[phenixbb] Error of Sculptor

[Gabor Bunkoczi]

Hi Fish,

your line endings cause trouble. I assume you are running sculptor on 
either linux or mac, but your line endings are from windows (dos). I will 
change the parser so that it is independent of line endings. In the 
meantime, you can use the dos2unix utility to convert the linebreaks, and 
go ahead with your calculation.

Thanks for your help, Gabor

On Apr 25 2012, Zhang yu wrote:

>Dear Gabor,
>
>The error message shows nothing but part of the alignment file. I tried
>both Phenix 1.7.3 and 1.7.1.
>
>Thanks,
>Fish
>
>2012/4/25 Gabor Bunkoczi <gb360 at cam.ac.uk>
>
>> Dear Fish,
>>
>> can you let me know what the error message is and which Phenix version 
>> are you using? Your alignment file looks OK to me.
>>
>> Thanks, Gabor
>>
>>
>>
>> On Apr 25 2012, Zhang yu wrote:
>>
>>  Dear Phenixer,
>>>
>>> When I used Sculptor to generate a new model, there is a error which I
>>> can not figure out. I input a PDB file (*.pdb) and an alignment file
>>> (*.aln).
>>>
>>> The following is the log file (contents in ######). There seems
>>> something wrong with the *.aln file.
>>> #################
>>> Reading PDB file
>>> ----------------
>>>
>>> File name: **/**/******/******/**.pdb
>>> Separating solvent from macromolecules...
>>>
>>> Reading alignment files
>>> -----------------------
>>>
>>> 1. **/**/**.aln
>>>
>>> #####################
>>>
>>>
>>>
>>>
>>> The following is the content of the alignment file:
>>>
>>> **_** MVYSYTEKKRIRKDFGKRPQVLDVPYLLSI**QLDSFQKFIEQDPEGQY----GLEAAFRSV 
>>> **_** ---------**MEIKRFGRIREVIPLPPLTEIQVESYRRAL** QADVPPEKRENVGIQAAFRET
>>>                           * **: :*: :* * .**::*::: :: * : *::****..
>>>
>>> What is the problem with the alignment file?
>>>
>>> Thank you in advance!
>>> Fish
>>>
>>>
>> --
>> ##############################**####################
>>
>>    Dr Gabor Bunkoczi
>>
>>    Cambridge Institute for Medical Research
>>    Wellcome Trust/MRC Building
>>    Addenbrooke's Hospital
>>    Hills Road
>>    Cambridge CB2 0XY
>> ##############################**####################
>>
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>