Hi,
I think this practice (requesting the data) is getting more and more
common these days with some scientists having published fake
structures. You are far more protected from scientific misconduct when
you provide the data to referees (this takes place through an editorial
system - you
Hi,
If you have the correct solution, clashes may be due to loops. It may be
an idea to clip these off for the molecular replacement calculations
(loops might be shorter in the structure-to-be-solved than in the search
model, they may have different conformations in the
Hi there,
I am not certain that the thread is P321 space group reindex problem
any more.
But: trigonal (and hexagonal) space groups are (usually?) polar. The
cell axis c can go up or can go down, and in order to get a
consistent indexing you need to check both indexing systems when you
:55, Vellieux Frederic frederic.velli...@ibs.fr wrote:
Hi there,
But: trigonal (and hexagonal) space groups are (usually?) polar. The cell
axis c can go up or can go down, and in order to get a consistent
indexing you need to check both indexing systems when you scale additional
data
Hi Lisa, hi all,
Please do not discard the alternative method(s) of conventional heavy
atoms. Co-crystallisation or heavy-atom containing mother liquor soaks.
You may remember that monster complexes have been solved in the past
by such methods, and sometimes there are difficulties in
Dear colleagues,
Information just received here through the AFC channels: the UN general
assembly has declared that 2014 will be the international year of
crystallography.
Their statement (in French) as an attachment (sorry about including an
attachment).
F. Vellieux
IYCr-FR.pdf
The press release in English:
http://www.un.org/News/Press/docs/2012/ga11262.doc.htm
Boaz: perhaps the crystallography congresses and events taking place in
2014 will be attended by UN peacekeeping force members as well (with
their blue helmets) ?
F.V.
Boaz Shaanan wrote:
Et alors, what
Do you mean we should crush the helmets and solve the structure of the
resulting powder blue coloured powder by crystallographic methods ?
Sounds like a good proposal to be put forward to the UN to help them get
rid of their used helmets !
David Schuller wrote:
On 07/04/12 08:03, Vellieux
Hi there,
Not much information provided. How was the initial model refined ?
Phenix ? It could be a problem with the Refmac refinement protocol
(difficult to say with so little information) if you switched from
Phenix to Refmac.
How certain are you 1 - of the space group; 2 - that the
Hi all,
Just a (naive?) question: how does one manage to introduce (and deal
with) improper non-crystallographic symmetry in DM ? Or does one has to
go to DMmulti for that (because, by definition, going from one crystal
form to another crystal form is improper NCS) ?
Ta,
F. Vellieux
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
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,
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)
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
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
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)
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
Hi Paul,
I've seen that type of behaviour before for low resolution structures.
On such structures,
either I have a very hard time getting at the same time a good geometry,
good R-factors and satisfactory electron density,
or things go very smoothly and all the statistics (model geometry,
Hi Andy,
I'd say fairly common, and there can be several reasons. One is that the
entrance of the active site (in case of crystal soaks) is blocked in
some subunits. Also, different affinities in the different active sites,
plus allosteric effects, are possibilities to consider.
The latest
Hi Christian,
Had exactly the same problem (converting an mmCIF file into a PDB). I
located and installed CIFTr . The version I have running here is
ciftr-v2.053 . I am afraid I can't remember exactly where I downloaded
it from. I think it one of the PDB associated files.
Fred.
Christian
This has been told (written, in fact) on this bb many times. The purpose
of refinement is not to bring the R-factor down, but to obtain a model
that satisfies best all available data (including biochemical data).
