Hi, Peter,
Does the radition damage have such a large effect? There are many positive
peaks seeing from the difference map, seems abnormal. But I have seen
such difference maps before which are OK for modeling and refining.
Actually when I try to modelling the Se-met into the positive peaks, the
Got it.
Turn down the resolution of the monitor. The characters will be large enough
to see. But the map looks not so soomth as before.
On 3/20/07, Jiamu Du <[EMAIL PROTECTED]> wrote:
Dear All:
I have a question about the new version O.v11.
In the new version, the characters displayed on the t
Hi Peng Zhang,
The presence of radiation damage might cause some problems.
Do so see any obvious features in the difference map?
Another problem (although I doubt it would cause such a big difference) might
be the fact that f' andf f" prime are incorrect.
Try and refine them (CNS or phenix.refin
Maybe I did not make the questions clear, which leading to the misleadings.
Firstly, I have collected the mad data and get the phase at synchrotron,
the phased Se is quite good for modelling, and get over 70% of the
molecule run with resolve autobuilding.The density seems also good for
building. Bu
Hi
it seems I overestimated what's in my little mac mini.
Its a g4 not a g5, so the g5 binaries would not really
be expected to work.
Thanks for the responses
Ulrich
Hi,
I just installed ccp4 6.0.2 with ccp4i 1.4.4.2 on a mac mini.
no matter what little job I try to run (importing mmCIF file,
calculating structure factors from pdb), the execution fails
with a note in the log file saying:
has failed with error message
child killed: illegal instruction
**
Actually, the structure is not mine. I just wanted to check the
structure before using it for my work!
The unit of the structure is: a = 141.59, b = 141.59, c = 43.68
alpha = 90.00, beta = 90.00, gamma = 120.00
So, it is H3 not R3!
Checking the structure after editing the space
I'm not a big fan of restraining chiral volumes, except for models based
on low resolution data (maybe up to 2.7A). In my experience, if a refinement
results in the flipping of a chiral center the true solution is almost never
to flip it back. If a CA flips then probably a neighboring peptide
Call For Speakers
Gordon Research Conference on Diffraction Methods in Structural Biology
July 13-18, 2008 Bates College, Lewiston, Maine, USA
Co-Chairs: Elspeth Garman & Andrew Leslie
The 2008 Gordon Research Conference on Diffraction Methods in Structural
Bio
are you mixing R3 with H3 ?
in the current pdb R3 has a=b=c, al=be=ga
while H3 has a=b, al=90, be=90, ga=120
this was not consistently used in the earlier pdb
examples
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: R 3
REMARK 290 SYMOP SYM
Dear All,
I wanted to check some structure using the validate server
http://deposit.pdb.org/validate/
In the validation summary file I got a list of close contacts
based on crystal symmetry:
In case anyone here did not hear about our upcoming session on
microcrystallography, here is some information.
Please note that the ACA has extended the deadline for abstract
submission to April 1. We are still in the process of choosing final
speakers, so if you have interesting science or
Dear all,
I am running a very long phaser job (using the keyword FINAL SELECT ALL). It
found and refined 30370 solutions, and now it is in the very last stage (PRUNE
DUPLICATES). How long could take this step on a machine with a xeon 3.2GHz cpu?
Days, weeks, or months? I have no clue from the
On Tue, 20 Mar 2007, Robert Sweet wrote:
I'm pretty sure that the crystallographer was David Sayre.
Indeed it was. He is mentioned explicitly in this article:
http://inventors.about.com/od/bstartinventors/a/John_Backus_4.htm
Regards,
Peter.
Regarding David Sayre, Ed Lattman once opined in a Sayre's Equation
lecture to graduate students that if only David Sayre would focus his
attention on macromolecular crystallography again, that perhaps the
phase problem would be solved.
Lofty praise indeed.
Thanks for the anecdote Bob.
Steve
SFTOOLS has a random number generator that produces a uniform
distribution between 0 and 1, which you can than use in different ways.
You could then select all non-centric reflections and asign their phase
as RanU*360.
For the centric reflections you can first set them to the P-variable in
the
I'm pretty sure that the crystallographer was David Sayre. I also believe
(not documented well enough for wikipedia, but perhaps for here)
that IBM were so pleased with this performance that they made David an IBM
Fellow, which meant that he could do anything he wanted for the rest of
his life.
All - I'm refining some structures in SG P22121 and I lots of warning
msgs from Refmac: "===> Warning: No such space group in ASYLIM".
