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Thanks Tom.<br>
I guess the file terminator line '--' was missing.<br>
It seems to be working fine now.<br>
<div class="moz-signature">
<div class="moz-signature"><br>
A quick question: If I use the other simpler format, does its
file extension need to be different or will .ali do?<br>
</div>
<br>
<font color="#000099" face="Times">
Thanks, <br>
Abhinav </font>
<p>
<font size="-1" color="#0099aa" face="Verdana">
JCSG@SSRL, SLAC <br>
Phone: (650) 926-2992 <br>
Fax: (650) 926-3292 <br>
</font></p>
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<br>
On 10/11/2011 12:57 PM, Thomas C. Terwilliger wrote:
<blockquote
cite="mid:51971.128.165.72.7.1318363079.squirrel@webmail.lanl.gov"
type="cite">
<pre wrap="">Hi Abhinav,
This format is very unforgiving. It has to have exactly 5 lines:
## TARGET SP_3n91
# hhsearch
scores_from_program: 0 1.00
0 --DDDEVTMNSK....
0 GSDNEFPDFDYQ....
--
also note I changed SP 3n91 to SP_3n91. Your PDB file name must also start
with SP_3n91 in this case. You need a pdb file name with at least 5 chars
before the ".pdb" and these 5 characters have to match the 5 characters
after TARGET on the first line.
Note that the other format read by mr_rosetta is a lot easier:
</pre>
<blockquote type="cite">
<pre wrap="">title text for sequence of target to follow
</pre>
</blockquote>
<pre wrap="">VDFNGYWKMLSNENFEEYLRALDVNVALRKIANLLKPDKEIVQDGDHMIIRTLSTFRNYIMDFQVGKEFEEDLTGIDD
</pre>
<blockquote type="cite">
<pre wrap="">title text for sequence of template (supplied PDB) to follow
</pre>
</blockquote>
<pre wrap="">-AFSGTWQVYAQENYEEFLRAISLPEEVIKLAKDVKPVTEIQQNGSDFTITSKTPGKTVTNSFTIGKEAEIT--TMDG
All the best,
Tom T
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">Somebody helped me out with the format. Thanks.
My alignment file looks like:
## SP 3n91
0 --DDDEVTMNSK....
0 GSDNEFPDFDYQ....
But phenix says
******************* ERROR ENDING ***************
Sorry, the alignment file ['xx.ali']
does not seem to have the correct format?
It can either start with '##' or with '> title of target seq here'
******************* ERROR ENDING ***************
I do have the file starting with '##'!
Thanks,
Abhinav
JCSG@SSRL, SLAC
Phone: (650) 926-2992
Fax: (650) 926-3292
On 10/11/2011 12:23 PM, Abhinav Kumar wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi,
I am looking for file format for alignment file (*.ali) used in
mr_rosetta.
The description on the Phenix web site is not clear.
Can someone please describe the file format with an example?
--
Thanks,
Abhinav
JCSG@SSRL, SLAC
Phone: (650) 926-2992
Fax: (650) 926-3292
</pre>
</blockquote>
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<pre wrap="">
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