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"<[log in to unmask]> 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"<[log in to unmask]> 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<[log in to unmask]> wrote:
>>>>> I think they fudged the data in this paper...
>>>>>
>>>>> JPK
>>>>>
>>>>> On Thu, Aug 11, 2011 at 6:30 PM, David Schuller<[log in to unmask]> 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)
>>>>>>
>>>>>>
>>>>>> --
>>>>>> =======================================================================
>>>>>> All Things Serve the Beam
>>>>>> =======================================================================
>>>>>> David J. Schuller
>>>>>> modern man in a post-modern world
>>>>>> MacCHESS, Cornell University
>>>>>> [log in to unmask]
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> *******************************************
>>>>> Jacob Pearson Keller
>>>>> Northwestern University
>>>>> Medical Scientist Training Program
>>>>> cel: 773.608.9185
>>>>> email: [log in to unmask]
>>>>> *******************************************
>>>>>
--
*******************************************************
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: [log in to unmask]
WWW: www.genzentrum.lmu.de
*******************************************************
|