Anyway, as to what you can do: it's always possible to question the
choice of
There is an option in Phenix to generate the necessary cif file for
Phenix refinement. But that's a Phenix file, not a REFMAC file (I think,
I never tried taking the cif file generated by Phenix to use it in
REFMAC). As an example, I am enclosing a cif file that was generated by
Phenix for
Received from Peter Zwart:
Original Message
Subject:Re: [ccp4bb] creating new ligand cif file
Date: Mon, 21 Jun 2010 07:08:18 -0700
From: Peter Zwart phzw...@lbl.gov
To: Vellieux Frederic frederic.velli...@ibs.fr
References: 4c1f4f26.2070...@ibs.fr
R.Srinivasan wrote:
Dear All,
I have got initial crystals in a condition with PEG 1000. The
PEG 1000 stock we had in our lab was rock solid and when i heated it
to about 50 degrees for 15 to 20 minutes it became a solution. We
thought the compound has got out dated or something like
Hi there,
If there are a few clashes (acceptable - usually surface loops that
enter the surface part of another molecule or subunit) then you can
delete the parts of loops that usually have poor density and that clash,
refine, compute a new map and see if the loop can be traced (usually it
Dear all,
I think we all think that macromolecular structures are the best there
is... And now we have a chance to prove it to the world.
The Scientist is organizing a competition to elect the best website.
One of the competitors is the Proteopedia web site
(http://www.proteopedia.org).
Hi,
No such thing as a stupid question. If the resolution is sufficient,
arp_warp does a good job. But it is a reconstruction and REFINEMENT
program. But checking the proper packing (that there are indeed contacts
in the 3 dimensions of space to form the crystal): takes only 10 seconds
using
Dear all,
An obituary for Prof. Lodovico Riva di Sanseverino (in English, written
by Prof. Carlo Mealli) can be found on
http://www.cristallografia.org/uploaded/181.pdf
(www.cristallografia.org is the web site of the Italian Crystallographic
Association, Associazione Italiana di
Dear all,
A tribute to Lodovico (pictures + letters + a song) can be found on
http://www.crystalerice.org/Erice2010/Lodovico/index.htm
Fred.
Vandu Murugan wrote:
Dear all,
I have collected a 2.7 angstrom home source data with Cu-Kalpha
source for a protein with 6 cysteines, with a multiplicity of around
23. I need to know, is there any significant anamolous signal present
in the data set, since there is no good model for my
Petr Kolenko wrote:
Dear all,
I am working on crystallization of a protein purified using
intein-chitin binding domain. There is 86% identity with protein with
already known high-resolution structure, but I am not able to get any
crystals. I heard that reversed phase chromatography is not
Hi Hui,
I think most of us can't do much with rar archive files.
This is a Windows thing I believe and my Linux system tells me
Archive type not supported...
Fred.
hui yang wrote:
Hi all,
I just collected a data set from a long-spindle-shaped crystal. The
data has been scaled to P1
Hi,
If you do not know anything about peptidase (protease) classification,
I'd suggest you have a look first at the Merops peptidase data base:
http://merops.sanger.ac.uk/
Will tell you what (type of) classes there are, for example (and based
on what).
Fred.
Gowriishankar Raju wrote:
Hi,
Can't rotate the picture so that I can't see the distance between the
nitrogen and the green blob.
The green blob is elongated. Sometimes what happens is that you can have
2 waters (partial occupancies), in some unit cells in your crystals the
water occupies site 1, in the other unit
News just received from the French Crystallographic Association (and
thus forwarded to ccp4bb):
The fifth Max Perutz Prize of the European Crystallographic Association
goes to to Professor Claude Lecomte from Nancy Université and CNRS, France.
Claude Lecomte is recognised for his
Hi,
I think the MAXCHN errors has been fixed in recent versions of CNS.
You must be using CNS v1.0 or v1.1.
So either you download and install a recent version (the latest is
v1.3), or you do as the error message suggests: you edit your anneal.inp
file, you locate MAXCHN= or MAXCHN = (or
Vandana Kukshal wrote:
hello sir ,
recently i have collected one data of 3.0 A of a protein having no
sequence homology with any known PDB .
but
while fold prediction i got 100 % identical fold with some of the
protein .
space group of my protein is P622 and showing 6 molecule in a
Non-symmetric tetramers: you can check out Tete-Favier et al (1993),
Acta Cryst. D49, 246: the quaternary structure was assumed to have local
222 symmetry. It turned out this was not exactly the case: the actual
symmetry of the object (the molecule) was pseudo 2t2t2t. So in
addition to 2-fold
Hi,
To quote you: even my P222 experimental envelop does have a 4-fold
axis - this is not suprising, a particle with 222 symmetry does not
have 4-fold symmetry. There are 3 mutually perpendicular 2-fold axes
that intersect at the origin (of the particle, of the molecule) [and
for the
Hi,
You take the output mtz from the refinement program (let's assume it's
called refine_1.mtz).
