<div dir="ltr"><div><div>Thanks for suggestions again!<br><br></div>Could you tell me as well<br>1) what should I provide to the below ali.py script to copy HETATM from the template to the model<br><br>env = environ()<br>
aln = alignment(env)<br># Read in HETATM records from template PDBs<br>env.io.hetatm = True<br>env.io.hydrogen= True<br><br>mdl = model(env, file='3eml', model_segment=('FIRST:A','LAST:A'))<br>aln.append_model(mdl, align_codes='3emlA', atom_files='3eml.pdb')<br>
aln.append(file='od_r.ali', align_codes='od_r')<br>aln.align2d()<br>aln.write(file='result3.ali', alignment_format='PIR')<br>aln.write(file='result3.pap', alignment_format='PAP')<br>
<br>2) how salt bridges can be defined in the model taken from the template with the homology
cysteins in the same positions?<br><br><br></div>James<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">2014-04-15 23:03 GMT+04:00 Modeller Caretaker <span dir="ltr"><<a href="mailto:modeller-care@salilab.org" target="_blank">modeller-care@salilab.org</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="">On 4/15/14, 2:05 AM, James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I've followed 1st modeller tutorial making alignment of my target<br>
against 1 template (with the inclusion of hetatm from the template). As<br>
the result I've obtained the below alignment<br>
</blockquote>
<br></div>
As pointed out already, you haven't told Modeller to put the ligand in the model. Is it possible that you modified the 2rh1.pdb file? Your template sequence doesn't match the one in 2rh1 from PDB (there's an extra sequence in the official PDB from residue 1002:A to 1161:A that isn't in yours). Maybe you removed the ligand by mistake too.<br>
<br>
Ben Webb, Modeller Caretaker<span class="HOEnZb"><font color="#888888"><br>
-- <br>
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</font></span></blockquote></div><br></div>