Hi,
In fact the problem was solved with the help of Ivica Dilovic from
Zagreb who suggested some changes to the shelxl .ins file. After these
modifications the cryptic error message was still there, but the
modifications made me try to remove one card. That did it.
So the part that is
Dear all,
Perhaps a reader of the bb will have a solution for this problem. ccp4
is version 8.0 and is up to date. All graphics programs (coot, but also
other non-ccp4 software such as chimeraX, Pymol...) run fine on the
Alma-Linux 9.3 system. There is a problem however with ccp4mg: the
Hi and thanks for the reply.
In case others on the bb face the same problem before july 2024, this is
what I can write about the process of migrating to a more recent Linux
distro:
"elevate-release", not "elevate-linux"... Poor memory of mine.
The debtakeover and debootstrap route failed
Hi,
Last time I needed to do this the most convenient for me was to use
Coot, with a very large coordinate file. Coot pre v1 (v0 something) to
read in coordinates in the mmcif format and write out coordinates in the
PDB format.
HTH,
Fred.
On 2022-04-19 14:01, Abhilasha Thakur wrote:
Hello,
I am posting this summary in case anyone else encounters the same
problem. Replies were received from David A. Case, Morpholino Peligro,
Arunabh Athreya, Tushar R. and Walker Olivier (through Adriana Miele).
The problem: how to get MD runs when you are not a specialist (first
time
Hello,
I think what you are alluding to is model bias in (macromolecular)
crystallography. What you should consult are the publications associated
with this topic, and those on the map coefficients used to compute
electron density maps (e.g. SIGMAA weighting), OMIT maps, current
refinement
Hello,
Which version of Phaser are you using ? As you must be aware, not all versions
of Phaser deal in the most appropriate manner with cases of translational NCS
if this is what you mean by pseudo translational symmetry. Personally I'd go
for the latest version of Phaser...
HTH,
Fred.
I'd google for Bart Hazes and SSBOND myself. There is (or was) a server,
and the publication is Prot. Eng. 1988, 119, 25 (PMID 3244694). The server
seems to be down or has moved.
HTH, Fred.
Message du 04/03/12 05:07
De : Naveed A Nadvi
A : CCP4BB@JISCMAIL.AC.UK
Copie à :
Objet :
Hi,
Your email mentions drop.
What about trying another technique where you do not have drops, such as the
liquid interface diffusion method (in capillaries), or the use of dialysis ?
Crystallisation
under oil (injection of the 2 components under oil) could also be tried.
Fred
Message du
Hi,
What you must deposit is what is present in the asymmetric unit of the crystal.
The HEADER cards (and the publication) can describe the most likely biological
assembly.
Why is that: there is no reason why the crystal should conform to the
biological function (and associated quaternary
P4(1) and P4(3) are enantiomorphic space groups. The only difference is the
helix (one way, or another). No difference in the diffraction pattern. Hence a
program (or a
crystallographer) cannot distinguish the 2 based on the diffraction pattern.
Once you start phasing, e.g. by molecular
Well you could have a monoclinic space group with beta = 90....0001, which
for everyone would mean 90.0 degrees. You could also have beta = exactly 90 by
pure chance. Normally the R-sym values should tell you which of the two
possibilities is the correct one.
If you obtain (an example)
Quoting you:
I wish to solve a monomeric protein in P21 where there are 2 monomers in
asymmetric unit.
How do you know that if you haven't solved the structure? Matthews coefficient
calculations?
Remember that the solvent content in protein crystal structures can go from ca.
15 % to ca. 85
Looks to me as if you have what we call ice rings, i.e. crystalline powder
diffraction. Plus what we call salt, i.e. strongly diffracting small molecule
crystal(s).
Fred.
Message du 20/02/11 14:47
De : Vandu Murugan
A : CCP4BB@JISCMAIL.AC.UK
Copie à :
Objet : [ccp4bb] Strage image
Hi,
I suggest that you check out the lanthanide compounds investigated by a number
of people including Richard Kahn. Papers can be found using the iucr web site
(and its search function). Commercially available.
Fred.
Message du 31/01/11 17:02
De : Jan Rashid Umar
A :
Hi,
How sure are you of the space group ? What are the data processing Rsym values
(which if high may indicate mis-indexing due to an incorrect choice of detector
origin for
example) ? There are many places where things can go wrong before reaching
the molecular replacement calculation
I can't see any problem switching from Refmac to Phenix refinement. You just
provide Phenix with the current model (if you have refined using TLS there is
an additional
step, using I believe tlsanl to generate the proper PDB file as you would for
data deposition with the pdb), the initial mtz
Hi,
In our hands, the crystallisation droplets of glycosomal pyruvate phosphate
dikinase had a 'skin' of what I thought was denatured protein at the surface of
every crystallisation droplet. We had to learn to use the crystal microtools
(such as a microknife, or a micro-needle can't remember
In CNS v1.2, you have the input file called model_fcalc.inp. So what I would
do is to generate these Fc's from the model, then insert them into an mtz
that contains your Fo's, and use SIGMAA to generate the Sigmaa figures of
merit. Or use another program to generate e.g. Sim weights.
