from iron.
-James Holton
MAD Scientist
On 6/2/2013 8:47 AM, Edward A. Berry wrote:
Is Ethan Merritt's anomalous scattering page at:
http://www.bmsc.washington.edu/scatter/
down or moved, or the firewall I'm behind is blocking it?
I want to check feasibility of a native-iron MAD experiment
The idea of RAID (redundant array of inexpensive disks) must seem
pretty silly to the Brits- disks may be inexpensive but they're
not free- why waste money on a redundant system?
Ethan Merritt wrote:
On Tuesday, May 14, 2013 01:58:06 pm Colin Nave wrote:
The use of the term redundancy (real
herman.schreu...@sanofi.com wrote:
I would process or expand the data to P1, also expand your pdb file to P1 and
refine in P1 to see what happens. I would also run Phaser or some other
molecular replacement program on the P1 data to see what comes out.
process or expand? I don't understand
Hope you already finished your presentation, but if not here is anther way.
You don't mention whether you have predicted secondary structure or you want
to base it on actual structure for one or more of the sequences.
If the latter, CCP4's procheck makes such a cartoon in its postscript pages,
Yes- this has happened to us so often recently that I've taken to checking every
new crystal form against the nearest cell server before starting heavy atom
search.
That would account for the poor reproducibility.
Yeast glutamate-cysteine ligase (e.g. 3LVV) crystallizes with nearly identical
Robbie Joosten wrote:
Hi Martyn,
I think the question is where the error was made - seeing the uploaded file
would clear this up. But it seems unlikely to me that the depositor saw a huge
R factor discrepancy at the end of refinement and just blithely uploaded it.
So scenario 3 :-
PDB : we
Opher Gileadi wrote:
Hi Theresa,
To add to Anat's comments: Although the AUG codon for the first methionine and
all other methionines in a protein coding sequence look the same, they are read
in a very different way by the ribosomal machinery. The first AUG is recognized
by the initiation
Maybe this thread still needs some more pedagogy/explanation for those newbies and for biologist/ wanna-be
crystallographers like me. My original reaction was- if the true space group is P21 you wouldn't want to expand from
data reduced in higher symmetry, because you would be enforcing that
want to start translation if there isn't ample resources to finish the
job. Perhaps Met concentration is a proxy
for anabolic potential of the cell? Or at least was primordially and QWERTY'd
in?
/wild speculation
Shane Caldwell
McGill University
On Tue, Mar 19, 2013 at 9:46 AM, Edward
In the mitocondrial inner membrane (which is very protein-dense) I believe the most abundant protein is the adenine
nucleotide transporter. (e.g. pdb1OKC). Single chain or homodimer, but apparently its not very easy to crystallize.
Jacob Keller wrote:
Dear List,
Does anyone know of a source
Or give it to arp/warp, either with the current model to improve or with phases
from the current model to build new model?
Phoebe A. Rice wrote:
What happens if you solvent-flatten/flip/massage that map, but tell the
software the solvent content much lower than
what you think it is now? Maybe
and redundant
email.
A.
On Sat, Mar 9, 2013 at 1:02 PM, Edward A. Berry ber...@upstate.edu
mailto:ber...@upstate.edu wrote:
Still, I would second Lisa's question. Your google search gives a lot of
false hits, and one doesn't want to
download and install a dozen programs
Still, I would second Lisa's question. Your google search gives a lot of false hits, and one doesn't want to download
and install a dozen programs (with license forms to fill out in some cases) to see which one works, when Partha can tell
us that Pro-origami will do it and provide a link to the
try cheating by something like:
ln -s /usr/lib64/libXaw.so.7 /usr/lib64/libXaw.so.8
?
[berry@sbserv ~]$ ldd `which xplot84driver`
linux-vdso.so.1 = (0x7fffb936)
libXaw.so.8 = /usr/lib64/libXaw.so.8 (0x003f8600)
libXmu.so.6 = /usr/lib64/libXmu.so.6
Raji Edayathumangalam wrote:
(3) Inconclusive no diffraction situation, which could indicate a million
things including the possibility that your
cryoprotectant was sub-optimal for data collection done using flash
cryocooled/flash frozen crystals in a stream of
gaseous nitrogen.
