Clemens,
I don't think anyone suggests to use unmerged data and such. I think
there is important difference in what Mohinder describes.
Let's say I have a ligand on symmetry axes and so it appears in two
conformations. If I reduce symmetry, there are two possible scenarios.
a. In lower symmetr
There is nothing fundamentally wrong with refining in P1 even if the
P21212 symmetry is present. An effective way to reduce the number of
parameters wold be to introduce tight restraints. If you decide to
lower the symmetry, go with P21 as it still keeps your ligand off
symmetry axes. You can th
A couple of twinning-related questions.
I have a protein-DNA complex in P65. Protein binds DNA as a dimer, DNA
itself is not palindromic and has sticky ends located asymmetrically
with respect to the protein (dimer).
DNA contains a single fluoro-uracil which is flipped into the active
site. Thi
To upgrade the Refmac version that I am running from inside the CCP4i, I
did the following
mv $CCP4/bin/refmac5 $CCP4/bin/refmac5.5
cp refmacgfortran $CCP4/bin/refmac5.6
ln -s $CCP4/bin/refmac5.6 $CCP4/bin/refmac5
It seems to have worked fine. Is there more intelligent way of doing
this?
--
E
Thanks, Ian, this is excellent. It appears that depending on the
sequence the "ideal target rmsd" may vary from 0.018 for a poly-H to
0.024 for a poly-P. Except for some really short sequences, in PDB the
variation is generally between 0.021-0.022, indeed undetectable.
On Fri, 2010-10-15 at 10:2
raints as covalent bonds you need to specify type 1 (type 0 means
> dictionary values will be overwritten and type 2 is external restraints for
> non-covalent bonds)
>
> I hope it helps
>
> regards
> Garib
>
>
> On 14 Oct 2010, at 21:51, Ed Pozharski wrote:
&g
On Thu, 2010-10-14 at 23:31 +0200, Tim Gruene wrote:
> you observe that each photon decides on exactly one slit
> that it goes through.
That is if you observe which slit it goes through.
--
"I'd jump in myself, if I weren't so good at whistling."
Julian, King of L
On Thu, 2010-10-14 at 23:31 +0200, Tim Gruene wrote:
> I would like to understand how the notion of a photon being scattered
> from all
> electrons in the crystal lattice explains the observation that
> radiation damage
> is localised to the size of the beam so that we can move the crystal
> along
It appears that external restraints are included in bond_rmsd
calculation. When they are used to restrain the hydrogen bonds to
maintain the Watson-Crick pairing in a 3A resolution structure of a
protein-DNA complex, the bond_rmsd is inflated about 5 times. To verify
this, the refmac run was done
On Thu, 2010-10-14 at 09:11 -0700, James Holton wrote:
> I wonder if anyone on this
> thread can explain to me the difference between a matrix and a
> tensor?
Matrix is a 2nd order tensor. Tensors may have any number of
dimensions, including zero. Tensor is just a fancy name for a
multidimensi
or, a vector quantity in the old
> coordinate system can be transformed into the new one by using exactly
> the same operator. This is the correct definition of a vector.
>
> G.
>
>
>
> On Thu, 14 Oct 2010 10:22:59 -0400, Ed Pozharski
> wrote:
> > The definition
On Thu, 2010-10-14 at 08:41 +0200, Tim Gruene wrote:
> This sounds as though you are saying that a single photon interacts
> with several
> electrons to give rise to a reflection.
Not only with several - it shouldn't be much of an exaggeration to say
that the photon senses all the electrons in th
The definition game is on! :)
Vectors are supposed to have direction and amplitude, unlike scalars.
Curiously, one can take a position that real numbers are vectors too, if
you consider negative and positive numbers having opposite directions
(and thus subtraction is simply a case of addition of a
Lei,
1. Consider making the complex and then purifying the excess peptide
away by dialysis (size exclusion may be tricky since complex may be
diluted in the process).
2. Conventional wisdom would be to try to minimize the amount of excess
peptide as it may "interfere with crystallization". But c
You don't need twinning to invalidate the Rmerge as a criterion for the
resolution cutoff, there are other reasons why you should use I/sigma
instead. If you process data all the way to 3A, what's the I/sigma in
the highest resolution shell?
