.
Stewart, D. E., Sarkar, A., and Wampler, J. E. (1990) J. Mol. Biol. 214, 253–260
D. Pal, P. Chakrabarti, Cis peptide bonds in proteins: residues involved, their
conformations, interactions and locations, J. Mol. Biol. 294 (1999) 271–288.
(and I'm sure that is far from complete)
On 02/16/20
Well let me further muddy the waters by insisting that the 1 IS DEFINITELY a
place-holder, telling you that there is no rotation (greater than 1-fold) along
the a or b axes, and that the 2 therefore refers to 2-fold rotation along the
next axis, the ab diagonal (no the -a,b diagonal which is pe
Ethanol? You weren't setting up drops with liquor on your breath, were you?
On 02/23/2015 12:20 PM, Keller, Jacob wrote:
Dear Crystallographers,
I've got a strange blob hanging off an arginine--see attached. Any ideas?
Nothing weird in the prep; cryst+prot conditions: NH4SO4, TRIS/HEPES, CaCl2
If you use restraints to fix outliers, I strongly suggest to refine to convergence without
restraints after they are "fixed". If some outliers return, and "% favored"
decreases, so be it.
For one thing, depositing a structure with dihedrals restrained gives an unfair
impression of higher quali
----
Van: Edward A. Berry <mailto:ber...@upstate.edu>
Do you have evidence that the oil blocks diffusion of O2? O2 is a nonpolar
molecule, generally much more soluble in oils than in water. I'm not sure about
silicone oils, but I would think they also dissolve O2 readily.
eab
On 03/18/2015 08:02 AM, Patrick Shaw Stewart wrote:
Hi Steve
I have o
Actually I may have misunderstood the original post. Patrick never said oils
block O2 diffusion:
On 03/18/2015 09:47 AM, Edward A. Berry wrote:
The microbatch-under-oil method is very handy for anaerobic work:
(In a glove box, of course)
1. You can keep the microbatch
To be sure it is protein, it would be nice to see some spots at resolution less
than (spacing greater than) ~12 A. The pattern is somewhat consistent with a
unit cell with two very short axes and one long axis. If so, then when you
rotate so that the long axis is in the plane of the picture (pe
On 04/01/2015 08:47 PM, Shane Caldwell wrote:
I guess the next, probably more general question for the bb is: which utilities
export an NCS transformation matrix with more precision?
TAJones' "O" program allows you to specify output format like
write .LSQ_RT_m2m ncs.odb (3f16.10)
which gives
One of my projects was caught in the transition- as long as we didn't have
crystals diffracting to high resolution, the project was highly significant
but was denied (continuation of) funding for lack of confidence we
would get the structure. After we got good crystals and phased them
they said su
On 04/20/2015 06:44 PM, xaravich ivan wrote:
Hi CCP4eans,
solvent based HPLC system?
Do you mean like acetonitrile:water:TFA on reverse-phase columns? I think this
is
routinely used for analytical runs or to obtain material for protein chemistry,
but the concentration of acetonitrile required
Also collect while rotating around the long axis, which you nearly are in this
shot assuming the Phi axis is horizontal.
That way the close separation is in x,y where you can see it rather than in Z
which puts the spots on top of each other requiring thin slicing and (low
mosaicity!) to separat
Some details of one controversy Prof. Rich became embroiled in are available
on the wikipedia page for his colleague Sung-Hou Kim
(http://en.wikipedia.org/wiki/Kim_Sung-Hou).
Especially references 6-8, which are scanned copies of correspondence exchanged
with the folks at MRC, e.g. the initial a
On 05/02/2015 12:23 PM, Imre Berger wrote:
Dear Edward -
Would you be so kind and explain why you went ahead to post that comment
about Alex Rich on CCP4, in a thread which announced the sad news of his
passing away?
Yes- I realized after posting it that it was inappropriate. If there is any w
Thanks, these are great! I installed the ttf font on a windows box, and the
symbols are available in MSWord and Photoshop (and presumably powerpoint and
everything else). No more designing my own symbols in photoshop!
eab
On 05/08/2015 02:43 PM, Mooers, Blaine H.M. (HSC) wrote:
Hi Nick,
These
iser wrote:
Good points. But also, the traditional isomorphous difference map is not as susceptible
to model bias issues compared to a real space difference map (or a "vector"
isomorphous difference map).
On Tue, May 12, 2015 at 11:37 AM, Edward A. Berry mailto:ber...@upstate.edu>&
If I remember correctly, there are two different ways to calculate a surface by
rolling a ball over it, and i think that I want a program to calculate the
non-conventional one.