The job seems to run fine & I can't see anything untoward with the
results or the output files, so I was just wondering whether I need be
concerned about the mes
You can do that to some extent by scattering random atoms about and
calculating phases from them..
Then the centrics will be sensible.
That is how some direct methods programs get their "random starting set"
of phases..
Depends on how flat you want the starting map to be
Eleanor
David Briggs
The storey also made it to the CNN business page and they add...
The Fortran programming language, which was a huge leap forward in
easing the creation of computer software, was released in 1957, said the
report.
Backus launched his research project at IBM (Charts) four years earlier,
assemb
Hi Li, There is nothing wrong with your opinion the expected redundancy
is indeed 4 because, as you say, each reflection intersects the Ewald
sphere twice, once through the top and once through the bottom
(redundancy will actually be a bit less due to the missing cusp region).
Bart
yang li wrot
Hi y'all.
Excuse that rather "noddy" question, but I've been googling this for hours
now and I've finally lost patience...
How can I generate a random phase set for either a .mtz or .hkl (cns format)
reflection file (if possbile with sensible values for centric reflections).
That's it.
Thanks
A bit of history: NY Times obituary for John W. Backus, 82, developer of
Fortran, without which CCP4 and much else would not have been possible.
http://www.nytimes.com/2007/03/19/obituaries/20cnd-backus.html?ex=1332043200&en=adde3ee5a1875330&ei=5124&partner=permalink&exprod=permalink
Pete A
-
The scales files is opened NEW, then overwritten by REWINDing for each
refinement cycle.
It is not explicitly closed, but relies on the compiler correctly flushing
& closing the file on exit.
This may be a compiler bug I suppose.
I can change Scala to close the file explicitly, which might fix t
Hi Phil,
Looking at the file it is clear that the end is missing - the files are
identical to a certain point then the last few 0 values are missing and
there is no newline at the end of the ppc version...
I have just run it again on the firewire disk and got the same error,
which is odd. So the
The SCALES file is plain text so you should be able to check it with an
editor
Phil
> Hi Folks,
>
> Sorry this is slightly off topic. I have an OS X PPC mac mini and I have
> noticed some very strange behaviour. When I run scala for one example
> the scales file that is produced is exactly 16384 b
Hi:
I am confused by a idea for a long time, and it maybe an easy question.
That is, if a cryst with p1 spacegroup, after 360 degree data collection,
what the redundancy should be? I was told that it is 2, and the 2 are
F(h,k,l) and F(-h,-k,-l), but I think if the reciprocal lattice rotated 360
Hi Folks,
Sorry this is slightly off topic. I have an OS X PPC mac mini and I have
noticed some very strange behaviour. When I run scala for one example
the scales file that is produced is exactly 16384 bytes, and when I try
and restore this scala dies. Now running the same scaling job on an
intel
CCP4 is a collaboration between many and varied authors, so the exact
answer depends on which bit of the ccp4 interface you are talking about!
Generally, most CCP4 programs will work with "standard" PDB files. The
spacegroup on the CRYST1 line is only needed if a program can't get the
symmetry inf
yang li wrote:
Hi:
Now I need to input a heavy atom pdb file in the ccp4 interface, does
ccp4 has a special format for all the programs in the package? I used
heavy atom file from shelxd but it seemed not right. where can I get a
model of such pdb file? Thanks!
SHELX has its own interpretati
Whatever you do it is good practice to do your first run of refinement as
Review Restraints"
Under the Monitoring folder set the level to many (default medium)
and set the sigma cut off for chirals to 3.00 say to get a god list
Then run the job and you will get a list of violations of restraints
On Tue, 2007-03-20 at 08:57 +0100, Laurent Maveyraud wrote:
> Dear list,
>
> another question related to stereochemistry, but concerning coot.
> When using the RSR zone button, which should "improve geometry and fit to
> map", it seems that the geometry is not always improved : some chiral
> cent
You can run the pdb file through pdbset, supplying cell and spacegroup,
that's probably the quickest way to fix it.
Tim
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Tue, 20 Mar 2007, yang li wrote:
Hi:
Now I need to input a heavy
Dear list,
another question related to stereochemistry, but concerning coot.
When using the RSR zone button, which should "improve geometry and fit to
map", it seems that the geometry is not always improved : some chiral
centers can be inverted. The surprising thing is that using the "regularize
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