On Wed, 2010-10-06 at 11:28 +0200, fulvio saccoccia wr
On Wed, 2010-09-22 at 22:46 +0200, Gerard DVD Kleywegt wrote:
> > ...constraints are just a special case of restraints in the limit
> > of infinite weights
> If you impose "infinitely strong" NCS
> restraints,
But "in the limit" means that the restrained refinement can be made to
approach the re
It's best to have dedicated NVIDIA (don't have much experience with ATI,
but it is my understanding that they may be more difficult to configire
sometimes). However, Intel on-board graphics has gotten much better
recently (in fact, Intel releases drivers as open source (guess because
they are not
Sure. But if I start with model that has no hydrogens, they will be
generated but not passed to the output, right. just like refmac.
On Wed, 2010-09-15 at 14:52 -0700, Pavel Afonine wrote:
> Dear Ed,
>
> On 9/15/10 2:47 PM, Ed Pozharski wrote:
> > On Wed, 2010-09-15 at 16
On Wed, 2010-09-15 at 16:26 -0400, Phil Jeffrey wrote:
> So the riding hydrogen model is imperfect. At least with
> phenix.refine
> you can measure it, unlike the default behavior of REFMAC. (But you
> can
> tell it to write hydrogens out, I believe).
>
My impression is that default behavior
On Wed, 2010-09-15 at 13:13 -0700, Pavel Afonine wrote:
> I can't agree with this, sorry. A change to a model content
> (especially
> the one that changes Fcalc) is a model manipulation.
>
That is not what I asked. Do you agree that using the riding model does
not add additional refinable parame
On Wed, 2010-09-15 at 10:50 -0700, Pavel Afonine wrote:
> I wouldn't dare calling a model manipulation that typically changes
> the
> R-factor by 0.5 ... ~2% as "nothing". Although, you are may be right
> -
> "who cares"?
It's not a manipulation because no parameters were manipulated in the
mo
On Wed, 2010-09-15 at 09:14 -0700, Dale Tronrud wrote:
> I know that in my refinements I manually move the hydrogen
> from one nitrogen to the other in a couple Histidine side chains,
> and have created my own rules for hydrogen generation in co-factors.
>
Excellent point. And I believe in this
On Wed, 2010-09-15 at 07:57 -0700, Pavel Afonine wrote:
> if you refined your structure with H, then you should deposit it with
> H
sure. But the structure is not *refined with hydrogens* when they are
in predicted positions. Following the same logic one could suggest that
electron density shou
Mark,
On Tue, 2010-09-14 at 13:34 -0400, Dr. Mark Mayer wrote:
> Where does the crystallographic community stand
> on deposition of coordinates with riding
> hydrogens?
Surely community is divided on this. There could be arguments made both
ways. Personally, I think that riding hydrogens can
On Mon, 2010-09-13 at 15:52 +0100, Paul Holland wrote:
> that has very high sequence similarity to the search model
How high exactly?
--
"I'd jump in myself, if I weren't so good at whistling."
Julian, King of Lemurs
David is absolutely right. There is no design, Jacob, we just
instinctively look for it everywhere because seeking purpose instead of
understanding mechanism conveys advantage to our species. Your
rationale is flawed - just because it is imaginable (with caveats) does
not mean that it must exist
is k=2 the maximum likelihood estimate of the best approximation
of the true map in the following form
DFc + k*(mFo-DFc)
Ed.
On Wed, 2010-09-01 at 10:49 +0100, Ian Tickle wrote:
> On Wed, Sep 1, 2010 at 4:26 AM, Ed Pozharski wrote:
> > The
> > reason you see the missing region in
Ian is, as always, absolutely right. The only comment/correction I have
is that Hailang was apparently referring to severely incomplete model,
for which the poor phases will dominate the mFo map. Under such
circumstances, even 2fo-fc map will not correctly reflect the actual
relative contribution
If I understand correctly, the only difference between "mFo" and "Fo"
map will be weighting in different resolution shells according to
figure-of-merit. While this will presumably downweigh the less reliable
resolution shells, it will hardly make up for the heavy model bias. The
reason you see th
On Tue, 2010-08-31 at 13:15 -0400, Hailiang Zhang wrote:
> Is the difference
> between mFo and Fo maps supposed to be very small?