But before
Maybe a silly question, but -
Is this standard deviation of bond lengths that of each bond type in
the Eng and Huber paper, or the standard deviations in the structure
being validated?
Robbie Joosten wrote:
Note that we discuss rmsZ values in the paper, not rmsd. This is done on
purpose; rmsd
Nat Echols wrote:
On Sat, Jan 19, 2013 at 4:14 AM, Qixu Caicaiq...@gmail.com wrote:
Could you please teach me any method to present the relationship between
resolution and B values of all the x-ray structures in Protein Data Bank.
Can the PDB statistics in RCSB do it?
Perhaps, and I'm pretty
http://www.computerhistory.org/revolution/timeline
And this paper describes their use of a digital computer as if it were rather
routine:
Sternberg, J., Stillo, H. Schwendeman, R. (1960). Spectrophotometric Analysis of Multicomponent Systems Using the
Least Squares Method in Matrix Form.
Edward A. Berry wrote:
http://www.computerhistory.org/revolution/timeline
And this paper describes their use of a digital computer as if it were rather
routine:
Sternberg, J., Stillo, H. Schwendeman, R. (1960). Spectrophotometric Analysis
of Multicomponent Systems Using the
Least Squares
I think one may need to distinguish between three different kinds of dehydration experiment, because of the different
forces they will exert on a crystal to shrink the unit cell, creating new stabilizing crystal contacts or perhaps
causing contacts to fail in a chaotic manner, disordering the
But I think the original poster meant partially overlapped after applying
the ncs- operator- i.e. they are not ncs related but occupy partly the same
position (in the two non-overlapping copies of the binding site).
Then I guess it depends how clear the density is- If the density is not very
: bshaa...@bgu.ac.il
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Edward A. Berry
[ber...@upstate.edu]
Sent: Monday, January 07, 2013 6:12 PM
To: CCP4BB
No, No- in scientific circles we go from MSB on the left to LSB on the right:
2012 12 20 (still a sort of palindrome).
as in
Release: 2012-12-19 Classification: Lipid Transport
Experiment: SOLUTION NMR Residue Count: 216
but right to left can be used if there is no
to mis-represent the resolution of the structure.
Regards,
Mitch
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Edward A.
Berry
Sent: Friday, December 07, 2012 8:43 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] refining against weak data
file.
The message can be eliminated in the way I suggested by inserted a CALL XYZINIT
before the call to RBFRO1 in almn.f .
Cheers
-- Ian
On 10 December 2012 21:47, Edward A. Berry ber...@upstate.edu
mailto:ber...@upstate.edu wrote:
I am experimenting with ALMN cross-rotation using some old
I am experimenting with ALMN cross-rotation using some old known structures.
I was surprised to see what seems to be a requirement for the cell dimensions
of the two crystals to be the same. Is that the case?
Excerpts from the log follow.
eab
Data line--- CROSS 5 30
. ..
OPENED INPUT MTZ FILE
Does this mean that, when placing the first (or only) copy of a model,
the score will not be elevated by presence of tNCS (Unless the model contains
domains separated by more or less exactly the distance of the tNCS vector)?
(In general, using a generic MR program that does not correct for TNS.)
Yes, well, actually i'm only a middle author on that paper for a good
reason, but I did encourage Rebecca and Stephan to use all the data.
But on a later, much more modest submission, where the outer shell
was not only weak but very incomplete (edges of the detector),
the reviewers found it
Another consideration here is your PDB deposition. If the reason for using
weak data is to get a better structure, presumably you are going to deposit
the structure using all the data. Then the statistics in the PDB file must
reflect the high resolution refinement.
