Dear all,
Is there any software which will print the RMSDs (residue wise, and
not chain wise) for more-than-2 chains (having similar/same sequences)
superposed together?
Thanks in advance,
sreetama
Dear Sreetama,
theseus can superpose multiple structures and reports RMSD per residue.
http://www.theseus3d.org/
If your sequences are not identical and you want least squares
superposition, run it like this:
theseus_align -l -f *.pdb
This will produce several output files. The file
Hi all
This structure has the following ncs (output via phenix.simple_ncs_from_pdb)
OPERATOR 1
CENTER: 18.3443 -55.4605 23.0986
ROTA 1:1.0.0.
ROTA 2:0.1.0.
ROTA 3:0.0.1.
TRANS: 0.0.0.
OPERATOR 2
Dear All,
We are organizing an EMBO Practical Course on the Structural
Characterization of Macromolecular Complexes.
The course is primarily intended for Ph.D. students and postdocs
working on
challenging structural projects involving macromolecular complexes.
WHEN: 4-9 June 2012
WHERE:
Hi,
I'm sure there's a way to do this in CCP4, but using some little jiffy programs
I've collected over the years...
That's a 133 degree rotation around an axis defined by the unit vector
0.290647, 0.624977, 0.724519, and there's a small screw component of about 2.4A
along the axis, so it's
Hi Francis,
a quick insertion of your rotation matrix into CONVROT (by Alexandre
Urzhumtsev) gives the following equivalent polar rotation angles
(definition as in X-PLOR/CNS or Rossmann, 1962):
phi,psi,kappa : 111.86 128.68 133.38 291.86 51.32 226.62
For a proper two-fold,
Francis,
It's very easy to spot a 2-fold rotation or screw because the matrix
must be symmetric (or nearly so)**. Your matrix very obviously is not
(i,e, A12 ne A21, A13 ne A31 etc).
** Proof:
A rotation matrix is orthogonal, which implies inverse = transpose: A^-1 = A~.
A 2-fold rotation is
I've had a couple of requests for the jiffy program that interpreted the
transformation, so here's the FORTRAN source code for decomp.f, for anyone who
is interested. It's very simple, so all you should need to do is something
like:
gfortran decomp.f -o decomp
to get an executable (or
Sounds exactly like something is off in your site.def file. I would look to
the beam center.
Also, have you tried indexing with another program? Mosflm perhaps. I find
that if one program cannot index the data, another usually can (as long as
the data isn't too horrible!). Thus I always try to
Hi, everybody,
In addition to all comments, just as a pleasure to remind an old-fashion no
computer way to calculate the rotation angle. The trace of a rotation matrix
(the sum of its diagonal elements) is always equal to 2*cos(kappa)+1. Calculate
it yourself for kappa = 180° and compare with
Hello Peter-
Is it possible that you are shooting close to an axis? If you are shooting near
parallel to one of the crystal axis, you will get values that are reasonable
for 2 cell lengths but extremely low values for the third. Try indexing a frame
that is say 30 degrees into the collection
Is the direction of rotation correct? I got some data that were going
the wrong way once.
JPK
This is a possibility, but probably you should be able to get the initial index
in this situation. The integration is a different story. To fix that problem,
usually you can change the def.site fix with: {alig,1} {180} as opposed to 0.
-Todd
-Original Message-
From: CCP4 bulletin
Dear All,
Please see below details of a data analysis scientist post available within the
scientific software team at Diamond. For full details please go to the web
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Hi peter,
I agreed with Kelly, You should try indexing your data in
different program. I recently collected a diffraction data which showed
problem in indexing in HKL2000, but data indexed very fine in imosflm
giving right cell parameter. So it is worthfull to index your data in
Hi all,
I recently encountered a modified surface cysteine residue in one of my
structures. The protein is expressed in E.coli and my data is to 1.7Å so I am
positive of the number of extra atoms. It really look like one of the tails
(the Propanoic acid) of a TCEP molecule. TCEP was added
Hi Folks,
As crazy as it sounds, if you have crystallized and managed to solve the
structure of a protein from aggregated protein, please could you share your
experience.
