riya doreen wrote:
Hello:
Can someone tell me if there is a relatively straightforward way of
transferring Free R flags between two CNS format reflection files ?
Thanks
Dear Riya,
You can do it either by using CNS (merge.inp: keep the flags Rfree(A:
dataset A), Fobs(B: dataset B) for examp
Dear Fred --
just to check... are you sure you have the His-tag? Might have been
cleaved somehow? You might want to increase the number of His in the
tag as well.
HTH.
-- Leo --
On 27 Jan 2009, at 21:00, Fred wrote:
Hi ccp4 list,
I am trying to purify a his-tag protein by metal affinity
Dear Jesse,
The current version of BALBES can only find MR models of a protein
complex from its own internal database. I guess in your case, BALBES
did not find the complex models (assembly as shown on the balbes log
file). What you expect BALBES to do is under developing within the new
version of
Hi Allison,
How sure are you of your spacegroup? Have you tried P212121? It is a much more common
spacegroup. How did you look for your systematic absences? It is possible that the
systematic absences are also present along the third axis even though all the reflections
have not been measu
Hi all, a non-CCP4 question:
Are there any good free programs for the design of one's own sparse
matrix screens?
I am looking for something in the lines of a set of mixtures of what
gives you the best coverage of, say, seven variables with five states
each in 96 experiments.
Thanks,
Jose
Hi Alison,
At how many (and which) wavelengths were data collected?
How much data at each wavelength?
Which option was used in scaling with HKL2000 ("anomalous", "scale
anomalous" or neither)?
Any indication of radiation damage during data collection (i.e.
disappearing higher resolution spots) or
Not sure if it's been mentioned, but I personally use EnzymeX(http://mekentosj.com/enzymex/
) .
Also, I find their PDF library organizer Papers (http://mekentosj.com/papers/
) to be exceptional.
Cheers
FR
On Jan 28, 2009, at 1:47 AM, Darren Hart wrote:
Hello,
After several years of offering
I like the consurf coloring scheme the best. I forget things so I had to write
down the instructions which I copied off of some website which I can't seem to
find at the moment. The other program is ESPript which I've also included my
cheat sheet.
Mapping conservation onto your structure (C
Hello:
Can someone tell me if there is a relatively straightforward way of
transferring Free R flags between two CNS format reflection files ?
Thanks
Dear All,
Thanks to all that replied in private and in the bb!
Answers are and will be 'permanently' summarized at:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Mapping_sequence_alignment_to_a_structure
(a nice opportunity to c
We recently collected a complete 2.5A MAD dataset. However, finding a
solution has not been as straightfoward for reasons unclear to us. We would
be grateful for any helpful advice or suggestions.
The thin plate shaped crystal was grown from a relatively small protein (90
residues).
The crysta
AL2CO ( http://www.ncbi.nlm.nih.gov/pubmed/11524371 ) may be what you need.
It takes the multiple alignment (made by user, so it isn't a black box)
that must contain the sequence of your structure, and maps the positional
conservation in the B-factor column of the structure. To see whether this
On Thu, Jan 29, 2009 at 1:25 PM, Anastassis Perrakis wrote:
> Dear all,
> I was wondering what is the state of the art for this old dark art ... are
> there any good servers / programs that allow to easily upload your own
> sequence alignments or create a 'transparent' alignment (I want to see th
Dear all,
I was wondering what is the state of the art for this old dark art ...
are there any good servers / programs that allow to easily upload your
own sequence alignments or create a 'transparent' alignment (I want to
see the alignment first and not a total black box) and then allow yo
On Thursday 29 January 2009 10:59:23 Bernhard Rupp wrote:
> Ok, following seems to be correct:
>
>
>
> a) interaction length = mean free path : relevant for absorption
>
> b) correlation length = time correlation between photons : relevant for
> multi-photon scattering
>
> c) c
Thank you Fei for your input. Your response inspired me and I found the
error I was making (a poorly truncated PDB file).
However I have another question regarding BALBES for the brains out there.
As I mentioned before, I have a two protein complex with a nice homology
model for Protein 1 and th
Ok, following seems to be correct:
a) interaction length = mean free path : relevant for absorption
b) correlation length = time correlation between photons : relevant for
multi-photon scattering
c) coherence length = longitudinal coherence length : relevant for
single photon s
Bernard
I guess this came from
"Aren't detwinning methods appropriate only in the case of true twin
domains which are larger than the X-ray photon correlation length in
order for the assumption to be valid that |F|^2 from each domain can be
summed? This wouldn't give rise to the apparent 'diffuse s
So it would seem that the five-fold periodicity in the spot intensities
along the long axis is probably due to a short-range, 34 Ang pseudo-repeat
(the decamer) along the true 170 Ang cell axis (170 = 34 x 5).
