Dear all,
going through some previous lab member's data and trying to make sense
of it, I was wondering what kind of solutions exist to simply the
archiving and retrieval process.
In particular, what I have in mind is a web interface that allows a user
who has just returned from the
Do you want the frames to be accessible too ?
If not, then a.wiki would be an easy solution.
Alternatively a Filemaker database would do the trick too.
Jürgen
..
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry Molecular Biology
Johns
I did something like that for plasmids by putting together a web
interface, php, and MySQL. It was simple, maybe a little ugly, but
worked nicely. The problem was convincing anyone to actually use it was
virtually impossible.
--paul
On 08/18/2010 04:52 AM, Andreas Förster wrote:
Dear all,
Dear all
As CCP4, we are currently developing the new CCP4i that will include a database
application that will store project and job data. The database schema has
already been designed but its design is not final and can be modified depending
on user feedback. Now, we are in the process of
Hello All,
I am currently solving a structure at 2A resolution with phases obtained from
molecular replacement. Using the MR solution, I began refinement with Refmac
using NCS restraints. I am currently building the parts of the model that were
left out of the MR search model, and have just
Michael Thompson wrote:
Hello All,
I am currently solving a structure at 2A resolution with phases obtained from molecular replacement. Using the MR solution, I began refinement with Refmac using NCS restraints. I am currently building the parts of the model that were left out of the MR search
On 08/18/10 08:25, Michael Thompson wrote:
Hello All,
I am currently solving a structure at 2A resolution with phases obtained from
molecular replacement. Using the MR solution, I began refinement with Refmac
using NCS restraints. I am currently building the parts of the model that were
Knowing where all the important files are is really all that is needed.
Sofistication can come later.
I would welcome a CCP4 database-assisted data archive system.
Here is my contribution to the discussion:
I agree with Paul Paukstelis that getting users to use any
database-assisted data
Dear All,
I would just like to add to Enrico's mention of ISPyB. This LIMS
system will log all your data collected at the beamline (experimental
parameters, screening images, data sets, edge scans, xrf spectra,
crystal snapshots etc) automatically and is stored indefinitely. Your
Dear Jerry,
On Tue, Aug 17, 2010 at 04:26:14PM -0700, Jerry McCully wrote:
Dear All:
I am currently using autoBuster to refine my structure. I notice that
autobuster generates a new column in the MTZ data file with the label of
FreeR_flag.
Because my MTZ file has already had
Hi all,
I know scaling up from a hit found from a high throughput screen is an
empirical process, but does anyone have a good rule of thumb as a starting
point when it comes to scaling up from a hit observed in an Intelliplate to
a Linbro plate (i.e., change in volume ratios, amount to add to
There is an image archiving system called TARDIS (http://tardis.edu.au/)
that sounds more-or-less exactly like what you describe.
I agree that it would be nice if you can get your synchrotron to do it
for you, but since every single beamline and home-source setup in the
world has already been
What about XTrack?
http://xray.bmc.uu.se/xtrack/
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of James
Holton
Sent: 18 August 2010 16:54
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] database-assisted data archive
There is an image archiving
Hi Mo
What you need to remember is that a relatively large amount of protein
is lost from smaller drops. The ratio of surface area to volume is
greater. With 100 + 100 nl drops about half of the protein is lost,
either as skin on the drops or on the plastic of the plate.
So when you
There are three more vacancies coming up at the Protein Data Bank in Europe
(PDBe; pdbe.org):
- Head of PDBe Deposition and Annotation
http://ig14.i-grasp.com/fe/tpl_embl01.asp?s=MbkMjPUrEcTFkHhTczjobid=40182,2388233441
- 50% Oracle DBA/50% Senior Software Engineer
Thank you Patrick for your reply.
As a note to others who might be interested, I found a few comments about
scaling up interwoven in a long thread about which robot to buy that was
posted on this bb a few years ago. The most salient link is probably:
The Protein Data Bank in Europe (PDBe; http://pdbe.org/) is pleased to
announce the availability of PISA assembly files, summaries and associated XML
descriptors for all relevant entries in the Protein Data Bank (PDB) archive
for download and in-house analysis.
PDBePISA
Dear Andreas,
If you really want to do this, and want to define what is
the data is, it's not _so_ difficult to do it yourself, with Ruby on Rails (
http://rubyonrails.org/)
You have to know how to script a bit, and know a bit about
Model/View/Controller frameworks.
I assume you're sure you even *need* to scale up? Most of our
structures come from crystals from small (150-300nl) drops, we
consider a 100um crystal already huge. And if a smaller crystal
doesn't diffract far enough on a modern beamline, chances are a large
one won't either (quite apart
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