There are I think three places
Without F000 we cannot get absolute density level vs zero, but still
I think electron density in units of e-/a^3 above the mean is much more
meaningful than sigma above the mean. I think the last one of these
mystery density questions generated a lot of discussion until someone
pointed out that
Appu kumar wrote:
Dear all,
Please guide me on right track in weired confusion. I have
model structure(available in pdb)
and a structure solved by molecular replacement as a dimer . Our structure
does not giving correct tetramer by
symmetry mates. Strangely when i am
Thanks to all for the suggestions! We will try, this weekend at macCHESS,
all those conditions for which we have reagents, and order the others now.
On Oct 16, 2012, at 9:01 PM, Edward A. Berryber...@upstate.edu wrote:
Would someone suggest a cryoprotectant for index screen #59? It contains
Would someone suggest a cryoprotectant for index screen #59? It contains
0.02 M MgCl2
0.1 M HEPES pH 7.5
22% polyacrylic acid 5100, Na salt
Adding glycerol tends to dissolve the crystals.
Thanks,
Ed
Not to worry- since you carefully preerved the original files,
you can easlily recover. You just need to boot a live CD
like DSL or fdora live (or maybe even Tom's Root Boot disk)
to bring up a system that can mount your filesystem and allow you to
undue the failed experiment.
Recent fedora live
Shya Biswas wrote:
Hi,
Thanks, I think the problem is with the EDS server as I tried numerous pdb
files (not just the 3TVN) and none of
them worked so far.
Shya
I suppose that when the first message in this thread came out yesterday morning,
it was a signal for hundreds of thousands of WW
Ian Tickle wrote:
below the noise threshold. This does make the tacit assumption that
the unmeasured reflections are distributed randomly in reciprocal
space, which is clearly not entirely true, but it's hard to see how
one could account for the non-random distribution. Again, in any case
Oh - you meant how one could take nonrandom distrubution
into account in the analysis-
funny how I always understand what someone meant after
i push send on an inappropriate reply
Edward A. Berry wrote:
Ian Tickle wrote:
below the noise threshold. This does make the tacit assumption
Are all the software packages consistent in their (mis)use of these
symbols? Recently I scaled data (scalepack) as R3, imported to ccp4 as H3,
and had to make a link in $ODAT/symm from R32 to H32 (which it turned out to
be).
Ian Tickle wrote:
If we're all agreed that ITC(A) is taken as the
Iron sulfur proteins tend to absorb less (although not zero) in the visible
when reduced. We see this with succinate dehydrogenase when we reduce with
dithionite to see the heme spectrum- the difference extinction coefficient
at the beta peak is actually negative because the baseline absorbance
narayan viswam wrote:
Hello CCP4ers,
In my data, the highest reolution shell 2.8-3.0 A has I/sigmaI 2.5 Rsym
224.3 %
for multiplicity 7.8 and completeness 98.2 %. I solved the structure by MAD
refined it
to Rfree 27.3 %. Ths crystal belongs to P622 space group and it is not twinned.
The
How low does O2 have to get to be dangerous?
To reduce the oxygen concentration by a factor of two, you would have to mix
equal
volumes of air and nitrogen. Now since the nitrogen is coming off at about 70K,
assuming equal heat capacity for N2 and 80% N2, the temperature of that mixture
would
googling dityrosine suggests thaey can be formed by osidation by Cu or Ni
ions.
In structures of cytochrome oxidase, Tyrosine forms a covalent bond
from the same meta carbon to NE2 of a histidine. see Fig 1 of:
http://www.sciencemag.org/content/280/5370/1723.long
And histidine is ligating a
Good to know about this ISC operon!
Do you know if it is specific for Rieske-type His2/Cys2 Fe2S2 clusters,
or for FeS clusters in general?
Thus wild-type E. coli is already making three types of ISC clusters
for succinate dehydrogenase or fumarate reductase (although some help
might be needed
Bosch, Juergen wrote:
Dear CCP4 community,
what's the general opinion regarding sharing old published data sets ?
Would you be offended if I asked you for your raw images from say a 5-10 year
old structure ?
