<div dir="ltr">Phil<div><br></div><div style>You have a few choices and I'm happy to discuss in detail but the two main choices are</div><div style><br></div><div style>1. Use a SMILES string for each molecule.</div><div style>
<br></div><div style>2. Use REEL to edit the molecule and run eLBOW directly.</div><div style><br></div><div style>In both cases, you can fit the molecule to your model using GLR.</div><div style><br></div><div style>Sorry for the short answer but I can easily help you directly.</div>
<div style><br></div><div style>Nigel</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Apr 25, 2013 at 1:01 PM, Phil Jeffrey <span dir="ltr"><<a href="mailto:pjeffrey@princeton.edu" target="_blank">pjeffrey@princeton.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">I've got homologues of small molecule compounds I want to generate restraints for. The changes I'm looking at are converting O to S and moving a substituent around on a phenyl ring. I expect them to have similar conformations overall.<br>
<br>
Is the best method to:<br>
<br>
1. create a new PDB file of the homolog, change atom types and do some primitive modeling, assuming that the --opt method will fix geometry snafus<br>
<br>
~or~<br>
<br>
2. use a SMILES string, edit the numbering of the PDB file and regenerate the restraints from that<br>
<br>
<br>
Thanks<span class="HOEnZb"><font color="#888888"><br>
Phil Jeffrey<br>
Princeton<br>
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</font></span></blockquote></div><br><br clear="all"><div><br></div>-- <br>Nigel W. Moriarty<br>Building 64R0246B, Physical Biosciences Division<br>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>
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