Hi all, <div>I used Modeller in the past to create small loops from scratch. Now I have a protein-DNA complex, and I have to build and model 4 loops of my protein.</div><div>My first problem is that MODELLER does not support DNA, so I have to strip the DNA from the PDB and use the protein alone.</div>
<div>Considering the problem that I have to &quot;paste&quot; the DNA to the modelled structure, I use the options</div><div><u>a.md_level= None</u> to keep the rest of the protein fixed and the option <u>a.loop.md_level</u> to model the loops.</div>
<div>Now, these two commands work on three of the 4 loops, but I have another problem now: I have a very long loop to build (35 aa) and using these two commands, MODELLER create a very strange hairpin loop to connect these two positions. I know which will be the correct structure of this loop because I have a similar protein that present this loop, and the modelling is wrong.</div>
<div>Finally, if I don&#39;t usage a.md_level=None, MODELLER builds a very good loop, but all the protein is in a complete different position with respect of the starting one.</div><div>Any suggestion?</div><div>Best regards</div>
<div>Rubben</div><div> </div><br clear="all"><div><br></div>-- <br>PhD Student, Prof.Glen Group<div>University of Cambridge,</div><div>Unilever Center, Lensfield Road CB2 1EW</div><div>Cambridge, Cambridgeshire,</div><div>
United Kingdom</div><div>University Phone : <span style="color:rgb(128, 128, 128);font-family:Verdana, Arial, Helvetica, sans-serif;font-size:11px;line-height:16px">+44 (0)1223 336432</span></div><div>Cell Phone: +44 (0)774 3358973</div>
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