And then the more tricky question, what if I find something you overlooked and
I would
Maybe figure 4 in
Viatcheslav Berejnov et al. Vitrification of aqueous solutions
J. Appl. Cryst. (2006). 39, 244–251 ?
JORGE IULEK wrote:
Hi, all,
I thought I could easily find a reference to comment upon the relative
intensity of
rings in an image due to diffraction by polycrystal
Sorry to come late to this discussion-
I think the actin and tubulin people already reverted polymer
to its etymological use- google actin polymerization
Another example of infinite polymers formed by domain swapping
(and the surprises you can get trying to engineer a molecular switch):
Yes! I want a copy of this program RESCUT.
REMARK 200 R SYM FOR SHELL(I) : 1.21700
I noticed structure 3RKO reported Rmerge in the last shell greater
than 1, suggesting the police who were defending R-merge were fighting
a losing battle. And this provides a lot of ammunition to
In the meantime we could follow Phoebe Rice's example and put
the resolution at I/sigma=2 in REMARK 2 resolution of structure
but put the actual bleeding-edge resolution we used in the
reduction and refinement statistics (At least if the PDB
will allow us to have different values in these three
--
From: Edward A. Berry ber...@upstate.edu
Sent: Thursday, May 31, 2012 2:59 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Death of Rmerge
Yes! I want a copy of this program RESCUT.
REMARK 200 R SYM FOR SHELL (I) : 1.21700
I noticed structure
sreetama das wrote:
Dear All,
I have a PDB file which does not have the REMARKS cards 465 (for missing
residues) and 470
(for missing atoms). This is not a deposited PDB file. Is there any program to
figure out
the missing residues and atoms (some programs complain about missing atoms) ?
Or
Jacob Keller wrote:
Just to make sure I understand pH correctly: isn't it true that the
[OH-] should always be the same at a given pH (by definition)?
Maybe not by definition but by equilibration with [H+] to make water:
[H][OH]/[H2O] = Kw
[OH] = Kw[H2O]/[H]
if [W]
A protein would only scatter but not diffract
or Diffract but not scatter? isn't diffraction a kind of scattering?
But yes, the atoms in the unit cell may seem random in that
distance range (in fact this is assumed in wilson scattering)
but in a perfect crystal they will be the same in each
Did you locate the Iodine(s)? Did you have iodotyrosine, or I^- bound
at anion binding sites? There are two distinct methods based on I2/I-.
Florian Sauer wrote:
Dear Rajesh,
another method to incorporate Iodine into your crystal is by simply
placing a drop of KI/I2 solution next to the
We also use the US portal. Can't speak to the solvent content as we never
had a value much over 70%.
As for the resolution range, I never saw any place to enter this
user-defined resolution of the structure.
As far as i know it comes from the record:
REMARK 200 RESOLUTION RANGE HIGH (A) :
Bosch, Juergen wrote:
To pick a bit on George's point with MR citation.
Here's how you can read it in the paper from your favourite competitor:
A homology model was generated using [fill in any program for ab initio
prediction] and subsequently used for molecular replacement with Molrep.
The
I would say yes. In any case you need to examine each mutated
residue to be sure the correct conformation is chosen, so you might
as well do the mutagenesis in coot or O. The ccp4 chainsaw program
is sometimes used to prepare models for MR, but it truncates the mutated
residues to variable
Dear Sunil,
I think you can do this with the ccp4i gui-
In the category Reflection Data Utilities
select Edit mtz file (sftools)
One of the panels is Change column labels and types with options to
edit labels or add new label. But Surprise, there are no labels in the list!
This is because the
Florian Schmitzberger wrote:
Dear Toby,
I don't think there is a basic problem using glycerol in
crystallization. Glycerol will affect the vapour pressure (if it is not
present in the well/precipitant solution) and 10 % glycerol is ~ 1.3
molar concentration. During equilibration the drops may
If I recall correctly cytochrome oxidase, which I believe was
the first protein purified with DDM, requires about 10x cmc
in column buffers to keep it soluble. Check for papers from 1970's or 80's
by S. Ferguson-Miller.
