One of the early references for mFo- nFc is:
Vijayan, *Acta Cryst.* (1980). A*36*, 295-298
You may also like to read the book on Fourier transforms in crystallography
by Ramachandran and Srinivasan.
Shekhar
On Fri, Jul 30, 2010 at 4:25 AM, Pavel Afonine wrote:
> Hi Ian,
>
> please correct me
On Jul 29, 2010, at 4:00 PM, CCP4BB automatic digest system wrote:
Date:Thu, 29 Jul 2010 13:49:12 +0100
From:Simon Kolstoe
Subject: CIF format frustrations
Dear all,
What's the best way to convert a coordinate cif file to a pdb (without
compiling a program, installing new utilities,
Hi Ian,
please correct me if I'm wrong in what I'm writing below...
My reasoning for writing it like this
2Fo-Fc = Fo + (Fo-Fc)
is:
1) the map (Fo, Pcalc) shows density for missing atoms at half size
(approximately)
2) the map (Fo-Fc, Pcalc) shows density for missing atoms at half size
(ap
On Thu, Jul 29, 2010 at 8:25 PM, Pavel Afonine wrote:
>
> Speaking of 3fo2fc or 5fo3fc, ... etc maps (see classic works on this
> published 30+ years ago), I guess the main rationale for using them in those
> cases arises from the facts that
>
> 2Fo-Fc = Fo + (Fo-Fc),
> 3Fo-2Fc = Fo +2(Fo-Fc)
>
>
Got the references, and I will check them out. Thanks a lot!
Best Regards, Hailiang
> These papers might help:
>
> J. Appl. Cryst. (1997). 30, 396-399, F. M. D. Vellieux and B. W. Dijkstra
>
> J. Appl. Cryst. (1997). 30, 400-401, F. M. D. Vellieux
>
> Speaking of 3fo2fc or 5fo3fc, ... etc maps
These papers might help:
J. Appl. Cryst. (1997). 30, 396-399, F. M. D. Vellieux and B. W. Dijkstra
J. Appl. Cryst. (1997). 30, 400-401, F. M. D. Vellieux
Speaking of 3fo2fc or 5fo3fc, ... etc maps (see classic works on this
published 30+ years ago), I guess the main rationale for using them i
Hi,
I frequently find 3mFo-2DFc maps have been used for model building. I am
not sure whether they have less model bias than 2mFo-DFc maps, and I
appreciate for any references.
Best Regards, Hailiang
No, constraints do not improved the Chis, but also don't harm them much.
Which NSDs, from selection or superposition (damsel or damsup)? The
superposition ones:
>>> P1
egp1p_04-1.pdb !! Reference file
egp1p_12-1r.pdb !! NSD = 0.912
egp1p_05-1r.p
So, that was my previous question.
Em 29-07-2010 14:14, Phoebe Rice escreveu:
You don't have to keep the same number of symmetrical
contacts.
Original message
Date: Thu, 29 Jul 2010 14:13:56 -0300
From: Fred
Subject: Re: [ccp4bb] non-symmetric tetramer ? 2nd round
To: CCP4BB@JISC
Clarifying... That's happened because I was talking about the symmetry
of the SAXS envelop/particle. I understand that if you consider the
symmetry of the whole particle, say a tetramer of identical subunits,
you can have the 4-fold axis when asking for 222 symmetry envelop, which
gives you a 4
Fred,
Two cents - I think the P1 SAXS solution should strongly guide your choice
of symmetry constraint above all else in this case: do any of the
symmetry-restrained shape reconstructions *improve* the statistics (chi) and
stability of the shape (NSD) when compared to the P1 result? Also, it soun
Of course, 222 has not a 4 axis, otherwise it would be a 4-fold axis.
But that's the output of the program. P4 exp. model has a 4-fold axis
along the longest axis, while the P222 MODEL has a 4-fold axis along the
smallest, which doesn't make any sense. Can you imagine something build
up with 4
Hi,
To quote you: "even my P222 experimental envelop does have a 4-fold
axis" - this is not suprising, a particle with 222 symmetry does not
have 4-fold symmetry. There are 3 mutually perpendicular 2-fold axes
that intersect at the origin (of the "particle", of the molecule) [and
for the nome
Thanks all of you who promptly replied my question.
I should have been more precise. I was referring to the symmetry of the
tetrameric particle (point symmetry) at the molecular level not at the
atomic level. This question has arisen because I have collected some
SAXS data of my protein in solu
Here is another example of a tetramer with neither 222 or 4 fold
symmetry:
http://www.ncbi.nlm.nih.gov/pubmed/7792597
Thierry
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Vellieux Frederic
Sent: Thursday, July 29, 2010 03:35 AM
To: CCP4BB@JISCM
Sanjeev Munshi
Notice: This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates Direct contact information
for affiliates is available at
http://www.merck.com/contact/contacts.