Command line mode:
sftools
read refine_1.mtz col 1 2 3 4 # assuming the mtz contains H K L 2FOFCWT
PHI2FOFCWT FOFCWT PHI2FOFCWT
cal col 3FO2FCWT col 1 col 3 +
set types
F
P
F
P
R F
write
AM, Vellieux Frederic
frederic.velli...@ibs.fr wrote:
Hi,
You take the output mtz from the refinement program (let's assume it's
called refine_1.mtz).
Command line mode:
sftools
read refine_1.mtz col 1 2 3 4 # assuming the mtz contains H K L 2FOFCWT
PHI2FOFCWT FOFCWT PHI2FOFCWT
cal col 3FO2FCWT
I would like to know the accuracy (error) of the position of the
coordinates
This is provided by the output of the refinement software.
An example (CNS-refined structure, from the pdb header, there is an
input file called xtal_pdbsubmission.inp
REMARK 3 ESTIMATED COORDINATE ERROR.
To: Vellieux Frederic frederic.velli...@ibs.fr
References: 4c57c841.2080...@ibs.fr
Dear Fred,
I think the Cruickshank Diffraction Precision Index and its specific
reformulation by David Blow are a better estimate of overall coordinate
errors.
These two papers are in Acta D.
Greetings
anna delprato wrote:
Hello All;
I've just started using XDS and have scaled three data sets from the
same crystal - unmerged. It was a SAD experiment
My question is concerning which R values to use as data processing
statistics. I don't find any Rsymm or even Redundancy values in the
LP
Hussain Bhukyagps wrote:
Dear all,
i want to know that how can we find Rmerge from the refinements done
in CNS..??
Hi,
I think you have the terminology wrong: Rmerge (or Rsym nowadays when
most diffraction data is recorded from a single crystal) is provided by
the data frame diffraction
POST-DOCTORAL POSITION
DATE OF AVAILABILITY : starting as soon as possible, for 2 years (ANR
contract).
TITLE : purification and crystallization of ABC transporters
POSITION: the position is opened at the Institute for Structural Biology
(IBS) in Grenoble in the team of Jean-Michel Jault
Dear ccp4bb subscribers,
I have just learned that Proteopedia (the wikipedia-style encyclopedia
of macromolecular structures) has been voted winner in this year's
competition organized by the Scientist ( http://www.the-scientist.com/
, readers and judges choice).
So thanks to all who voted,
Dear all,
Giuseppe Zaccai showed me an interesting article about science funding
(from F.T.). I thought it could be of interest to all of us since we
have to apply for funding, and succeeding in securing funds is getting
more difficult all the time.
The scan of the article can be found on:
What you could try to do is print out the pdf file, then locate a
scanner with a suitable scanning software. Several scanning software
have the possibility of generating word processing program output or
ASCII format. Since the pdf file is text only (no figures etc) then it
should be OK. You
ccp4i
Reflection Data Utilities
Convert to/modify/extend MTZ
Input reflection file is in XPLOR/CNS format etc
Fortran format (7X,3I5,6X,E12.4,7X,E12.4,6X,I2) Skip first 6 lines (if
# is part of the .cv file)
[I think, I have counted the space before the INDEx for example giving
me
Another possibility is with sftools, set spacegroup option
Fred.
PS not in ccp4i
Graeme Winter wrote:
Hi Tim,
Is it as easy as
reindex hklin a.mtz hklout b.mtz eof
symm P43212
eof
This will simply (and correctly) reassign the symmetry operations. Is
this what you meant?
Best wishes,
Hi,
I did a little bit of modeling in your density (starting from a
nicotinamide ring, the positioned nicotinamide is enclosed). The middle
part looks suspiciously like a 6 membered ring. Could it be a molecule
in a half-chair conformation? There is only the blob that is
perpendicular to the
Hi,
Frankly, any vendor or assembler of PC's will do. Things to make sure to
have on your PC: an NVIDIA graphics board in order to get nice graphics
(their Linux drivers are fine; I don't know their current range of
boards, here we buy middle-range boards, not the cheapest ones that are
Rex Palmer wrote:
Can anyone reccomend a free download program that will calculate the
energy of a protein/ligand complex? The ligand has been modelled in.