Cytochrme bc1 complex, on the other hand, is perfectly clear in 1 cmc
and
Jim Pflugrath wrote:
In addition to reducing the beam divergence, you may wish to use a
smaller beam size by using a smaller collimator or making the slits
smaller. A smaller crystal can also help to spatially separate the Bragg
spots as can moving the detector closer to the crystal. Yes, closer
Roger Rowlett wrote:
No. Kw = [H3O+][OH-] = 1 x 10^-14 at 25 deg C.
So at pH 7.0, you have 10^-7 M each at equilibrium no matter how you slice it
or whatever
else is in solution. If equilibrium [H3O+] goes up [OH-] goes down
commensurately.
The pKa of water as an acid is based on Kw and
Bosch, Juergen wrote:
Hi Dirk,
I remember a neat paper don't recall who wrote it. I think it was in Acta D
where the
authors made a tiny probe the size of an elongated crystal glued to a
[/Advertisement on]
Hampton loop [/Advertisement off]. The probe was a temperature sensor and they
Deepak Thankappan Nair wrote:
~~~
Can anybody tell me a method to quantitate shape complementarity
between two surfaces? Sc program in CCP4 is not running properly.
thanks and regards
Deepak
I think SC is THE way to calculate it.
If not working in the current release, we should get it fixed.
Deepak Thankappan Nair wrote:
Dear Dr. Berry
thanks for the mail. maybe the syntax that I provide is not correct.
i assume you have to write
MOLECULE1 CHAIN A to define the first surface
but i get the following error:
MOLECULE1 CHAIN A
No molecule number given
BFONT
megha goyal wrote:
Our recombinant product is formulated in 10 mM sodium acetate buffer at pH 4.0
and the std
composition mentions sodium 0.035 mg and acetate 0.59 mg per ml of sample. It
mentions
Sodium acetate is formed by titrating glacial acetic acid with sodium hydroxide.
Can anyone
Does trimethyl lead tend to lose the Me in aqueous buffers?
A colleague is preparing to deposit a 2.9A structure that
was refined against the TML derivative (higher resolution than native).
Since the Pb was added as trimethyllead, the first inclination is
to report the heavy atoms as TML, ligand
Maybe the His Tag is blocked by the folded protein.
Try using 6M Guanidine-HCL and see if it sticks.
Then you will need to find some way of refolding your protein,
if you want to crystallize it.
Theresa H. Hsu wrote:
Hi all
I have a His-tagged soluble protein (8 His residues added to 90 kDa
It seems some 32-bit libraries need to be installed to get recent versions
of O to run on 64 bit architecture. There is a 64-bit version undergoing testing
now, so you might want to just wait for it. or volunteer to be a tester.
Subscribe to o-info mailing list (at the below site) to keep up with
I suppose you mean the pipetman and similar, and having it calibrated
by a professional rather than pipetting into a weighing boat to see
if it is OK-
Unless i'm missing something, there is very little that can be done in
the way of calibration- the diameter of the stainless steel shaft and
the
Hmm- I wonder if B-factor unsharpening (applying a large POSITIVE B-factor to
the data)
would have the same effect?
Francis E Reyes wrote:
On the other hand, shooting a lower resolution crystal may get you the
conformation of the disordered domain.
Surprising at first thought, but was true
The program:
http://sb20.lbl.gov/berry/for/pdbdist2b.for
does this.
If you run it by the wrapper pdbd2b:
echo 'Find distances greater than threshold between corresponding atoms in 2
PDB files'
echo 'Usage: pdbd2b file1 file2 startres# [thresh]'
pdbdist2b eof
$1
$2
$3 1
$3
$4 3.0
eof
then
No! the divide by 2 part is for a 2-fold rotation- not 8*.
Sorry, and hope the O.P. didn't waste any time trying to implement this.
Edward A. Berry wrote:
Would this work?