For an essentially correct model, yes. The major advantage of (2mFo-DFc)
maps is suppression of model bias, so if you don't see much difference
then your model is very
On Tue, 2010-08-31 at 11:57 -0500, Jacob Keller wrote:
> I just don't want this guy to get misled into perhaps wasting
> months/years on something not particularly promising.
Trouble is, of course, that one never knows if a particular trick will
work this time. We routinely get PEG/fluoride salt
Well said. I've seen three cases by now when switching to a homologue
from a different organism led to solving a structure (and way too many
cases when crystals just did not diffract, either at all or well
enough :).
On Tue, 2010-08-31 at 18:48 +0300, Tommi Kajander wrote:
> Or might be worth goi
Unfortunately, some crystals don't diffract at all. You may want to try
to 100% verify that it's protein either by SDS-PAGE or mass-spec
(100x100x100 micron crystal could contain ~0.5mcg of protein, so you my
need to use silver staining). If it is, I'd consider trying to get
diffracting crystals
On Thu, 2010-08-26 at 11:35 -0400, Roger Rowlett wrote:
> We routinely polish protein preps on Q-sepharose (Mono-Q should be
> even better) with at least 10 CV gradients over a narrower range of
> NaCl concentrations, maybe 0-0.5 M or even smaller.
Just wanted to add that in my experience the reso
I don't see what George's attempt to point out that pure-phenix
questions should be asked in phenix bb (and the point itself may be
subject to different opinions) has to do with renaming Moscow streets
and subway stations (unless you thought that the proposition to rename
ccp4bb is serious).
You
On Fri, 2010-08-20 at 18:50 +0200, Charles W. Carter, Jr wrote:
> Is there a program that will read in a pdb coordinate file and re-order the
> side chain atoms in each residue according to a standard order?
>
> I've a program that compares two files for the same structure, but requires
> that
There are many ways to test if the two test sets are identical. For
example (using CCP4i):
Go to Reflection Data Utilities -> SF file analysis
and then perform data correlation between your two FreeFlag columns. If
they are identical, the resulting R-factor should be 0 and correlation
coeffici
> 38, 1734.
> 39, 1778.
> 40, 1822.
> 41, 1866.
> 42, 1910.
> 43, 1954.
> 44, 1998.
> 45, 2042.
> 46, 2086.
> 47, 2130.
>
>
>
> --- On Thu, 12/8/10, Ed Pozharski wrote:
>
> > From: Ed Pozharski
> > Subject: Re: [ccp4bb] PEG in
Nevertheless, what do you have in mother liquor/protein buffer?
On Thu, 2010-08-12 at 17:24 +0200, wrote:
> Dear All,
>
> I am refining structure of protein at 1.7A. It is enzyme with 3
> histidine residues in the active site, which are chelating metal (at
> the moment I built in calcium but
On Thu, 2010-08-12 at 08:57 +, MARTYN SYMMONS wrote:
> Zero occupancy is generally a deprecated way of dealing with missing
> density as it is confusing for less experienced user of the
> coordinates. I think zero occupancy can be useful during refinement as
> the atoms help fill space (or for
PEG solutions contain fragments of all sizes - it is the average size
(however defined by the manufacturer) that is 1000. So technically it
is incorrect to claim that you have PEG1000 molecules bound to your
protein, it is most likely much shorter fragments that can penetrate the
channels in prote
Take a look at MAMA from Uppsala Software Factory
http://xray.bmc.uu.se/usf/mama_man.html
It can generate the mask from the PDB file. This will, however, leave
internal cavities belonging to "solvent". If you don't want that, the
following MAMA script will fix it giving you the mask of the pro
Pure translation NCS?
On Fri, 2010-07-16 at 20:04 +, Marie Lacroix wrote:
> Hi everybody,
>
> I just calculated a self rotation function from the data used for
> molecular replacement (what by the way did not worked) and saw no peak
> at all. Does this not mean that there is only one molecule
The problem is the unrestrained nature of the grouped b-factor
refinement itself. Read this thread
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg14133.html
In a nutshell, just stick with (properly wighted) individual B-factors.