As I understand, the ASA is defined as the surface traced out by the _center_
of the rolling sphere, i.e. one radius
al Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Edward A.
Berry
Sent: Friday, May 15, 2015 3:08 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Two kinds of solvent-accessible-surface ?
If I remember correctly, there are two different ways to calculate a surface b
Is it possible to distinguish P64 from P62 without having basically solved the
structure?
Given that it is P64, is the +ive direction of the c axis arbitrary? A
left-hand helix is left hand either way you point it, and the molecules in the
asymmetric units could be pointing the opposite way.
In other words, the free set for each complex must be
such that reflections that are also present in the apo dataset retain
the FreeR flag they had in that dataset.
A very easy way to achieve this- generate a complete dataset to ridiculously
high resolution with the cell of your crystal, and ass
Neat! It's true the PDB will choose a unique code for you,
but they will use what you supply if it is already unique,
and it is nice to be able to choose something that can help
you remember what it stands for.
Gone are the days when we could choose meaningfull pdb ID's
(like 1PRC, 2PRC, 3PRC etc
A number of superposition programs allow to superimpose specified atoms (such
as CA).
Once you get the operator, comparing two different operators is not a job
for a conventional superposition program, since you are superimposing a
line on a line which has the extra degree of freedom- rotation ab
You raise some good points, but as far as better confidentiality
pre-publication goes. unreleased entries are not secret in any case- if the
second group is at all nervous about competition, they will be searching the
unreleased entries database (http://www.rcsb.org/pdb/search/searchStatus.do),
I can't imagine a journal doing that can you? When I work on my
supplementary material in a paper I don't expect that the journal will
take a bit out and publish it separately to support the work of my
competitors. Not out of spite that I was beaten - but because I don't
want to take the respon
A little bit confused about the 30 molecules. Superimposed models from the nmr
structure in
one or two copies ofone ensemble?
Anyway, Arp-warp just uses the model to calculate phases for an initial map.
How about forgo the model and give it a map with phases from the successful
phaser run?
It l
Another criterion for cutoff, also requiring the structure to be solved,
is the agreement between data and structure, e.g. Rfree or CCfree.
I think it is very unlikely that you could get Rfree =.2493 in a shell
which contains only noise. So I would suggest doing paired refinement
to 2.2 and 2.1 A
: Edward
----
*Va
I think it is part of ccp4:
$CCP4/bin/topdraw
On 07/05/2015 10:30 AM, Faisal Tarique wrote:
Dear all
Can anybody provide me the link to download or install " TopDraw " a topology
drawing interface in CCP4..?
Thanks
--
Regards
Faisal
School of Life Sciences
JNU
est wishes, Tobias.
On Fri, Jun 19, 2015 at 4:54 PM, Edward A. Berry mailto:ber...@upstate.edu>> wrote:
A number of superposition programs allow to superimpose specified atoms
(such as CA).
Once you get the operator, comparing two different operators is not a job
fo
What about China? Singapore?
On 11/09/2016 12:45 AM, Tom Peat wrote:
I don't know about Europe, but it is very tight Down Under...
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of William
G. Scott
Sent: Wednesday, 9 November 2016 4:38 PM
To: CCP
On 11/17/2016 08:36 AM, herman.schreu...@sanofi.com wrote:
Dear Shijun,
The reject.hkl file is the file with all rejected reflections. The first three
numbers are h, k and l. For the other items you have to consult the HKL manual.
As I said, I am not familiar with HKL2000. However, in your cas
On 11/30/2016 10:16 PM, Keller, Jacob wrote:
If you fine slice and everything is then a partial, isn't that *more* sensitive
to lack of synchronization between the shutter and rotation axis than the
wide-frame method where there's a larger proportion of fulls that don't
approach the frame edge
When faced with a program requiring HL coefficients, and having
phases from a (partial) model, I used to run a ccp4 program called
sigmaa to generate the HL coefficients. I'm not sure if this is
theoretically a good idea, but at least it allows the program to run.
On 01/19/2017 11:10 PM, Vikram D
Uma's use of quotes around "di" suggests a related question about PDB
convention. It was my (perhaps not very good) understanding that ligands should be
identified by what is actually present in the crystal, and not by what can be modeled.