Take the rot-trans operator from superpose or lsqman and express
the rotation matrix as polar coordinates of rotation axis
Would this work?
Take the rot-trans operator from superpose or lsqman and express
the rotation matrix as polar coordinates of rotation axis (and angle about it).
Get the rotation axis as direction cosines, which will be a vector along
the rotation axis of the matrix. Now take the component of the
Ho Leung Ng wrote:
There is at least one paper describing the success of PEG precipitants
for complexes, but I can't find the reference right now.
Is this it?
http://scripts.iucr.org/cgi-bin/paper?S0021889802013973
J. Appl. Cryst. (2002). 35, 674-676[ doi:10.1107/S0021889802013973 ]
Gerard Bricogne wrote:
. . . . the view, expressed by many and just now
supported by George, that developers could perfectly well do their job on
the basis of relatively small collections of test datasets that they could
assemble through their own connections or initiative. I mostly agree with
I integrated data with mosflm using the lowest symmetry implied by
the lattice- P4. Scaling with scala confirms that symmetry.
Now I want to test P422, but scala doesn't seem to have a SYMM
or SPACE GROUP keyword. I'm sure there is an obvious way to do
this, which everyone else knows, but i don't
Thanks! That does it.
Harry wrote:
Hi Ed
reindex is your friend here -
reindex hklin jumbo.mtz hklout dumbo.mtz eof
symm p422
eof
should do it.
On 18 Oct 2011, at 22:18, Edward A. Berry wrote:
I integrated data with mosflm using the lowest symmetry implied by
the lattice- P4. Scaling
Now it would be interesting to refine this structure to convergence,
with the original free set. If I understood correctly Ian Tickle has
done essentially this, and the Free R returns essentially to its
original value: the minimum arrived at is independent of starting
point, perhaps within
Tim Gruene wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
On 10/11/2011 09:58 PM, Ethan Merritt wrote:
On Tuesday, October 11, 2011 12:33:09 pm Garib N Murshudov wrote:
In the limit yes. however limit is when we do not have solution, i.e. when model errors are very large. In
the
If the ice rings are really sharp, they trigger the bad
background rejection in denzo/HKL2000. To reject more spots,
increase the reject fraction 0.7 parameter to something
greater than .7. This rejection is on a spot by spot basis,
so spots with good background between the rings should not
be
Jacob Keller wrote:
I actually looked at an EtBr MSDS a while ago, and was shocked at how
benign it was. I also heard from someone that they used to feed it to
Argentinian cows routinely a few years back...
Wikipedia says it was used as a trypanosomacidal - It's being
discontinued not because
Jacob Keller wrote:
Dear Crystallographers,
I would like to soak my crystals in bicarbonate (a possible
substrate), but the crystals have grown--and only grow--in pH 5.2-6.0,
so the bicarb/CO2 will just keep evolving out of the solution and
reliquishing its hydroxyls until the pH is elevated
What does ProCheck say?
Xiaopeng Hu wrote:
Dear all,
I just notified that there is a big difference between the Ramachandran plot
analysis results produced by Coot and Morprobity (or Phenix). For the structure
I am working now, Phenix(Morprobity) gives out Ramachandran outliers 0.2%,
The outputfile appears to have additional line feeds (see picture) which,
however are not seen in the windows notepad.
What application ARE the extra lines seen in?
Sounds like a problem with different newline conventions-
CR vs LF vs CRLF -
although I shouldn't have thought extra carriage
A real UV microscope requires quartz optics, right?
Probably conventional microscopes use glass.
And you can't see 280 nm (and its not good for your eyes)
so you need some kind of phosphor screen to view the image?
Bosch, Juergen wrote:
I'm replying here to myself :-)
So in an off-board
Gregory Bowman wrote:
Yes, but I don't actually want to swap a and c (convention that a is shorter
than c), but instead flip k and keep h and l the same. Incidentally, it is not
immediately obvious to me why in matrix I cited below that the new l is h+l:
-1 0 0
0 -1 0
1 0 1
Greg
Because -a
Sorry for adding confusion- of course in reciprocal space beta* should be
acute. The figures should have been labeled a, c not h,L.