On Fri, 2010-07-16 at 10:57 -0400, hongjunyu wrote:
> Hi，
>
But of course. This is what mixed refinement is for - the easiest was
to get it to work is probably somehow generating anisou records for all
the atoms and then doing something like "egrep -v 'ANISOU|HOH'" on the
pdb file. Mixed refinement will then refine only the atoms with
pre-existing anisou
I just compiled the latest coot (0.6.2-pre-1.3011) on 64-bit Lucid (it
appears that the gtkglext issue is gone). I don't know what you mean by
so many compiling issues. Are you using autobuilder script?
On Sun, 2010-07-11 at 12:28 -0700, Michael Hothorn wrote:
> Hi,
>
> can someone point me to
Given your unit cell parameters + high Rsym I'd say you have an indexing
problem. If you try P2, what happens? I suspect that you might have
something as simple as incorrect beam center position and while
integration works, scaling fails (the only way you are getting away with
it is by choosing P
On Fri, 2010-07-02 at 13:35 -0400, Douglas Jacobsen wrote:
> My opinion is that attached images in bb posts should be allowed:
> 1) Storage & network bandwidth is cheap
Glad to hear that University of Michigan administrators agree with you.
However, you should not forget that cheap is a compl
gt; >>>> e.g. mutt, pine, etc, which address the very same problem.
> >>>>
> >>>> It's is a lot easier to show a jpg-image a few kB in size than to
> >>>> attempt to
> >>>> describe what you see with words.
> >>&g
Several recent posts with decently sized attachments (now in cross eyed
stereo too!) prompt this (annual?) anti-paperclip-button rant. Lucky
for me, I can just recycle the old messages:
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg11949.html
Cheers from the self-appointed thought police,
When refmac encounters new ligand, the default behavior is to report it
in the log file and exit. But it also apparently creates the output
pdb-file (with coordinates the same as the input file). Is there some
way to change this behavior so that no output pb file is generated?
What I need is the
http://en.wikipedia.org/wiki/SGI_Octane#Available_Operating_Systems
just googled "linux sgi o2"
On Tue, 2010-06-01 at 10:18 -0600, Brennan Bonnet wrote:
> Hi All,
>
>
>
> I just obtained a Silicon Graphics O2 Unix workstation from 1996. I
> want to use it for 3D modelling of protein crystals
http://sw-tools.pdb.org/apps/CIFTr/
On Tue, 2010-06-01 at 15:21 +0200, Christian Engel wrote:
> Dear All,
>
> I am looking for a ccp4 program that reads in cif-files and converts
> them into pdb-files, including the CRYST1 card. Can anybody suggest a
> solution? I didn't find any in ccp4i, e.g.
You should take a look at DIFFMODE COMPARE keyword in AREAIMOL manual,
it allows for buried surface area calculation (you have to prepare the
two pdb files with complex and receptor only). If you can easily use
command line and scripts (i.e. you are running CCP4 on non-micro$oft
OS), try the follo
On Tue, 2010-05-18 at 07:03 -0700, Miller, Mitchell D. wrote:
> The decrease in missing reflections are due to the fact that
> the output file does not include the missing reflections that
> are lower resolution than the lowest resolution observed
> reflection. Thus, this file is no longer "uniq
I just checked a recent refmac job and it seems that in the output mtz
the has indeed changed. what's more interesting, the number of
missing reflections has changed too (disturbingly, it decreased so that
the dataset looks more complete 97.07% to 97.17% in this case).
But if the same overall an
On Fri, 2010-04-30 at 13:35 +0100, Nicholas Keep wrote:
> If anyone has a piece of software that would do this it would be
> great.
>
How about this (this is a single line)
---
grep 'ATOM\|HETATM' file1.pdb file2.pdb |grep -v REMARK | cut -d: -f 2 |
cut -c 13-54 | sort | awk 'BEGIN {FIELDWIDTHS
On Thu, 2010-04-29 at 16:23 +0530, Jhon Thomas wrote:
> This is a strange behaviour of the protein complex.