HTH,
Bart Hazes wrote a program (and published as well, Hazes Dijkstra perhaps)
called SSBOND I think. I cannot remember exactly what the computer program
does, but it certainly has a data base of possible disulphide bond
conformers. Hence I would myself certainly check your second didulphide to
I am not sure that I understand your question perfectly... You can add/remove
waters automatically during refinement using the proper options. After
refinement, then
you can also (i.e. you should also) take the output mtz file and use a graphics
program (with PDB and MTW file) for modelling
Hi there,
The way to fix or freeze an entire section of a protein molecule will
depend on the refinement program used.
For example, in CNS, I would go to the = atom selection = section in the input
file(s) and change the parameters
there. You can fix atoms, or apply harmonic restraints.
Hi,
I never carry out grouped B-factor refinement at that resolution... Also you
(probably) will want to do TLS
refinement. I think that is not possible in the current (v1.2) CNS. Implemented
in Refmac and Phenix, I don't know
if it will be implemented in the upcoming CNS v1.3.
Fred.
Hi,
There are differences in the algorithm used by Phenix and (for example) Refmac
for the solvent treatment. These can
account for a 3 to 4 percent difference in Rfactor. I do not understand why
there is such a large discrepancy in
your case, unless you have for example a solvent model in
Received from Peter Zwart:
Message du 13/07/10 22:02
De : Peter Zwart
A : Frederic VELLIEUX , Pavel Afonine
Copie à :
Objet : Re: [ccp4bb] differences Rfactor calculations
Also, at such a high resolution you might want to do individual atomic
anisotropic temperature factor
Rsym is 0.6
I'd be seriously worried about this. An R-sym value of 0.6 in the entire
resolution range (I assume) means that your
reflection intensities do not match. This is the value of the Rsym I could
expect in the high resolution bin - in
the age of maximum likelihood refinement, not in
The rule is that the average isotropic temperature factor for your protein
atoms should not differ too wildly from the Wilson B-factor of the data set
(when you convert your anisotropic B's to isotropic B's). Otherwise there is no
such thing as an acceptable or unacceptable value, the value is
Which own web page??? I don't have an own web page from my internet
provider, there is one at work (not everyone
at work has a such web page, in my case dedicated to PX), in order to get
something added to that web page I have to
provide the material to the person in charge of the web pages
Could it be that for some reason (like the components of your solutions) you
have Mg2+ in that site? Also, Magnesium
is a common contaminant, trace amounts are usually present in one chemical or
another.
Subtle differences in the site might make it a better site for another
lighter ion (we
To reply to the original question, can the calculated Matthews coefficient be
wrong?:
have you read the paper by Matthews? There is a distribution of solvent content
in macromolecular (protein)
crystals. It has a peak and tails on both sides. Meaning that there are
outliers in the
Hi,
I suggest you check the following publication: Morales, R. et al. (2000),
Crystallographic studies of the interaction between the ferredoxin-NADP+
reductase and ferredoxin from the cyanobacterium Anabaena: looking for the
elusive ferredoxin molecule, Acta Cryst. D56, 1408-1412.
Here is
Hi,
I don't think you need a web server to do that. Jorge Navaza's program Amore (a
version of which is in CCP4) computes these for the search model and reorients
the search model according to these axes.
So you just need to run a fake molecular replacement calculation...
Fred.
Message du
Anisotropy in the diffraction pattern could simply be due to the shape of the
crystals. The intensity of diffraction is a function of the volume of
diffracting matter that is hit by the X-ray beam. Think for example of a thin
plate crystal, which you rotate in the X-ray beam. When the plate is
Holes in the diffraction pattern, to make it simple, means holes in the
electron density maps. So the resulting
electron density maps will be more noisy than electron density maps computed
with complete data sets.
It is possible to replace the missing amplitudes by non-random estimates during
Hi,
Padova: Giuseppe Zanotti and Paola Spadon (Universita degli studi di Padova);
Verona: Ugo Monaco (Universita degli studi di Verona, I think).
I don't think there is any protein crystallography in Venezia. If you go
further east, then there is Trieste...
Fred.
Message du 27/04/10 19:28
Hi Phil,
Indeed it does, both during integration (INTEGRATE, only if you ask for it
with the proper keyword) and in the post-refinement step (CORRECT). Normally
this should be quite sufficient. I haven't seen a single case where this was
not sufficient.
Fred.
Message du 25/04/10 09:55
De :
Hi Zhiyi,
There are two ways you can go about this (RT data collection). Either mount the
crystals in capillaries (not all beam lines at synchrotrons have sufficient
space on the goniometer setup to allow data collection on capillary-mounted
crystals) or use a Humidifier (the latter is briefly
Hi James,
Both Rsym and Rmerge are agreement factors. Rmerge is used in the case when you
have data from multiple crystals (because you are merging data coming from
these different crystals). Fairly unfrequent nowadays with the high flux beam
lines at SR sources. Otherwise what is quoted is an
Hi,
Replies to your specific queries are interspersed with your text below.
