[phenixbb] Error of Sculptor

Zhang yu phenixzyfish at gmail.com
Thu Apr 26 13:55:58 PDT 2012


Hi Gabor,

It works now. Thank you for your suggestion!

Fish

2012/4/26 Gabor Bunkoczi <gb360 at cam.ac.uk>

> 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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>>>
>>
>
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