Why is this strange? 20 mg/ml is fairly high, just dilute the protein
to 10 mg/ml and repeat the screen. Or better yet, repeat the screen
with 1:2 protein:reservoir ratio for precipitated
I may be mistaken, but there appears to be no "chainid" in CNS atom
selection syntax. Standard topology generators will convert chain ID to
segid, which could then be used.
On Wed, 2010-04-28 at 18:50 +0530, AMIT wrote:
> Just type in CNS refine.inp in the atom select option:
>
> {===>} atom_sel
Transferring crystal into mother liquor minus lithium sulfate plus
ligand may work (consider both direct and stepwise transfer). Worked
for us recently when 0.2M sodium malonate was competing out the ligand
(which is ironic given that sodium malonate would be my first choice of
replacing ammonium
On Wed, 2010-04-21 at 17:21 -0700, James Holton wrote:
> The "0.3% chance" of a peak being above 3
> "sigmas" assumes that the histogram of electron density values is
> Gaussian. It is not! In fact, it is a funny-looking bimodal
> distribution (the peaks are protein and solvent regions).
Ind
Couldn't they simply be too thin? After all, unit cell dimensions are
routinely about 0.01um, so if these needles are only fraction of a
micron thick, there is simply not enough material for diffraction.
Nice looking but non-diffracting protein crystals are too disordered
(i.e. while packing is p
I second Tim's opinion. In the days of CNS/O, there was a popular rule
to place waters in 3 sigma peaks that make chemical sense, then
re-refine and keep those waters that produce more than 1 sigma in 2fo-fc
map. (With Coot the default cutoff is 5).
There could be a bizarre probabilistic argumen
Use bond command
bond atom1, atom2
once you do that, any subsequent line and stick renderings will connect
the atom1 and atom2 (you can right-click on the corresponding atom to
see their full string representation). I assume you are trying to do
something like this
http://tinyurl.com/y2cdezj
I
Katherine,
all good questions and all discussed previously on this very discussion
board. My personal opinion did not change much since 2007:
http://www.dl.ac.uk/list-archive-public/ccp4bb/msg19777.html
although I would probably amend couple of minor things. As for riding
hydrogens, take a look
Hussain,
http://137.189.50.96/kbwong/teaching/pymol/pymol_tutorial.html
which is the top hit when you google "pymol electron density". Using
google (and not to appear biased, other available search engines) is the
most valuable advice (per word) that you may possible get.
On Tue, 2010-04-13 at
On Thu, 2010-04-08 at 23:26 +0100, Daniel Bonsor wrote:
> both the Rfactor and Rfree get stuck at 30% and 36%
according to
http://xray.bmc.uu.se/gerard/supmat/rfree2000/plotter.html
these are higher than expected. With that said, R/Rfree should not be a
fetish, and your model may be fine (i.e. a
It is also possible that mother liquor prevents binding (although often
in such cases you would see some precipitant component in the active
site.
I would generally bet on need for conformational change. And you expect
to see the product complex, right?
Ed.
On Fri, 2010-04-09 at 11:15 +0200, Pa
On Thu, 2010-03-18 at 12:51 -0500, Jacob Keller wrote:
> Does anybody have a good way to understand this?
Sure, it just depends on what would one consider a "good" way to
understand. For a pure empiricist, it's good enough to see one of those
two-dimensional phase swap pictures. For a "mathemat
On Fri, 2010-02-26 at 16:50 +0100, Gerard DVD Kleywegt wrote:
> But it still won't solve Miri's problem. I think what she is asking
> for is a
> program that detects which atoms should be matched to which,
> irrespective of
> their names (i.e., not assuming they are called " CA ") and order
> (i.
Ethan,
manual handling of the mosaicity seems to help. There are now plenty of
other things to sort out, but at least scalepack does not crash anymore.
I used lower fixed mosaicity setting in denzo and fixed it in scalepack.
Another issue is that there was apparently something funny about first 5
calepack
> in postrefinement sees this as a serious case of "slippage" and is
> unable to postrefine a value of crystal rotx that is compatible with
> all the frames.