Message du 19/12/09 05:19
De : Jinzhong Lin
A : CCP4BB@JISCMAIL.AC.UK
Copie à :
Objet : [ccp4bb] merge data from multiple isomorphous crystals.
Dear all,
I have a crystal that can diffract to 3.0A for the
In fact, if you want the truth, what I now do is to download the sf.cif file,
use ccp4i to regenerate the MTZ (with the same Free R-factor flags that the
authors have used for structure refinement). Then feed that into Phenix for a
few rounds of positional and temperature factor refinement with
Ibrahim Moustafa wrote:
This will help to educate the non-crystallographers how to look at the
structures critically.
The first thing that a non-crystallographer should be aware of is the existence
of the temperature factors. It is a pity that the displays of biological
macromolecules on
Hi Rui,
I am at home so this is all from memory. In coot.
Use the control key (pressed down) to translate the map and get the center
point on top of your positive density (using the mouse at the same time, left
button I think). Do not hold cntrl any more to rotate the map by 90 degrees.
Cntrl
Dear Bulletin Board,
I received this information from Axel Bruenger, who rightly corrected me on the
modification to be made to the bindividual.inp file:
As an fyi, the sigmas should be made smaller to get a narrower B-factor
differences.
My previous post:
You modify the file
Hi,
Looks as if you want to do rigid body refinement 'a la CORELS'.
What about rigid body refinement in Phenix? From the Phenix manual:
If one have many rigid groups, a lot of typing in the command line may not be
convenient, so creating a parameter file rigid_body_selections, containing the
If the problem is B-factor refinement, you can do that easily at low resolution
with CNS. You just give tight restraints.
You modify the file bindividual.inp
This section:
{* target sigma values for restrained B-factor refinement *}
{* mainchain bonds *}
{===} bsig_main=1.5;
{* mainchain
Hi there,
2 things:
Are you sure that the relative orientations of your components are the same in
the different crystal forms? If you haven't done it already, it would be worth
while trying to search for the individual components as well (could be
difficult because your components are not so
Dear All,
For those of you who may worry about the future and future availability of
PyMol, this is the information I have received from Elizabeth Pehrson (Warren's
wife, DeLano Scientific LLC):
I would like to reassure all who fear for PyMOL's future that DeLano
Scientific still exists, we
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 Boltzmann
distribution)
through to
It it Inès Kahlaoui and Dominique Sauter who should be thanked. The first one
(Inès) located this jewel and was kind enough to inform me. The second person
(Dominique) directed the movie. My (small) contribution was to realise how
important this movie was.
Fred.
Message du 14/11/09 23:21
De
Dear all,
I have received this from Axel. I did not see the [ccp4bb] tag on it, so I pass
it on. I think that this is important, since Warren has done so much for us
all. I'll see how I can contribute (I hope it is easily done from abroad).
Fred.
Message du 15/11/09 01:09
De : Axel Brunger
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
in the credits? It just shows how ubiquitous his
program was.
Best, BR
From: Frederic VELLIEUX [mailto:frederic.velli...@orange.fr]
Sent: Friday, November 13, 2009 2:01 PM
To: b...@ruppweb.org
Subject: Re: [ccp4bb] video that explains, very simply, what Structural
Molecular
Sorry if this is a bit off topic. But I have found it useful. Members of the
ccp4bb might be interested in the biomedexperts network ( www.biomedexperts.com
). Once you join (as professionals of biomed science who have already
published) you have a homepage that gives you recent publications of
Sorry about starting a new thread (this is not a new thread in fact but I
mistakenly erased all the relevant ccp4bb messages).
for dogfish LDH and binding of cofactor fragments see J Mol Biol. 1973 Jun
5;76(4):503-518.
Fred.
Hello there,
Don't you have extinctions along the axes allowing you to distinguish between
the possible space groups? Or are the reflections along the reciprocal axes
missing from the data set you have collected? Normally this is how one decides
on the space group in orthorhombic 222, by
Hi,
One I remember (did my Ph.D. on it at the end of the 80s under the supervision
of J. Drenth W. Hol) is quinoprotein methylamine dehydrogenase. Also, the
old yellow enzyme, photoactive yellow protein and I am sure there are plenty
others.
Fred.
Message du 21/10/09 02:25
De : Artem
Hi again,
If you are certain about your NCS operators (well refined operators) and about
your envelopes, then why don't you forget about solvent flipping gamma
perturbation and phase combination? Just use the experimental phases once (to
compute the initial electron density maps) and throw
In fact the stats will be exactly the same: the only difference between P222
and P212121 are the extinctions along the a* b* and c* axes.
Given that you have thousands of reflections that are not extinct and only a
few that are, the stats will be the same.
Fred.
Message du 15/10/09 22:43
De
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