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Hi Jenny and Iain,
But my understanding is that Iain's procedure gives the rmsds of the
_aligned_ C-alphas, whereas Jenny actually seems to be more interested
in those that she excludes from the alignment. I may be wrong, but in
these cases, I use
On Thu, May 10, 2007 at 02:46:44PM +0100, Kolstoe S.E. wrote:
The most useful aspect of the ccp4i GUI is its automatic generation of
com files. However, I would prefer the GUI to output a .com file into my
working directory (rather than the obscure location they are saved to
now) every time I
Hello Scott,
hmmm - it is quite difficult to do a good analysis of your problem,
remotely. You've tried the enantiomorphic space group I4(3), just to be
sure? In principle, the molecular replacement solution given by Phaser
sounds good, but this is no proof of whether it's correct. What
Hi
Maybe any parameter setting unchanged from the values in the
$CCP4/ccp4i/tasks/*.def file should be internally flagged as being at
the 'default value' - resulting in them _not_ being written to the
com-file? This way any potential change in defaults inside the actual
program would have
Clemens Vonrhein wrote:
One thing I found very confusing though, is that the com-files created
by the CCP4i will often have (nearly) all possible keywords set, even
if I haven't changed any of the defaults in the gui. Often, a CCP4
program has defaults itself and only requires keywords if one
It is a bit clunky - you can use siperpose molecules - fit residues to
fit a selected range (1-40; 60-100 say) and write out a complete fitted
pdb file. Then you could use a VERY old program
compar xyzin1 original.pdb xyzin2 fitted.pdb (xyzin3 another.pdb)
and it will match all pairs with the
I would agree with Clemens that the Scala GUI task generates far too
many keyworded commands, for things which have sensible defaults in
the program.
One problem conundrum for the GUI (because it works by generating a
script without actually running the program) is that the GUI has no
Bernhard Rupp wrote:
Dear Coders,
Do I see this correctly that crossec.lib
is the XSECT.DAT file from Don Cromer's FPRIME
program? If so, has there ever been an update?
Mine is from some reel tape I got from him long ago
when I ported the code...seems to be the same.
Thx, br
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Excellent!
Thank you Gerard,
Miguel
Gerard DVD Kleywegt escribió:
But my understanding is that Iain's procedure gives the rmsds of the
_aligned_ C-alphas, whereas Jenny actually seems to be more interested
in those that she excludes from the
Hi all
Apologies for the non-ccp4 question - hopefully some of you who use CNS can
help me - I have a problem with anneal.inp in CNS:
When I run the anneal script for my structure containing novel ligand, the
program fails before the start of the torsion dynamics with no error message
-
Hi Emmanuel,
Perhaps a little more information ?
What was the Z-score and LLG in PHASER ? I take it the translation
function solution is fairly well separated from the rest ? Are you sure
the spacegroup is correct ? How complete is the model before refinement
?
Not to be paranoid, but
I think the filament from one of our x-ray generators must be a record
breaker. Yesterday it clocked up its 6000th hour or 250th day on the
job, not counting down / holiday time.
The intensity had only dropped by around 25 % of the value it was when I
put it in, eight-and-a-half months ago...
Dear all,
I have a structure (with 6 dissulphide bridges) at fairly low
resolution (3A) that I am trying to refine with Refmac. I've used
phaser with a template with 72% sequence identity. RFZ was 3.4 and TFZ
6.6, without clashes, with 80.7% of completeness. Space group was
p3121 (pointless)
On Friday 11 May 2007 00:57, Bernhard Rupp wrote:
Dear Coders,
Do I see this correctly that crossec.lib
is the XSECT.DAT file from Don Cromer's FPRIME
program? If so, has there ever been an update?
I do not know the history of crossec.lib, but the X-ray scattering
server
Eleanor Dodson wrote:
It is a bit clunky - you can use siperpose molecules - fit residues to
fit a selected range (1-40; 60-100 say) and write out a complete fitted
pdb file. Then you could use a VERY old program
compar xyzin1 original.pdb xyzin2 fitted.pdb (xyzin3 another.pdb)
and it will
I would highly recommend Doug Theobald's program Theseus for this -
the pictures at www.theseus3d.org say it all. Theseus does maximum
likely hood superimpositions of multiple structures (i.e. NOT
pairwise against a master copy), and the real beauty of it is that
you don't have to pick
Jenny,
I of course would suggest that you follow Olve's advice, and use
theseus to do a maximum likelihood, simultaneous superposition of all
your structures ( http://www.theseus3d.org ). The variable bits,
like your loop, will be naturally down-weighted in a rigorous
statistical
does anyone know of any reports where heavy atom positions were identified
by any method (or mol. rep.) in a Laue data set (or sets)?
also - i thought there was some Laue work out there on watching virus
nucleic acids move around in a crystal, so again, if anyone knows any
references (or
WOW. There are so many ways to do it. Thank you all for replying.
Nian Huang
Department of Biochemistry
Univ of Texas Southwestern Medical Center
On 5/10/07, Charlie Bond [EMAIL PROTECTED] wrote:
Just to complete the set, in pdb-mode for emacs, if you do
pdb-increment-centroid 0 0 0 (e.g. to
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