I find this confusing also!
Phil Jeffrey wrote:
On 1/13/11 2:48 PM, J. Fleming wrote:
Hi All,
I'm about ready to deposit my structure and have used pdb_extract to
aid in the process. Unfortunately the following values were not found
and are required by ADIT:
1) Under Data Collection, Reflectio
Hi Jon -
- Observed criterion sigma(F) and sigma(I) means "what cutoff did your data
processing package use to consider a reflection not observed, i.e. throw it
out?" If you processed your data with Scalepack/HKL2000, the default cutoff
is on I, and it's negative 3 sigma. There is no cutoff o
Hi Jon,
a partial answer:
> 2) Under Refinement, Refinement Statistics section: Number unique
> reflections (all)
>
> I looked in my log files for HKL2000, PHASER, and PHENIX but am confused on
> where to find the required values above. I tried searching the logs for the
> mmCIF items but that
On 1/13/11 2:48 PM, J. Fleming wrote:
Hi All,
I'm about ready to deposit my structure and have used pdb_extract to
aid in the process. Unfortunately the following values were not found
and are required by ADIT:
1) Under Data Collection, Reflections section: Observed criterion
sigma(F) and O
Hi,
Generally if we use CCP4i we can find these details easily in scala log
files.
Gauri
On Thu, Jan 13, 2011 at 2:48 PM, J. Fleming wrote:
> Hi All,
>
> I'm about ready to deposit my structure and have used pdb_extract to aid
> in the process. Unfortunately the following values were not fou
Hi All,
I'm about ready to deposit my structure and have used pdb_extract to aid
in the process. Unfortunately the following values were not found and are
required by ADIT:
1) Under Data Collection, Reflections section: Observed criterion sigma(F)
and Observed criterion sigma(I)
2) Under Refi
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UNIVERSITY OF CALIFORNIA SAN FRANCISCO (UCSF)
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Postdoctoral positions in Ion Channel Structural Biology are available
immediately for highly motiva
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UNIVERSITY OF CALIFORNIA SAN FRANCISCO (UCSF)
Structure, Function, and Regulation of Ion Channels
Postdoctoral positions in Ion Channel Structural Biology are available
immediately for highly motivated individuals with a strong interest in
integrated approaches
One of my colleagues asked if I could post the following to the ccp4bb:
Thanks to very helpful feedback, there is now a fairly comprehensive
set of curations for the new 'Crystals, X-rays and Proteins' (Sherwood
and Cooper) at the following link:
http://www.ucl.ac.uk/~rmhajc0/
The first 6
It sounds a bit silly after that nice theoretical discussion, but I would try
poking the existing oily blobs with a hair. Since you may be close to xtal
conditions, stirring up the equilibrium a bit may help nucleate something.
I've seen this work more than once, although usually with things w
Hi Ruben,
Timing is everything - We are just going through the proofs of a paper entitled
"What's in a drop? Correlating observations and outcomes to guide
macromolecular crystallization experiments" by Luft, Wolfley and Snell to
appear shortly in Crystal Growth and Design. In putting this toge
Hi Chen,
Check SPDBViewer if it is of some help to you!
Gauri
On Thu, Jan 13, 2011 at 5:57 AM, Qing Chen wrote:
> Dear all,
>
> I have the wt protein structure that contains two domains. I want to creat
> a model with two glycerin inserted between the two domains.
> Which software or webserver c
Would anybody offer an older crystal cooling system to go?
--
Jan Dohnalek, Ph.D
Institute of Macromolecular Chemistry
Academy of Sciences of the Czech Republic
Heyrovskeho nam. 2
16206 Praha 6
Czech Republic
Tel: +420 296 809 390
Fax: +420 296 809 410
:
Subject: Re: [ccp4bb] What is the simplest method to analytically compute the
Solvent-Accessible Surface Area of a given atom in a protein?
My knowledge on this is probably quite out of date by now, but some years ago
there was a lot of research on this topic because such surfaces are import
Hello Qing Chen,
if by 'shift' you mean the actual coordinates you can do in coot as Herman
describes. If you want to shift the sequence numbering: Coot also has an option
to renumber a sequence by an offset and the offset can also be negative.
Cheers, Tim
On Thu, Jan 13, 2011 at 12:27:49PM +010
In that case, I would split your pdb file in two parts: Nterm to 101 and
99 to Cterm. With the rotate/translate zone option, you can move one
complete domain to have residue 101 of the Nterm domain overlap with
residue 99 of the Cterm domain. In a nex step you will have to delete
residue 101 of the
Let's say I need to insert two G between resi 98 and 99. I tried in the way
as Herman suggest: break the chain in the domain boundary, add terminal
residues at the N-terminus of the 2nd domain. But then there is no space to
accommodate the inserted residues, the two glycerin backbones overlap with
use coot: calculate - model/fit/refine - add terminal residue.
this will add alanines. you can change these to glycines with the simple
mutate option in the same pop up menu.
best,
HErman
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
Behal
Dear all,
I have the wt protein structure that contains two domains. I want to creat a
model with two glycerin inserted between the two domains.
Which software or webserver could do this?
Pls help.
Qing Chen
Dear all,
I'm trying to crystallize a small, soluble part of a protein (~15kDa, 152AA). I
did some standard screens (Crystal Screen I & II + Index screen) with a protein
concentration of 25 or 45mg/mL in an 1:1 (0.75µL)96 well set up. In most of the
conditions I got phase separation (mostly PEG
Dear Francois,
my starting point would be 'man areaimol' which also contains the references
REFERENCES
1. B.Lee and F.M.Richards, J.Mol.Biol., 55, 379-400 (1971)
2. E.B.Saff and A.B.J.Kuijlaars, The Mathematical Intelligencer, 19,
5-11 (1997)
http://www.math.vanderbilt.edu/~
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