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,
you could check your sequence for this ...
Best regards,
Dirk.
Am 12.08.11 11:16, schrieb Phil Evans:
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 blank. The next line contains your amino acid
sequence, which you can also close with an optional asterisk.
Sent from my iPhone
On 12 Aug 2011, at 10:06, "Antony Oliver"<antony.oli...@sussex.ac.uk> 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.
Tony
Sent from my iPhone
On 12 Aug 2011, at 09:14, "Phil Evans"<p...@mrc-lmb.cam.ac.uk> wrote:
Can anyone get this server to work? For me it keeps complaining that my
sequence file is not a PIR file. The file looks OK to me, but I've never really
understood what a PIR file is
Phil
On 12 Aug 2011, at 01:39, Kevin Jin wrote:
Should we really have some crystallographers to review and qc those structures
before the formal releasing? JCSG has set a very good mechanism for this issue.
There is a sever for self check.
http://smb.slac.stanford.edu/jcsg/QC/
On Thu, Aug 11, 2011 at 4:58 PM, Jacob Keller<j-kell...@fsm.northwestern.edu>
wrote:
I think they fudged the data in this paper...
JPK
On Thu, Aug 11, 2011 at 6:30 PM, David Schuller<dj...@cornell.edu> wrote:
link: http://iai.asm.org/cgi/reprint/IAI.05661-11v1
Ferric C. Fang& Arturo Casadevall
Retracted Science and the Retraction Index
Infec. Immun. doi:10.1128/IAI.05661-11
Abstract: Articles may be retracted when their findings are no longer
considered trustworthy due to scientific misconduct or error, they
plagiarize previously published work, or are found to violate ethical
guidelines. Using a novel measure that we call the “retraction index,” we
found that the frequency of retraction varies among journals and shows a
strong correlation with the journal impact factor.
...
(with special attention to Figure 1, Retraction Index vs. Impact Factor)
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David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu
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Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
cel: 773.608.9185
email: j-kell...@northwestern.edu
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Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.de
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