>
> It may be possible to turn of post-refinement with "POSTREFINE 0"
> or some such.
>
> E
I want to process bunch of frames with extremely short step - i.e. these
are 0.5degree oscillations but crystal only rotates by 1 degree over
1000 frames (I would have kept it at the same orientation if Rigaku
control software would allow zero step). Denzo can process the frames
all right, but sca
Nick,
there was a discussion of this three weeks ago. Check this thread
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg14133.html
I still maintain the view that appropriately tight restraints are the
way to go and not the grouped B-factor refinement (at least not the way
it is currently i
Pavel,
> Simply not true. Think why -:) Hint: in restrained refinement the
> weight applies to all terms - bonds, angles, torsions, etc... So if
> you choose tight weight in such refinement the torsions will be
> restrained as tightly as other terms (at least as it would be in CNS
> or phenix.refi
Pavel,
> - In general you are free to decide what you name a domain: it can be
> a residue, its part or the whole structure.
> - What would be "main" and "side" for non-amino acid molecule, like a
> whatever ligand?
I don't see how my freedom to explicitly define the terms I use in a
post is rele
On Fri, 2010-01-29 at 00:14 -0500, Xun Lu wrote:
>So, how can I tell Refmac not to sacrifice the geometry of DNA
> to fit my poor density? Or, how to fix the DNA (just like in CNS)?
> Anyone could share their experience and tricks about dealing with
> DNA?
>
Xun,
I needed once to restra
DISCLAIMER: When I say "grouped B-factor refinement" I mean CNS-style,
Bmain/Bside refinement. Not to be confused with more general "domain
B-factor refinement" where single B-factor is assigned to some part of
the structure.
> Apart from improving data-to-parameters ratio, another argument for
Jose Antonio,
I've seen similar behavior few years ago with grouped B-factor
refinement in CNS. The argument for the grouped refinement is as
follows:
This is better than individual B-factor refinement at low resolution
because you significantly reduce the number of parameters.
There are two h
http://hamptonresearch.com/documents/product/hr000175_what_is_tacsimate_new.pdf
turns up once you use google's "I'm feeling lucky" button.
On Tue, 2010-01-26 at 15:42 +, Zhiyi Wei wrote:
> Dear all,
>
> I got a problem with my crystals. I have two total different proteins
> that both can be
Phoebe,
my understanding is that power of UV illumination here is not in
salt-vs-protein test (which, imho, can only be finalized by testing
diffraction) but in improved contrast for protein crystal detection. I
haven't used UV microscopes myself, but images provided by manufacturers
are quite im
The increase in RFZ is relatively small and not entirely unexpected.
While hydrogens only contribute one electron (as opposed to carbon (6),
nitrogen(7), oxygen(8) and sulfur (16)), there are many hydrogens (in
fact, almost as many as all the other atoms combined). For instance, in
lysozyme you ha
My knowledge of Fortran is dated, but the ESU_R and ESU_RFREE are
calculated in refmac like this
HESU_CRUIC = SQRT(FLOAT(N_REFINED_ATOMS)/FLOAT(NREFMNPAR))*
+ COMPL**(-0.33)*HD_HIGH*HRFAC_SHELL_WORK(NB1)
HESU_FREE = SQRT(FLOAT(N_REFINED_ATOMS)/FLOAT(NREFA(1,NB1)))*
+
The electron density snapshots I can understand on some level - after
all, picture is sometimes worth thousand words. But it does take a
"windows person" to post Mb-sized picture instead of a one-line error
message.
On the substance, you should probably do what the program suggests -
check the m
With salt-based conditions sodium malonate is your friend:
Acta Cryst D59: 2356
On Tue, 2009-12-15 at 12:20 +, Natalie Zhao wrote:
> -Original Message-
> From: owner-c...@dl.ac.uk [mailto:owner-c...@dl.ac.uk] On Behalf Of Rafael
> Couñago
> Sent: 14 December 2009 20:22
> To: c...@ccp
se with the cutoff level selected, but it is
> the inconsistency of that level with Rmerge and the Rvalues for the
> highest shell.
