Dear All,
On behalf of the Faculty of Science and Technology
(http://www.unibz.it/en/sciencetechnology/welcome/default.html)
of the Free University of Bolzano
(http://www.unibz.it/en/public/university/default.html)
I am glad to advertise a position for a PhD on the structural biology of
PIR is fairly similar to Fasta, from addled memory the format is...
protein name;
empty line
MPREIL...rest of amino acid sequence with an optional asterisk to mark the
sequence end.
Tony
Sent from my iPhone
On 12 Aug 2011, at 09:14, Phil Evans p...@mrc-lmb.cam.ac.uk wrote:
Can
That's what I had
protein
GSP etc
...
SEN*
On 12 Aug 2011, at 09:19, Antony Oliver wrote:
PIR is fairly similar to Fasta, from addled memory the format is...
protein name;
empty line
MPREIL...rest of amino acid sequence with an optional asterisk to mark the
sequence end.
I was missing the semicolon, but it still fails
On 12 Aug 2011, at 10:12, Antony Oliver wrote:
Interesting iPhone formatting things going on... Let's try again...
First line is greater than symbol followed by some text about your
protein then closed with a semicolon. The next line is
NBRF/PIR Format:
A sequence in PIR format consists of:
1. One line starting with
1. a ** (greater-than) sign, followed by
2. a two-letter code describing the sequence type (P1, F1, DL, DC, RL,
RC, or XX), followed by
3. a semicolon, followed by
4. the sequence
Thanks Suku - forgot about the P1, F1 stuff.
Still don't understand why you just can't use the simpler FASTA format with all
these programs, or even just a plain text file!
Tony.
Sent from my iPhone
On 12 Aug 2011, at 10:18, sukanta mondal
Dear All,
Due to some last minute cancellations, we have a couple of places
remaining on the joint Astbury Centre for Structural Molecular Biology at
the University of Leeds and Rigaku Americas Corporation free BioSAXS
workshop to be held at the University of Leeds on Friday 19th August 2011.
Dear Phil,
I remember one case where reading a sequence file in PIR format failed,
although I did my best to have the right format. It turned out, that the
error message about the wrong PIR format was misleading - the real
cause was a non-standard amino acid letter, in this case a X. Maybe,
A few words on obsoleted entries and validation reports:
OBSOLETE ENTRIES
Obsolete entries remain available to the public through the PDB ftp archive at
ftp://ftp.wwpdb.org/pub/pdb/data/structures/obsolete/.
For example, for entry 1F83, you can access the coordinate file at
I think you'll find it works better if you use Fasta format:
http://en.wikipedia.org/wiki/FASTA_format
Chris
From:
Phil Evans p...@mrc-lmb.cam.ac.uk
To:
CCP4BB@JISCMAIL.AC.UK
Date:
08/12/2011 01:16 AM
Subject:
Re: [ccp4bb] Another paper structure retracted
Sent by:
CCP4 bulletin board
Chris,
I seriously think this sever should be available to folks. It is very
helpful for most students.
Will you and Abhinav keep improving it?
Kevin
On Fri, Aug 12, 2011 at 8:04 AM, Christopher Rife
christopher.r...@danisco.com wrote:
I think you'll find it works better if you use Fasta
Phil,
The sever was developed by Chris. Currently, Abhinav is taking care of it.
If you have any questions, you may contact Abhinav Kumar at JCSG.
Kevin
On Fri, Aug 12, 2011 at 1:14 AM, Phil Evans p...@mrc-lmb.cam.ac.uk wrote:
Can anyone get this server to work? For me it keeps complaining
The server has always been available to everyone.
Thanks,
Abhinav
JCSG@SSRL, SLAC
Phone: (650) 926-2992
Fax: (650) 926-3292
On 08/12/2011 11:10 AM, Kevin Jin wrote:
I seriously think this sever should be available to folks. It is very
helpful for most students.
Kevin
beta sheets in really well-phased low-resolution maps should look sort of like
walls, but in an imperfect map they might by rather spotty.
I'd be very leary of making any conclusions from molecular replacement at such
low resolution. For a good control, try solving your data set with a
Hi,
what is the completeness of the datasets across the whole resolution range
(not overall - single number). At these resolutions missing a few
reflections may be enough to hide quite a bit of structure.
Pavel.
On Fri, Aug 12, 2011 at 10:32 AM, Huiming Li huimin...@hotmail.com wrote:
Dear
We are looking to recruit an individual who will assume the role of PROGRAM
LEADER for one of several high-throughput (HT) programs within the Albert
Einstein Macromolecular Therapeutic Development Facility. At least three years
of experience with high-throughput approaches and automation, as
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