After many constructs, many many expression schemes and after the usual
rigmarole of optimization that is also often
Hey, it could be that you just have a big oligomer--any support for
that in the relevant literature? A 10-mer would probably beat out an
s200, no? Do you have any other way to ascertain the oligomeric state?
Jacob
On Tue, Feb 21, 2012 at 5:21 PM, Raji Edayathumangalam
r...@brandeis.edu wrote:
I probably it depends on whether you've got gunk or a functionally relevant
oligomer in that void volume. Is it active?
RecA and Rad51 both form open-ended head-to-tail oligomers and yet they still
crystallize.
=
Phoebe A. Rice
Dept. of Biochemistry
Hi,
Your idea does sound really crazy but actually Jacob had made a very good
valid point.
Question is do you think your aggregate still functioning or not, if not,
can you revive them in vitro and how effective is your refolding process if
you are going to refold them?
You may want to take a
Well, depends on what 'aggregated' really means. If it implies reasonably
weak oligomerization interaction - and it
might not be too strong given that the oligomers remain soluble - a
chaotropic crystallization agent (on the
extreme end certain high salts, consult Hofmeister for chaotropicity)
On Feb 21, 2012, at 4:00 PM, sreetama das wrote:
Is there any software which will print the RMSDs (residue
wise, and not chain wise) for more-than-2 chains (having similar/
same sequences) superposed together?
In UCSF Chimera you can use the Match-Align tool to create a
On Feb 21, 2012, at 4:00 PM, Jacob Keller wrote:
is there a good way to put text labels into movies from pymol or
otherwise? It would be helpful for conveying some ideas...
As Jason pointed out, PyMOL has some useful facilities for this.
Chimera has a tool for placing standalone text and
Colleagues:
This is a bit off-topic, but there are two positions available in our group
for scientists with experience in biophysics and SPR. The description of each
position follows as does application instructions. The first position listed
is for an experienced Ph.D.-level scientist;
Hi,
Did you try using a different column like Superose 6? This column works
well to separate large molecular weight proteins including oligomers.
Ideally if your solution is not cloudy (coming out of void volume) those
are not aggregates those might be oligomers.
HTH,
Shya
On Tue, Feb 21, 2012 at
Dear All,
Will you please tell me a server of software which can draw a curve for the B
factor of the atoms in a protein PDB file from the first residue to the
residue?Or a server or software by which we can easily order the B factors of
the atoms in the PDB file according to the B factor in
Hi Dialing,
Will you please tell me a server of software which can draw a curve for the
B factor of the atoms in a protein PDB file from the first residue to the
residue?Or a server or software by which we can easily order the B factors
of the atoms in the PDB file according to the B factor in
Hi all ,
I will like to know which program we can use to calculate R-mergd-F( not
Rmerge) between two data sets, or more generally R factor between two data
sets.
Thanks in advance,
Regards,
ARKO
--
*ARKA CHAKRABORTY*
*CAS in Crystallography and Biophysics*
*University of Madras*
Hi all,
Can someone put in links of a few articles relevant to the above
discussion? ie where this kind of strategy was helpful in a specific
practical situation?
Thanks in advance,
Regards,
ARKO
On Tue, Feb 21, 2012 at 4:46 AM, ccp4 c...@ysbl.york.ac.uk wrote:
This is a case where it is
Hi all,
This is a general question regarding the formation of hydrogen bonds in
proteins. I have found hydrogen bond between the back-bone atoms of the
adjacent residues using computational methods, ie, between NH4-CO5 of
enkephalins. Is this kind of feature acceptable and is there any such
Hi all,
Thanks to all those who responded to my query about indexing my dataset. I'm
beginning to suspect that the crystals are twinned. the crystals initially
started as fused plates which were then optimized to single crystals that
diffracted poorly (3.5-4). I then set up an additive screen,
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