[phenixbb] phenix.mr_rosetta: Inconsistent query numbering

[Pietro Roversi]

Yes please!

I can replace that module only!

Thanks

Pietro
________________________________________
From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] On Behalf Of Dr G. Bunkoczi [gb360 at cam.ac.uk]
Sent: 06 July 2011 15:46
To: terwilliger at lanl.gov
Cc: PHENIX user mailing list
Subject: Re: [phenixbb] phenix.mr_rosetta: Inconsistent query numbering

Hi Pietro,

the parser complains because sequence positions are numbered in an
unexpected way, e.g.:

Q Japanin           1 -------
Q Consensus        17 ~~~~~~c

I do not fully understand the meaning of these numbers, but until now in
all sample .hhr-files these numbers were identical and were stored only
once (after a consistency check). This is the check that now fails. I am
wondering why these are suddenly different. Have you changed a setting on
HHPRED that could be the cause? (It would be great to see an .hhr format
description to see whether these numbers are supposed to be identical or
not, but I have not been able to find it yet.)

Anyway, from the parser point of view the solution is very easy. Both set
of numbers can be stored, and there is no need for a consistency check. I
have made this change and will be available in tomorrow's version. However,
since this is a very small change, I am happy to send you the affected
module, so that you can go ahead without reinstalling the full suite.
Please get in touch if this would be more convenient.

Best wishes, Gabor

On Jul 5 2011, Thomas C. Terwilliger wrote:

>Hi Pietro,
>
>There is something that phenix.mr_model_preparation cannot read in
>Japanin.hhr (attached):
>
> phenix.mr_model_preparation Japanin.hhr
>
>gives the same error. I'll copy Gabor Bunkoczi and see if he can help with
>this.
>
>All the best,
>Tom T
>
>>> Dear all,
>>>
>>> my run of phenix.mr_rosetta stops with:
>>>
>>> ******************* ERROR ENDING ***************
>>> Inconsistent query numbering
>>>
>>> ******************* ERROR ENDING ***************
>>>
>>> I attach script and logfiles.
>>>
>>> Any suggestions?
>>>
>>> Thanks
>>>
>>> Pietro
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>
>
>

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     Dr Gabor Bunkoczi

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