Thanks
Rex Palmer
Birkeck College
Hi Rex,
I think any refinement program such as CNS will do this - problem is,
since these programs
I second that. Incorrect space group assignment usually causes this
behaviour of having R and R-free stuck at very high values. It is useful
to go back to the data processing stage and carefully consider all
Bravais lattices (and associated space groups) that the autoindexing
routine finds
Hi,
For questions relating to a specific package (if it is in rpm format, I
don't know what the Uuntu installation software uses as packages), you
can use the rpm search web site http://rpm.pbone.net/ (in addition to
http://www.rpmfind.net/ , can't search in rpmfind.net at the moment, it
I do not know if that's really cynical: I've had the case of a referee
recommending manuscript rejection because the title of the manuscript
was not appropriate. The editor followed the advice of the referee. A
proper refereeing job would have been to suggest that the authors change
the title
I can direct you to PDB entry 1EWY, where the average isotropic
temperature factor for the major component of the complex is ca. 47 A**2
and that for the smaller component is ca. 69 A**2. Similar values than
the ones you are reporting. I am assuming some sort of disorder, or if
you prefer,
Hi,
I agree with what has been mentioned about fuzzy spots. But what seems
obvious as well is that the resolution for spot picking should be
limited (to 3.5 or 4 A resolution). It is difficult to judge from an
image of a diffraction pattern, but it seems to me from this image that
the spots
Muhammed bashir Khan wrote:
Dear All;
I have structures of two protein one full-length while the other truncated
at the c-terminus(one from prokaryote while the other from eukaryotes).
Now I want to do the sequence alignment of these two proteins from all
species in such a way that the
Hi Petr,
Usually IDXREF suggests more than one Bravais lattice that is consistent
with your diffraction images;
hence it is (sometimes) worthwhile trying to INTEGRATE in all possible
Bravais lattices and this allows you to eliminate a number of
possibilities (poor profiles during integration,
Hi,
Last couple of times I asked myself the same question (what does it
look like?) I used ssm (or PDBeFold as seems to be called now).
http://www.ebi.ac.uk/msd-srv/ssm/
HTH,
Fred.
Liu Zhao wrote:
The structure of my protein is as shown as the purple one. Another one
,as shown as
James Stroud wrote:
On Dec 20, 2010, at 1:53 PM, Jacob Keller wrote:
what is the .odp file extension?
http://tinyurl.com/mjokqs
A .odp file is an open document presentation. It is the open version
of a power point presentation.
http://en.wikipedia.org/wiki/OpenDocument
An .odp
Before re-inventing the wheel...
Is there anywhere some software (freely available software, I mean) that
can add some Gaussian noise to data. The data is currently stored in a
data column in an mtz (not phase data, but amplitudes, sigma
values...) but can be exported to another format if
Fsimulated which contains the value
of column Fcalc plus 10 times a random number from a Gaussian
distribution with average = 0 and variance = 1
Cheers
-- Ian
On Fri, Feb 4, 2011 at 12:40 PM, Vellieux Frederic
frederic.velli...@ibs.fr wrote:
Before re-inventing the wheel
Hi Rex,
There will be small differences in particular due to the different ways
of treating the solvent. How large of a difference are you talking
about? Normally the difference should not be very large... And if this
related to solvent effects, it will affect the low resolution
reflections
Ting-Wei Jiang wrote:
Dear experts,
Sorry for a simple question but confusing me so much!
Does it make bad effects on determining the number of identical
molecules in ASU by choosing low symmetry space group.
For example,If I choose lowest symmetry(p4) instead of higher
one(p43212).