I do not think that the streaks are helical layer lines, because the spacing
on the
>From memory, correlation length is the length during which the phase of the
electric field is preserved. It's typically computed by applying time (pulse
width)- frequency (converted to length) uncertainty principle.
V. Nagarajan
JAN Scientific, Inc.
-Original Message-
From: CCP4 bulletin
I always wondered - how is the X-ray photon correlation length defined
and where do I find it? This is not the interaction length, I assume.
So, to the physicists: How large is the 'X-ray photon correlation length'
for a given wavelength in a given material?
I had the impression that
<6d56f0ec21490b4db31a8ff1f0cb2914014ce...@ffpw10.f2.enterprise>
<4981d8a7.6000...@gmail.com>
From: "Ian Tickle"
To: =?iso-8859-1?Q?Andreas_Förster?= ,
Cc:
Return-Path: i.tic...@astex-therapeutics.com
X-OriginalArrivalTime: 29 Jan 2009 16:27:43.0581 (UTC)
FILETIME=[831110D0:0
Ian and Herman,
does one want to convolute the electron density at all? I was under the
impression that current thinking favors convolution of the model
instead, i.e. placing both the helices in both orientations at partial
occupancy and letting the refinement program figure things out?
An
Rana, to a large extent this depends on what you what to do with the
delta-F's afterwards (you didn't say). If all you want to do is
calculate a map, Patterson or Fourier, (which is probably what we do
most of the time with delta-F's) then you don't need to calculate the
difference as a separate s
You can use the CCP4 program sftools. You will need
to use the program twice if you want to keep the differences
positive ie
F1 - F2 if F1>F2
and
F2 - F1 if F2>F1
Adam
On Thu, 29 Jan 2009, Rana Refaey wrote:
>
> Hi,
>
> I was wondering if anyone knows what programme I need to use to
Hi Rana,
You probably have multiple options suggested to you. One is sftools
using the CALC command. If the subtraction includes a phase then sftools
can also do the calculation on the full structure factor.
Plain subtraction of amplitudes ensuring the result is >= 0
READ yourfile.mtz
CALC
Hi,
I was wondering if anyone knows what programme I need to use to subtract the
Fobs of two different crystals from each other.
Regards,
Rana
_
Invite your mail contacts to join your friends list with Windows Live Spaces.
It's e
For this discussion another relevant reference might be:
The 1.8 A crystal structure of a statically disordered 17 base-pair
RNA duplex: principles of RNA crystal packing and its effect on
nucleic acid structure.
Shah SA, Brunger AT.
J Mol Biol. 1999 Jan 29;285(4):1577-88.
-tommi
On Jan 2
Dear Ian and Margriet,
You are right, the correction needs to be done on F, not on |F|^2. If I recall
correctly (I did not do it myself), the assumption was that Fobs = 0.5*Fobs(A)
+ 0.5*Fobs(B), so Fcorrected(A) = 2*Fobs - Fcalc(B) where A and B are the two
orientations. Since one does not ha
Hi Herman
Aren't detwinning methods appropriate only in the case of true twin domains
which are larger than the X-ray photon correlation length in order for the
assumption to be valid that |F|^2 from each domain can be summed? This
wouldn't give rise to the apparent 'diffuse scatter' phenomeno
Dear Margriet,
>From your description and what James Holton wrote, it seems that you have 2
>types of unit cells:
A: with the "sense" strand in position 1 and the "antisense" strand in position
2
B: with the "antisense" strand in position 1 and the "sense" strand in position
2
If the crystal
The 34-34-34 cell does not predict all the spots, does it?
from the diffraction pattern it seems only the 34-34-170 or 34-34-340
cell can predict all spots, so the structure should be solved in the
one that predicts all spots.
The procedure I would use is to take a 180º dataset, sacrificing so
Hi
Nice of Jacob to mention the paper below but I don't think it is
relevant to these patterns (well it might not be relevant to anything!).
I think James has given the most likely explanation. The AB type
stacking disorder he mentioned is similar to the type in the paper I
referenced. I think Jam
Dear all,
There were some comments about detector issues, but these can be
ruled out, to my opinion, since the lines appeared on different
beamlines.
Default settings of mosflm (spot picking) finds the cell 34 34 34 90
90 90 (pointless indicating P41212)
Structure was solved by SAD ph
Hi Stephan,
If there were overflows on the detector, which cause lines due to the
spill over of the wells of the CCD, the lines would be visible in the
readout direction of the CCD detector, which generally is from bottom to
top or top to bottom. You can also see this with your own (pocket)
c
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