>
> BR
>
> -Original Message-
> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ed
> Pozharski
> Sent: F
Does anyone know if REFMAC has any SIGFP cutoff? I looked into manual
but perhaps missed it. What I mean is abnormal situation where some
FOBS are 0 or even negative - is there any intrinsic cutoff or
refinement will be done against all the reflections?
Thanks,
Ed.
--
Edwin Pozharski, PhD, Ass
I would like to point out that this outright fabrication remains an
isolated incident. There are over 50,000 crystal structures in the PDB,
which means that this is only ~0.02% of the total. This is all quite
bad, but let's not overstate the problem.
Maybe such report is not a great idea after a
Not to derail the thread, but there is nothing, imho, wrong with I/s=1
cutoff (you expect I/s=2, I assume?). R-factors will get higher, but
there are good reasons to believe that model will actually be better.
This has been discussed many times before and there is probably no
resolution, so why no
Ian,
On Mon, 2009-11-23 at 17:34 +, Ian Tickle wrote:
> Ed,
>
> > For instance, if angles are measured in degrees and x<<1
> > sin x ~ pi * x / 180
> > sin x ~ x
>
> Your equations cannot simultaneously be true & in fact the 1st one is
> obviously wrong, the 2nd is right. In the 1st case I
On Sun, 2009-11-22 at 23:33 -0800, Dale Tronrud wrote:
> I could be describing my angle as
> 1.5 radians, 1.5 degrees, or 1.5 cycles (or 1.5 of the mysterious
> "grad" on my calculator).
I thought that use of degrees is based on dividing a circle into 360
parts - roughly one per day (then in geo
ld do it (but with Emacs).
> But I guess the official way would be with Reflection Data Utilities -> Edit
> MTZ Datasets which will edit the dataset cells. It wraps keywords of CAD.
>
> Martyn
>
> -Original Message-
> From: CCP4 bulletin board on behalf of Ed Pozharsk
You may be able to open mtz files in a primitive text editor such as
nano (I just did). It's a little awkward, as there are no line breaks.
MTZ header is in the end of the file and it is plain text, so should be
easy to edit manually - just make sure you don't introduce extra space.
There are ple
Check if you have csh installed in your system. If it still fails, try
installing tcsh.
If I am right, then this is happening because automar-install script is
written for csh but which is not installed by default on your system
(most modern linux distros use bash).
On Mon, 2009-11-02 at 22:06 +
On Thu, 2009-10-22 at 10:18 -0400, protein.chemist protein.chemist
wrote:
> What is the Sigma Cutoff that one should use for Data Processing using
> HKL2000.
>
Since you say HKL2000, I assume that you mean the "Refinement Sigma
Cutoff" in index tab. The parameter, imu, determines which reflectio
I obviously didn't pay any attention to the specific numbers/space group
(and didn't read the rest of your message). Fred is absolutely right -
the only thing you can do in P21 is to switch a and c (and invert b to
maintain the right hand).
So maybe your crystal can be indexed both ways, but denz
On Thu, 2009-10-22 at 11:19 -0400, Yuan Cheng wrote:
> datasets in scalepack.I am wondering whether there is any way to reindex
> these two datasets to make their a/b dimensions match. Any suggestion
> will be highly appreciated.
Oh yeah, there is. It's on page 102 of the HKL manual (Scenario 5
Both pymol/align and coot/ssm (I presume) do the secondary structure
alignment first followed by structural alignment. So it only works for
proteins. In Pymol, there is "fit" command that instead matches atoms
with the same names; and "super" which does sequence alignment first.
You can try to pl
There is the shift_molecules.inp script in CNS. You can definitely do
this manually using pymol and/or coot. PHASER, I believe, does this
automatically.
On Wed, 2009-10-21 at 13:03 +0100, FRANCOIS XAVIER CHAUVIAC wrote:
> Dear crystallographers,
>
> After solving a structure by molecular replac
> > My resolution is 1.6A although I have cut it to 1.8A to bring the
> > R-factor down. I've been performing restrained refinement in refmac5
> > using the default settings. The solvent content is 40%
This sounds fundamentally wrong. Even the "Rmerge reduction by cutting
resolution" practice is
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