For example endogenous ubiquinone is likely to be UQ50
As I understood the problem, it is that automatic assignment comes out
differently for different structures of the same protein or proteins so close
that they should have the same secondary structure, due to differences in
quality of the structures. The question then is not how to determine sec
Does this count as an example?
grep SSBOND /a/pdb/pdb4e9m.ent
SSBOND 1 CYS A 39CYS B 39 1555 1555 2.05
SSBOND 2 CYS C 39CYS D 39 1555 1555 2.04
SSBOND 3 CYS E 39CYS F 39 1555 1555 2.03
Speaking specifically for succinate dehydrogenase, there are a number of
assembly factors required for insertion of flavin, iron-sulfur clusters
(SDHAF1,2,3 . . .). Since E. coli or Pischia make their own SDH, there is
a possibility the endogenous assembly factors and co-factors would work
with t
Yes, CM-Sephadex expands and contracts incredibly. For other than batch methods
you will be much better using CM-Sepharose. I guess it is cross-linked
sepharose, and doesn't swell up much even in distilled water.
What is happening is the negative charges of the carboxy groups repel each other,
On 03/09/2017 11:45 AM, Alice Dawson (Staff) wrote:
you can find a paper model of GFP at the RCSB PDB
https://cdn.rcsb.org/pdb101/learn/resources/gfp-model.pdf
Hmm- that seems to involve quite a bit of cut-and-pasting too - or rather
cut-and taping!
2D topology diagrams are really schematics
Raji Edayathumangalam wrote:
I have superimposed one structure on top of another. Now, I am
interested in only displaying the water molecules that are identical
between the two structures. MolA has ~3000 waters and molB has ~900
waters. There are ~330 water molecules identical between the two
Mapman (Uppsala software factory) allows you to subtract maps
if they are on the same grid. You may need to multiply one
map by a factor (again in mapman) to make the background flat
in the regions you believe to be identical.
Linearity of the Fourier Transform implies you could get
the same resu
Actually I was thinking of a somewhat earlier paper:
Rayment,I. Molecular relacement method at low resolution:
optimum strategy and intrinsic limitations as determined
by calculations on icosahedral virus models.
Acta Crystallogr. A 39, 102 116 (1983).
But thanks for bringing the Caliandro et a
-oops-
many missing REFLECTIONS are included.
Sounds like a pretty successful refinement, given the resolution!
The fact that releasing NCS improves R-free suggests there are
real ncs violations (otherwise releasing ncs increases R-free).
But they may be confined to a few residues in contact areas.
You can locate these violations by comparin
Kay Diederichs wrote:
the CPU (AMD versus Intel) does not play any role for crystallographic
computing, but you'll have to decide whether you want to install the
64bit or the 32bit version of RHEL4.
32bit programs run a bit faster on a 64bit operating system, and with a
64bit OS you can run p
It definitely could be the pin, assuming that projects in from the opposite
side as the beamstop shadow. Although the crystal is a major source of
background scatter, and obviously the pin cannot cast a shadow in that light,
air scattering is also significant, and the air at the tip of the collima
Dear All,
I'm doing molecular replacement with beast, using
the ccp4i gui.
Space group is P41 or P43 based on syst. absences.
Input mtz file is reduced in P41, but I want
to try the translation search with both. So,
Does beast automatically try both?
Is there a parameter I can enter to set p43 on
Ibrahim M. Moustafa wrote:
The last question: In the same paper, for the complex structure R and
Rfree are equal (30%) is that an indication for improper refinement in
these published structure? I'd love to hear your comments on that too.
Several times I solved low resolution structures using
?) to
compensate for the difference in resolution of model and data?
Carien
On 4 Jun 2007, at 19:38, Edward A Berry wrote:
Ibrahim M. Moustafa wrote:
The last question: In the same paper, for the complex structure R and
Rfree are equal (30%) is that an indication for improper refinement
in
Andrew Gulick wrote:
that the PDB file can be re-ordered? I realize I could use a sort command
in UNIX however that would be complicated by the presence of multiple chains
and splitting up the PDB by chain could be as tedious as manually editting.
Any other easy work-around suggestions from an
Ethan A Merritt wrote:
On Wednesday 08 August 2007 20:47, Ralf W. Grosse-Kunstleve wrote:
Implementations to generate intuitive, maximally backward compatible
numbers can be found here:
http://cci.lbl.gov/hybrid_36/
From that URL:
ATOM 8 SD MET L 48.231 -64.383 -9.257 1.0
Ralf W. Grosse-Kunstleve wrote:
I.e. the first 9 serial numbers are represented as usual. The
following atoms use a base-36 system (10 digits + 26 letters) with
upper-case letters. 43670016 (26*36**4) additional atoms can be
numbered this way. If there are more than 43770015 (9+43670016)
How about this (may be way off base):
Any transformation can be seen either as moving
of the coordinates in a fixed coordinate system, or as
a "change of coordinates" and expressing the position of
the same object with respect to the new coordinates.