Dear All,
Our group is recruiting an interdisciplinary postdoctoral fellow in structural biology/bioinformatics at the Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL) in Heidelberg.
For more details on the project and requirements, please consult:
http:/
This?
http://sw-tools.pdb.org/apps/CIFTr/index.html
Cheers
-- Ian
On Thu, Jul 29, 2010 at 1:49 PM, Simon Kolstoe wrote:
> Dear all,
>
> What's the best way to convert a coordinate cif file to a pdb (without
> compiling a program, installing new utilities, writing script files...)?
>
> Cif2mtz
Dear all,
What's the best way to convert a coordinate cif file to a pdb (without
compiling a program, installing new utilities, writing script files...)?
Cif2mtz works for the reflection file however coordconv doesn't have a
"cif" option. If I try using Coot I get a mangled pdb file that gi
As part of the recent Midsummer Make-over of the Protein Data Bank in Europe
website (PDBe; http://pdbe.org/), we introduced a new Wizard tool. The purpose
of the Wizard is to help novice users find "stuff" on the site, be it one or
more PDB or EMDB entries or information about PDBe tools, resou
Announcing: 2nd Biomics Hands-On Workshop & Conference
Location:Weizmann Institute of Science, Rehovot, Israel
Dates: November 14-19, 2010
Workshop & Conference Flyer ( http://biomics.weizmann.ac.il/flyer.html )
and Scientific Program
(http://biomics.weizmann.ac.il/2ndBIOmicsScienti
Hi,
My favourite is Phyre: http://www.sbg.bio.ic.ac.uk/~phyre/
A benefit of this is that it predicts your domains, makes sequence
alignments with the similar proteins, and makes homology models which are
sometimes good enough to start building with when you've phased the
structure!
Another bene
Tried with my protein and it says *very* difficult but I got crystals.
Quoting Albert Guskov :
Hi Vikrant,
I guess Xtalpred server might be of interest for you.
check it at http://ffas.burnham.org/XtalPred-cgi/xtal.pl
Cheers,
*Albert GUSKOV (Dr) *| Research Fellow | Division of Structural &
Co
Run your sequence through these predictors to get an idea of domain location
and disorder.
Disorder predictor links
http://dis.embl.de/
http://globplot.embl.de/
http://www.strubi.ox.ac.uk/RONN
http://bip.weizmann.ac.il/fldbin/findex
http://www.ist.temple.edu/disprot/predictorVSL2.php
http://iupred
Hi Vikrant,
I guess Xtalpred server might be of interest for you.
check it at http://ffas.burnham.org/XtalPred-cgi/xtal.pl
Cheers,
*Albert GUSKOV (Dr) *| Research Fellow | Division of Structural &
Computational Biology | Nanyang Technological University
Proteos 7-01, Biopolis Drive 61, Singapore 1
Peanut lectin, when we solved the structure in the 90's, had a very unusual
non-symmetric tetramer. Till we solved the structure, there were examples
only of symmetric tetramers 222 (say, ConA), or 4 (e.g. Neuraminadase) in
the literature. Peanut lectin had two dimers, each with a two-fold
symmet
Thurs., July 29th 2010
EBI
moreover..
the protein Andrew has suggested was determined several around
Goto
http://www.ebi.ac.uk/pdbe/
enter the uniprot P00362 in the middle box
"Retrieve PDB entries using an external database identifier "
(check UniProt)
and you get a more complete list.
click
I want to do cloning of a 40 Kd protein in pRSETA, and pGEX-KT vector. I don't
have any idea about protein solubility, its multimeric form, stability and
disorder etc. There is nothing known in the literature also. Is there any
software that can predict these parameters, so that i can decide
Thurs., July 29th 2010
EBI
Morning,
I think Andrew meant PDB 2gd1 and 1gd1 (has 4 NAD)
DOI10.1016/0022-2836(88)90130-1
Miri
On Wed, 28 Jul 2010, A Leslie wrote:
Hi Fred,
If your tetramer show negative cooperativity between the 4 sites for
ligand binding, then it is possible to g
Hi Fred,
If your tetramer show negative cooperativity between the 4
sites for ligand binding, then it is possible to get a tetramer with
(say) only one subunit occupied by ligand, which can introduce
considerable asymmetry if ligand binding gives rise to a hinge type
closure of
Non-symmetric tetramers: you can check out Tete-Favier et al (1993),
Acta Cryst. D49, 246: the quaternary structure was assumed to have local
222 symmetry. It turned out this was not exactly the case: the actual
symmetry of the object (the molecule) was "pseudo" 2t2t2t. So in
addition to 2-fold
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