Edward A. Berry wrote:
Gregory Bowman wrote:
Yes, but I don't actually want to swap a and c (convention that a is shorter
than c),
but instead flip k and keep h
Gregory Bowman wrote:
Hi all,
We have several primitive monoclinic datasets for the same protein with various ligands,
with essentially the same unit cell parameters. We would like to have these with the
molecules/density oriented the same way for easy comparison, but as chance would have
Andrea L Edwards wrote:
Hi all,
What are the most successful methods you know of for dehydrating a crystal
prior to freezing it? I am trying to push the resolution of my crystals.
Thanks,
Andrea
First of all, be aware that not all crystals are improved by
dehydration. Some need to be drier,
David Schuller wrote:
On 08/23/11 15:01, Ed Pozharski wrote:
On Tue, 2011-08-23 at 12:36 -0600, Francis E Reyes wrote:
Seems to be a quiet day on the BB
So you need an earthquake :)
Had one already, thanks.
Apparently sent from the vicinity of U. Maryland and JHSPH, thanks.
Yuri wrote:
Hello Everyone,
A little off topic but, what is a good way to show (publication
quality) multiple sequence alignment?
I am trying to show conserved regions in related proteins from
different organisms.
Thank you
--
Yuri Pompeu
or clustalw, e.g.
Edward A. Berry wrote:
If you have trouble with TCL/TK read below-quoted message.
Mosflm site has more suggestions.
better yet:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/CCP4_on_Fedora_12
which says: Now Tcl/Tk tools are bundled with Fedora 12, and they work well for
CCP4i
and ccp4i work (as far as I have tested)
Andreas
On 09/08/2011 2:46, Edward A. Berry wrote:
Edward A. Berry wrote:
If you have trouble with TCL/TK read below-quoted message.
Mosflm site has more suggestions.
better yet:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php
Edward A. Berry wrote:
That does look easier, but mainly because you are not
installing blt -
What do you get for which bltwish?
presumably in $CCP4I_TCLTK, since ccp4i works.
So that means $CCP4_MASTER/tcltk++/bin
But how did it get there?
maybe from here?
ftp://ftp.ccp4.ac.uk/ccp4/6.2.0
유상헌 wrote:
Dear all,
First I’m a beginner of linux and I’m trying to install CCP4 on my 64bit
Fedora 13.
If there is anyone who successfully installed ccp4 on 64bit fedora13,
please, instruct me how to install this program in detail.
I recently installed CCP4-6.1.3 from source on
My exabyte eliant 8 mm tape just went on the blink, so I've sent
it to Pacific Data (http://www.pacificdata.com/tape_drive.html)
for repair. They also sell tape drives, but looks like mainly newer ones.
Probably have some old ones from the repair business.
Search ebay for exabyte or dat tape and
If I recall correctly DATAMAN does Wilson scaling in which the scale
and B-factor are adjusted so the average reflection intensity in
resolution bins are the same. I suspect it may not be required if
all the data have been put on an approximately absolute scale by
e.g. truncate (although that
Its obviously not going to be possible to give a unique
chain letter for every chain in 27 cells, but forget renaminmg
the chains and its very easy to generate the models to look at-
might even do it in a triple-nested foreach loop in csh.
After generating the whole cell as suggested by David or
Jacob Keller wrote:
Dear Crystallographers,
what is the dogma with regard to affinities in crystals? For example,
if I soak three crystals in 1pM, 1nM, and 1uM compound X, and they all
show equivalent density, does that mean that the affinity is really
better than 1pM, or is the crystal of such
I suspect what your colleague wants is not a whole slew of homology models,
but for you to take a look at variable residues, see what they are doing in
the structure, and make comments like
The tyrosine is H-bonding the ligand, so mutating to phenylalanine may
weaken the binding or change
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