<div class="gmail_extra">Hi Gabor,<br><br>It works now. Thank you for your suggestion!<br><br>Fish<br><br><div class="gmail_quote">2012/4/26 Gabor Bunkoczi <span dir="ltr"><<a href="mailto:gb360@cam.ac.uk" target="_blank">gb360@cam.ac.uk</a>></span><br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Hi Fish,<br>
<br>
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.<br>
<br>
Thanks for your help, Gabor<div><div><br>
<br>
On Apr 25 2012, Zhang yu wrote:<br>
<br>
</div></div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div>
Dear Gabor,<br>
<br>
The error message shows nothing but part of the alignment file. I tried<br>
both Phenix 1.7.3 and 1.7.1.<br>
<br>
Thanks,<br>
Fish<br>
<br>
2012/4/25 Gabor Bunkoczi <<a href="mailto:gb360@cam.ac.uk" target="_blank">gb360@cam.ac.uk</a>><br>
<br>
</div></div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div>
Dear Fish,<br>
<br>
can you let me know what the error message is and which Phenix version are you using? Your alignment file looks OK to me.<br>
<br>
Thanks, Gabor<br>
<br>
<br>
<br>
On Apr 25 2012, Zhang yu wrote:<br>
<br>
�Dear Phenixer,<br>
</div></div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div>
<br>
When I used Sculptor to generate a new model, there is a error which I<br>
can not figure out. I input a PDB file (*.pdb) and an alignment file<br>
(*.aln).<br>
<br>
The following is the log file (contents in ######). There seems<br>
something wrong with the *.aln file.<br>
#################<br>
Reading PDB file<br>
----------------<br>
<br>
File name: **/**/******/******/**.pdb<br>
Separating solvent from macromolecules...<br>
<br>
Reading alignment files<br>
-----------------------<br>
<br>
1. **/**/**.aln<br>
<br>
#####################<br>
<br>
<br>
<br>
<br>
The following is the content of the alignment file:<br>
<br></div></div>
**_** MVYSYTEKKRIRKDFGKRPQVLDVPYLLSI<u></u>**QLDSFQKFIEQDPEGQY----<u></u>GLEAAFRSV **_** ---------**<u></u>MEIKRFGRIREVIPLPPLTEIQVESYRRAL<u></u>** QADVPPEKRENVGIQAAFRET<div><br>
� � � � � � � � � � � � �* **: :*: :* * .**::*::: :: * : *::****..<br>
<br>
What is the problem with the alignment file?<br>
<br>
Thank you in advance!<br>
Fish<br>
<br>
<br>
</div></blockquote>
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<br>
� Cambridge Institute for Medical Research<br>
� Wellcome Trust/MRC Building<br>
� Addenbrooke's Hospital<br>
� Hills Road<br>
� Cambridge CB2 0XY<br></div>
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