Does
The molecular replacement program does not know about your molecule
being a single polypeptide chain. The problem is fit two bodies
therefore the program fits two bodies. The centre of mass of whatever
you wish to position is placed the standard asymmetric unit used by
the program. If it
Hi Careina,
Just an example of a pir file which I just generated (using Bart Hazes
program mcfman):
P1;MALDH_
Just a title
TKVSVVGAAGTVGAAAGYNIALDIADEVVFVDIPDKEDDTVGQAADTNHGIAYDSNTRVR
QGGYEDTAGSDVVVITAGIPRQPGQTRIDLAGDNAPIMEDIQSSLDEHNDDYISLTTSNP
Judith Reeks wrote:
Dear All,
I am currently refining a structure using the latest experimental
version of Refmac (5.6) and there seems to be a problem with my Fo-Fc
map. There is a region where I have fitted residues to the electron
density but after refinement there is still positive
Hi,
A Laue diffraction pattern is a diffraction pattern recorded using
polychromatic (white) radiation. Hence the beam line optics is for
focusing the radiation onto the sample (the crystal) but not to select a
single wavelength (a monochromator). Just to make it simple to understand.
For myself, I decide on the high resolution cutoff by looking at the
Rsym vs resolution curve. The curve rises, and for all data sets I have
processed (so far) there is a break in the curve and the curve shoots
up. To near vertical. This inflexion point is where I decide to place
the high
Hi,
I don't think XDS generates an Rpim value, does it? The XDS CORRECT
strep provides the old fashioned Rsym (R-FACTOR) plus R-meas and Rmrgd-F.
The curves look all the same though
Fred.
Ed Pozharski wrote:
On Thu, 2011-03-03 at 16:02 +0100, Vellieux Frederic wrote:
For myself, I
Hi,
There's a whole bunch of programs that can help you out there.
The 2 methods I think of right now are DISPROT (there's a server I
believe, http://www.ist.temple.edu/disprot/ ) - Must admit I haven't
been to that one for quite a while; DISPROT provides areas of your
sequence with high
Afshan Begum wrote:
Dear All,
I have a severe prob lam to performed my ligand binding study with
corresponding protein. I have taking the native diffraction data at
1.75 A and after that i have performed soaking as well
co-crystallization experiment with my inhibitors.
Problem is that at the
Hi,
What about the ccp4 web page, from which you can follow the link to
http://www.ccp4.ac.uk/ccp4bb.php ?
HTH,
Fred.
Angela (Shaoxu) Li wrote:
Hi there,
I wish to unsubscribe to the mailing list. But I'm unsure as to how I
can do that. Your help will be greatly appreciated.
Best
Zhiyi Wei wrote:
Dear all,
I have a P2 derivative dataset with beta=89.6. I try to change the
beta to 90.4 to be consistent with the native dataset. Should I do sth
with the HKL, like applying a matrix? Thanks a million!
Best,
Zhiyi
Hi,
Personally I would use sftools (no ccp4i GUI), to
Hi,
I have a problem with the following sentence:
if I collect all spots I get good map, but it is impossible to solve
the structure by molecular replacement - if you have a good map (I
assume electron density map) then the structure is solved... for me a
good map is a map I can interpret.
the space group is I422 do you have any other suggestion?
Yes, how certain are you of the space group? For myself, I'm never
entirely certain of the space group until I have solved the structure...
I always keep in mind the other possibilities for space group
assignment, if need be. And
Hi,
The R-factor you mention, is it an R-factor before any refinement of the
model ? Like an R-factor at the very beginning of the entire modeling
procedure, right after molecular replacement ?
If this is so: you should always compare such initial R-factors to the
R-factors for the atoms
The distance to your modelled water seems to be in agreement with an
ionic interaction. What are the components of all buffers in the
crystallisation components ?
Fred.
ruheng wrote:
Dear all,
Recently we are working on an archaebacteria protein which was
expressed and purified from /E.coli
Plenty of old drives at ESRF, for that purpose. If you don't find any
other way, I could always read them there (the ESRF is in my backyard)
and burn the data to DVD for shipping (or upload to megaupload - but our
gov't is hunting down people who use such services, they think
megaupload and
Hi,
It's not a bad idea to read the Phaser manual for molecular replacement;
see http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement
Soon after the start, in a table on the right hand side, there is: TFZ
score 5, have I solved it ? No.