In molecular replacement it is convenient to
For nice crystals data processing is straightforward. For crystals with
large unit cells, high mosaicity, and diffuse scattering, processing
can be critical. It may be that future advances in integration
software will allow one to extract far better data from such a
diffraction dataset than can be
One other idea idea:
1. Solvent flattening on the hexagonal crystal
2. use the flattening mask to cut out the density of one molecule,
put in a large P1 cell for calculating structure factors
3. Use the structure factors from the density of the hexagonal crystal
to solve the triclinic crysta
Bernhard Rupp wrote:
Dear All,
I wonder about the exact use of torsion restrains and the effect
on phi/psi/w validation.
a) does refmac restrain phipsi at all (except vdw repulsion
which does not bias them otherwise)?
Isn't it the case that vdw interactions are turned off
between ato
I wrote:
Isn't it the case that vdw interactions are turned off
between atoms in a residue, and perhaps with the residues
before and after?
No it is not the case, at least in refmac5 and SHELLXL.
Thanks to those who clarified this.
Jim Naismith's earlier post, which I had not seen, suggests
a b
I just noticed there is a space between s and o in .so:
Robert Grant wrote:
Gtk-WARNING **: Unable to locate loadable module in module_path:
"libbluecurve.s o"
Probably a mistake in pasting the error message,
but if not it could be significant.
Ed
Clarification-
Someone wrote:
Ah- that's going way to fast for the beginners, at least one of them!
Can someone explain why the R-free will be very close to the R-work,
preferably in simple concrete terms like Fo, Fc, at sym-related
reflections, and the change in the Fc resulting from a step of
I'm currently struggling with what I think is a variation on this theme,
would appreciate comments as to whether my thinking is reasonable.
The space group is basically rhombohedral, but along the lines of spots
in the (hexagonal)L direction, with some crystals there are two weak
spots between eac
Better yet, RbBr? and pH MES, MOPS, and HEPES with RbOH?
I haven't checked the price.
Jacob Keller wrote:
Is there any reason why crystallographers have not routinely
substituted NaBr for NaCl in protein crystallization stocks, or even
pH'd their TRIS with HBr, if there is no NaCl? Wouldn't it m
Sean Seaver wrote:
Better yet, RbBr? and pH MES, MOPS, and HEPES with RbOH?
I haven't checked the price.
Including shipping in the US
RbBr: 50 g 99% pure is ~$150.
RbOH: 25g 99+% pure in 50 % water runs about ~$120.
It would be interesting to see how the substitution would influence the
crys
Arnon Lavie wrote:
~~~
We have been considering buying a Nanodrop machine (small volume, no
dilution needed, fast, easy).
However, while testing our samples using a colleague's machine, we have
gotten readings up to 100% different to our Bradford assay (all fully
purified proteins). For example,
In my experience ADIT (or ADIT2) is aware of symmetry mates,
and gives a different message for waters related to them- something
about these waters will be moved for you if you don't do it yourself.
I would go ahead and deposit, and when you are given the final file
to OK for release, if it erron
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 specif
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
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 E
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 does
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
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 sour
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
n a new terminal: imosflm 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-konst
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/
Seems to me the CCP4 change is exactly in line with the developers'
response to wgscott's bug report at:
https://bugs.launchpad.net/ubuntu/+source/blt/+bug/19148
You have to have the BLT package, whether you shell bltwish or wish.
Modern BLT package doesn't contain bltwish, because
"not a bug.
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.
http://npsa-pbil.ibcp.fr/cgi-bin/ali
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.
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 it,
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,
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 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 k
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 discu
>>> 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-
vs vs -
although I shouldn't have thought extra carriage return
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%,
favored
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 suf
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 a
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 limit
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 limita
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 <
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
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
t
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 ]
Crystal
yum install lesstif ?
but wouldn't the motif stuff be required for the X-server, i.e. your terminal, not for the
server running adxv?
Rajesh kumar wrote:
Dear Mark,
$ locate XKeysymDB - didnt come with any thing suggests probably openmotif lib
is not
installed.
I linux server has Fedora and
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
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 coordina
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
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 in
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 p
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.
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