marvelous
(thanks Paul).
I am having a little problem with it that is annoying me (I went through
the FAQ but could not find the answer). Coot does not allow me to insert
a terminal residue nor to real-space refine (I
Dear all,
I have a structure (2.25 A resolution) that was refined with CNS and I'm
trying to see if I can improve it ever so slightly using Refmac5.
The structure has 31408 atoms in the asymmetric unit.
The run of Refmac ends with the following lines:
WARNING : link:SS is found dist =
I don't think this has been placed on the bb yet. Please do not reply to me.
From: Liviu Movileanu [mailto:lmovi...@physics.syr.edu]
Sent: Sun 11-Oct-09 20:16
Subject: openings/request for help
Dear colleague:
I am trying to fill a couple of postdoctoral positions in the area of
Sometimes it is better that it takes time for crystals to appear.
Remember that crystallisation is a purification procedure. A way to
decrease the speed of crystallisation is to use Dunlop's and Haze's drop
dilution method (K. V. Dunlop B. Hazes (2003). When less is more: a
more efficient
---BeginMessage---
NCS. I don't think REFMAC can handle yet NCS (help me there Garib). CNS
FYI there's documentation for NCS options in REFMAC, although I haven't
actually used them yet (haven't been lucky enough to have NCS in my
structures).
Pete
---End Message---
attachment:
Dear all,
Sorry if this is a bit off-topic. But it concerns science.
There is a new initiative to launch a free TV channel in France
dedicated to science technology and innovation. They need support from
scientists I think. Can you spare 2 minutes? http://www.leonardtv.fr/ .
This is perhaps
Me again,
I've been asked privately what the leonardtv people are looking for.
I'll translate the letter I received from them and post it on the bb.
Btw, leonardtv is named after Leonardo da Vinci.
Hope all is well with all of you.
Fred.
Vellieux Frederic wrote:
Dear all,
Sorry
Dear Subscribers,
Here is the translation of the letter I received (as attached text
file). It was created from home on a Windows computer and saved in ANSI
format (don't know what ANSI format is but I can read it on my Linux
box). I did my best, knowing that the French write very long
Hi, thanks for your message. We have only progressed (we=mankind)
through knowledge, science and research. Not forgetting the humanities
of course. So if we don't do anything to stop this trend we're dead.
Fred.
b...@freesurf.fr wrote:
We all love science Fred, but are you sure you would
Hi again (I fell out of bed this morning).
Yoel Sussman advised me to look into Proteopedia (
http://www.proteopedia.org ) as a way to explain to students, scientists
and lay people what we (structural molecular biologists) do.
I never had the time to check that site before. But I did last
Perhaps you should tell us a bit more on refinement. What program, how
many reflections to refine against, how many atoms to refine, is there
any NCS that can be used as a constraint or restraint etc. This would
allow us to give you advice.
Fred.
Vandana Kukshal wrote:
hi
i am solving one
v_kuks...@cdri.res.in wrote:
number of atoms are 5113
and there are 2 chains
Now, you have 20215 reflections used as a target to refine against (I
assume this number does not include the Rfree reflections). You have
5113 atoms to refine, and you refine X Y Z B-iso (4 parameters per
atoms).
Dear fellow crystallographers,
(nice work on the ribosome, and this award is going to be good for our
science)
We have the following problem when running truncate:
FORMATTED OLD file opened on unit 45
Logical name: ATOMSF, Filename: /work/prog/ccp4/lib/data/atomsf.lib
TRUNCATE:
and H and retrieves their formfactors from ATOMSF.lib.
Has the H labelling been changed somewhere?
Eleanor
Vellieux Frederic wrote:
Dear fellow crystallographers,
(nice work on the ribosome, and this award is going to be good for
our science)
We have the following problem when running
your own,
what system and compiler.
Charles Ballard
CCP4
-Original Message-
From: CCP4 bulletin board on behalf of Vellieux Frederic
Sent: Wed 10/7/2009 2:24 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] problem with truncate
Dear Eleanor,
Hope all is well with you
- I guess it is a later version of truncate?
Vellieux Frederic wrote:
Dear Eleanor,
Thanks for taking a look at the data. The mtz file is still v4.2.2
(my own programs read that library and I only convert to the latest
MTZ definition once I have used my software --- I have no time to
keep up
Hi folks, hope all is well with you on this sunny day (well it is sunny
over here!)
I am trying to recompile some code on a machine that does not have the
ifc compiler installed. (The code did compile w/o problems on another
computer that has ifc). It all works fine except for one program
Dear subscribers to the CCP4BB,
On my previous computer, I had in my bookmarks (Firefox bookmarks) the
URL for an automatic 3D structure superposition server based some place
in Canada. Unfortunately that computer crashed and I lost all my bookmarks.
What was nice was that one could simply
for Tcoffee or EBI SSM, same functionality
Jürgen
On Sep 4, 2009, at 9:40 AM, Vellieux Frederic wrote:
Dear subscribers to the CCP4BB,
On my previous computer, I had in my bookmarks (Firefox bookmarks) the
URL for an automatic 3D structure superposition server based some place
in Canada
Hello all,
Until now I was using coot on my Linux box without problems.
Now I have a new structure (molecular replacement) that I try to mutate
to the correct sequence.
Coot crashes with the following error message:
Gtk-WARNING **: Failed to load module libgnomebreakpad.so:
Goettingen
GPG Key ID = A46BEE1A
On Mon, 2 Mar 2009, Vellieux Frederic wrote:
Hello all,
Until now I was using coot on my Linux box without problems.
Now I have a new structure (molecular replacement) that I try to
mutate to the correct sequence.
Coot crashes with the following error
Dear Colleagues,
I am looking for a program (if there is one...) that would allow to list
all interactions at a dimer interface (polar, ie hydrogen bonds and salt
bridges, and non polar).
Thanks in advance for your replies.
Best regards,
Fred.
begin:vcard
fn:Fred. Vellieux (Ph.D)
We've had lots of success with the additive screens (3 boxes of 24
additives) sold by Hampton Research
Vincenzo Carbone wrote:
Dear all,
I was wondering if anyone had some practical advice in regards to
increasing the size of a crystal. Currently my enzyme forms these
rather nice cubic
inserted residues at the end of the
PDB, so you miss it's there already.
HTH,
Mark.
On 30 May 2008, at 09:33, Vellieux Frederic wrote:
Dear All,
I haven't subscribed to the coot bb and hence thought I could get an
answer from this bb.
We cannot use the option Add Terminal Residue for the very
Dear all,
I am looking for some software (computer program) that would take a full
PDB file (including waters) and that would output a list of the water
networks (including the names of the atoms) at the surface of a protein.
Thank you in advance,
Fred.
begin:vcard
fn:Fred. Vellieux (Ph.D)
For HEW lysozyme: precipitant is 2 to 6 % (w/v) NaCl in 0.2 M Na acetate
pH 4.7 (the recommended procedure is to prepare a stock solution of 10%
NaCl). For the derivative, use para-chloro mercuri benzene sulphonic
acid. In 15 ml of the above stock solution, dissolve 0.123g of PCMBS.
Then use
Dear all,
What is the currently accepted view on the percentage of residues in
disallowed regions of the Ramachandran plot (for publication purposes) ?
This is because I have a structure where there are several stretches of
not so well defined density. As a consequence there are about 5% of
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