Hence with a TFZ score of 3.8 you do not
Quoting you: I type ccp4 and I get no error, what happens if you type
ccp4i (followed by carriage return) ?
Yuri wrote:
I downloaded the package for RHEL5. My default shell is sh. But I can
change environments. I have progrmas that I must run in tcsh.
I tried sourcing sh and csh setups.
james09 pruza wrote:
Dear CCP4BBers,
Refmac is giving the error No reflections in resolution bin??? It
seems there is no SigFP column. I wonder how to fix the problem.
Thanks in advance.
James
If the error is indeed due to a missing SigFP column, there are 2 ways
to go about it I
sadaf iqbal wrote:
Hello everyone,
Do anybody know the correct procedure for calculating omit map in
CCP4, if one need to reduce the bias from the Molecular Replacement
structure. I am confused about the two options, one is fft map
calculation while the other is OMIT map calculation in Map
Well in fact, it all depends on the type of detector these small angels
end up on and on the speed of this godly radiation. Only once you have
considered both these elements can you say poor little things.
My 2p worth.
Fred.
Ed Pozharski wrote:
The best X-ray related typo I ever seen was
Hi there,
In crystallography there are so many places where you can have problems
(and need to solve these problems) that I cannot list them all.
There is no twinning in the data - you probably mean the data does
not seem to indicate the presence of twinning but there might be
twinning;
Could be of importance to those who have to use the Lyon or Grenoble
airports (to ship in or out), check out the update from Sept. 27, 2011.
http://www.ill.eu/users/user-guide/safety/important-instructions-for-biological-samples/
Fred.
http://www.ill.eu/
Just to add to what has been said (written) before:
coiled coiled or simply helices can be very problematic for M.R.. Human
sacrifice has never given any positive result (as reported in the
literature as far as I know), but heavy atom sacrifice could be
attempted (heavy atom includes in my
Could you have an unexpected small subunit (or some other situation)
giving additional density that Phenix is building into ? In other words,
how sure are you of what is present in the crystal ? This is because I
remember the enzyme methanol dehydrogenase where there was a small
subunit which
Hi,
If, in your case, no possible asymmetric unit can contain A1-B2, then
you deposit A1-B1 (or I suppose A2-B2...) and indicate to the PDB (like
placing cards in the header cards) the operator to be used (and the
subunit it applies to) in order to generate the most likely biological
dimer.
D Bonsor wrote:
and allow someone else to have ago at solving the structure.
I'd be careful there if there was a motion to try to implement a policy
at SR sources (for academic research projects) to make it compulsory to
publically release all data frames after a period (1 year ? 2 years
I must say that there were some emails exchanged between me and Gerard
later, in which I pointed out that I wasn't against deposition of images
(data frames). In fact, if SR sources kept user's data there would be
one more structure from here in the PDB: HDD failure here, the data on a
mirror
A mixture between mathematical significance and biological significance
as a part of the reply:
you should also take into account the thermal vibrations of the atoms
present in that domain, i.e. the thermal ellipsoids when you have one
of the representations of anisotropic temperature factors
There are several ways to skin a cat. If you have processed your data
with XDS, XSCALE can also do the job (you have to think of the unit cell
parameters of the merged data set though - the default may not
necessarily what you wish to have), and I am certain other data frame
processing suites
For those of you interested, the reply to Tassos' question can be found
here:
http://www.iucr.org/resources/commissions/crystallographic-computing/schools/school96/ccp4-program-system
(on-line)
as well as here, http://www.*ccp4*.ac.uk/manual.ps (a ps file).
McLaughlin, Terry and Zelinka.
I believe Procheck generates drawings such as those. It generates
PostScript files, and if you need to have (eg) jpg files, a PostScript
interpreter, screen capture and there you are (Gimp to select only the
areas you're interested in)
HTH,
Fred.
WENHE ZHONG wrote:
Dear memebers,
Thank
Hi,
The refinement program generates an mtz file with map coefficients
(including difference Fourier coefficients) so you should use that one
for model rebuilding in coot;
for the next refinement rounds, at the beginning of each round you
should provide the initial mtz file coming from data
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