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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Dear Phenix community,
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<div>I was hoping if someone could help me with using Phaser correctly, since I can't seem to produce the desired search model.</div>
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<div>The first thing that I was wondering about is that the CLUSTAL alignment from the log file is quite different to the .aln alignment I made with phenix --> other tools --> multiple sequence alignment. Why is a sequence alignment required as input if sculptor
performs it's own internally?</div>
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<div>My model sequence aligned to my target sequence in the log file has several gaps in the alignment . For e.g.,</div>
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<div>MASTER ......AASFIMV...... </div>
<div>CHAIN_A ......AKM--MF....... </div>
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<div>I would like to great a search model in which the residues aligned to gaps in the MASTER chain are included, however the resulting sculptor .pdb file has these residues removed. Shouldn't <span style="font-size: 13.3333px;">they be inserted so that the
rest of the chain is in the correct register? </span></div>
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<div><span style="font-size: 13.3333px;">If anyone can let me know the parameters to allow this, I would greatly appreciate it. I tried unselecting 'gap' in main-chain deletion scope and some other variations, but this didn't seem to help. </span></div>
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<div><span style="font-size: 13.3333px;">I seem to get the same result even if I change the target index from 1 to 2 in the associated .aln alignment. Does anyone know why this is?</span></div>
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<div><span style="font-size: 13.3333px;">Apologies if this is quite obvious, I have been reading the documentation but can't seem to figure it out.</span></div>
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<div><span style="font-size: 13.3333px;">All the best,</span></div>
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<div><span style="font-size: 13.3333px;">Joseph.</span></div>
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<div style="margin:0px"><font face="Courier New" size="2"><span lang="en-GB">Joseph Brock |</span><span lang="en-GB"> PhD</span><span lang="en-GB"><br>
Division of Physiological Chemistry II</span><span lang="en-GB"><br>
Department of Medical Biochemistry and Biophysics </span><span lang="en-GB"><br>
Karolinska Institutet</span><span lang="en-GB"><br>
Scheeles v�g 2</span><span lang="en-GB"><br>
SE-171 77 Stockholm, Sweden</span></font></div>
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