Hey Jeremy,
I havent used this myself, but I believe APBS can do it. You can do it on
their server or locally after downloading the program.
Arti Pandey
> Hi, all
>
> Does anybody have experience with binding energy calculation of
> ligand-protein
> interaction? What are the good programs o
This usually leads to a mad
chase through all possible space groups, twinning refinements, etc. and,
in my experience, often results in a lot of time being spent for no
significant improvements.
If one has a model to refine, it is actually very straightforward to
test all possible merohedral
When you say you want an easy-to-get-easy-to-use binding energy/contact
area calculator I assume you mean a simple scoring function.
I have suggested that such functions cannot achieve reliable, accurate
general
affinity estimation (pdfs sent separately), and so far this seems to
be borne out (s
Forgot to mention that the NCSs are improper.
On Feb 21, 2007, at 6:22 PM, Jianghai Zhu wrote:
Dear all,
I have two low resolution (3.8 A) MAD data sets from two different
space groups. There are 4 copies of my molecule in one space group
and 2 copies in the other. The density-modified
Dear all,
I have two low resolution (3.8 A) MAD data sets from two different
space groups. There are 4 copies of my molecule in one space group
and 2 copies in the other. The density-modified maps from these data
sets are poor, but still allow me to build a crude model on them.
All the
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Hi Uhnsoo,
AMoRe will not run the translation function for the **first** body (an
hetero-dimer in your case) because in P1 the origin is arbitrary and
hence fixed by the first rotation solution. Now, if you think that the
first solution from the rotat
Uhnsoo,
Well you only have half of your 4-heterodimers, so your phases are poor,
particularly for the missing 50% of your structure. DM and NCS
averaging/solvent flattening will only work if the missing 50% can be
properly masked. One possible out from this hole is to try RESOLVE. If
you tell R
Dear all,
Recently, I've gotten a 3.1A data set with a P1 space group. Based on a Mattchew
coefficient, I have 4 hetero-dimer molecules in one asymmetric unit. Because one
of the dimers was known already, I tried MR with a program Phaser and molrep
(Amore doesn't calculate a translation function
I have some questions about the "NCS Phased Refinement" task run from
ccp4i:
Can one use this task if there are multiple nonidentical chains in the
NCS unit (e.g. a heterodimer), and if so, how does one define the NCS
units? I find that the default is to consider each chain as a separate
"NCS uni
Hi,
I think a problem I've had with my thesis project applies to this discussion:
My Rfactors, after having built a reasonable model into experimental maps in
P3121, were stuck in the upper 40s, and would absolutely not go lower. Trying
the other space group options (P31, C2) didn't help, and t
Hi, all
Does anybody have experience with binding energy calculation of
ligand-protein
interaction? What are the good programs out there ? I am aware of several
such
as AutoDock, Dock, Tinker, but they seem to be made for docking, I am
looking for
easy-to-get-easy-to-use binding energy/contact
oops didn't read that first one...
but from my own experience, twin refinement can lead to significant
improvements (10 percent drop in R-factors)
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Dear Eleanor et al:
mmtbx.xtriage, which is part of the full-blown ccp4 install, and
phenix.xtriage, which I think is basically the same thing, are also
options, and run a variety of twinning and other sanity checks.
mmtbx.xtriage --help tells how to run it, fairly painlessly.
All the best,
B
maybe interesting literature concerning this topic:
Lebedev AA, Vagin AA, Murshudov GN
Intensity statistics in twinned crystals with examples from the PDB.
Acta Crystallogr D Biol Crystallogr. 2006 Jan;62(Pt 1):83-95.
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Ideal f
-
It's very possible with any overlap of lattice points, even in the lower
symmetry space groups. To extend Eleanor's list: For example, I once had a
structure with the unit cell relationship 3c cos(beta) = -a. In cases like
that, it's not really a c
It's very possible with any overlap of lattice points, even in the lower
symmetry space groups. To extend Eleanor's list: For example, I once had a
structure with the unit cell relationship 3c cos(beta) = -a. In cases like
that, it's not really a clean diffraction, but looks very much like a
single
Dear all,
Please could you bring this advert to the attention of any potential
candidates.
Institute of Organic Chemistry and Biochemistry at the
Albert-Ludwigs-University Freiburg/Germany
A post-doc position and a PhD position in structural biology is
available in the group of
Prof. Diet
There are many and various reasons for unpleasantly high R values, and
twinning is undoubtedly one of them.
But you can only have twinning with apparently good diffraction if the
cell dimensions allow it.
It is always a possibility in trigonal, tetragonal and cubic cells.
Certain other comb
Hi Sue,
This reference has very useful info
Lebedev AA, Vagin AA, Murshudov GN.
Intensity statistics in twinned crystals with examples from the PDB.
Acta Crystallogr D Biol Crystallogr. 2006 Jan;62(Pt 1):83-95. Epub
2005 Dec 14.
PMID: 16369097 [PubMed - indexed for MEDLINE]
Roberto
On 21
Sue Roberts wrote:
Hello
A partially philosophical, partially pragmatic question.
I've noticed a trend, both on ccp4bb and locally, to jump to twinning as
an explanation for data sets which do not refine well - that is data
sets with R and Rfree stuck above whatever the person's pre-conceived
Hi,
here is a question for the crystallography jocks out there.
Stimulated by Sue Roberts' email here is a thought experiment that I
have puzzled about
in the past. Basically I think that if one has a wrong structure and
then assumes the
crystal is twinned one will get a lower R-factor.
No
Hello
A partially philosophical, partially pragmatic question.
I've noticed a trend, both on ccp4bb and locally, to jump to twinning
as an explanation for data sets which do not refine well - that is
data sets with R and Rfree stuck above whatever the person's pre-
conceived idea of an acce
Todd, Markus, Misha, Robi, Fabrizio,
thanks for the answers.
Indeed I'm scaling the data at the command line, now (good ol' way!).
The scalepackBig command does not exist anymore, but the ones you've
suggested work fine.
I was just wondering if there's a way to tell HKL2000 which command to use.
overlapmap does this for any set of coordinates and any map.
Eleanor
Charles W. Carter Jr. wrote:
Is there a CCP4 program that will calculate residue-by-residue
correlation coefficients for a molecular replacement solution and an
experimentally phased map?
Thanks,
Charlie
**UNCryst
Hi, you may want to try the Bias removal Server at tuna.tamu.edu
HTH,
Sid.
On 2/20/07, Charles W. Carter Jr. <[EMAIL PROTECTED]> wrote:
Is there a CCP4 program that will calculate residue-by-residue
correlation coefficients for a molecular replacement solution and an
experimentally phased map?
Bernhard Rupp writes:
> Mathlab image proc module probably would be the best choice but muchas
> dollares
> I found by accident that a cheaper alternative is any graphing package that
> can make
> contour plots.
Try Python with scipy/pylab/matplotlib. It comes with a full library
of numerica
Hi there,
does anyone know how to use HKL2000 with more than 2 million
observations (that would be the "scalepackbig" version of scalepack)?
At the moment, the scaling ends with "process died" when it reaches
the 200th observation read from the .x files.
thanks in advance,
Sebastiano
--
Hi Tim,
an R-factor of 0.64 does not sound like a solution. You may try submitting
your problem to our automated MR server CaspR and see if something pops up :
http://www.igs.cnrs-mrs.fr/Caspr2/
Kind regards,
Karsten.
On Monday 19 February 2007 17:15, [EMAIL PROTECTED] wrote:
> I would take
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