<div dir="ltr"><span class="Apple-style-span" style="font-size:large">Dear Luc and </span><meta http-equiv="content-type" content="text/html; charset=utf-8" style><span class="" style="font-family:Courier;border-collapse:collapse"><span class="Apple-style-span" style="font-size:large">Graeme</span></span><div>
<span class="" style="font-family:Courier;border-collapse:collapse"><span class="Apple-style-span" style="font-size:large"><br></span></span></div><div><font class="" face="Courier"><span class="" style="border-collapse:collapse"><span class="Apple-style-span" style="font-size:large">I have followed, what you all have suggested. I have downloaded and installed on my PC which is having DEBIAN OS.</span></span></font></div>
<div><font class="" face="Courier"><span class="" style="border-collapse:collapse"><span class="Apple-style-span" style="font-size:large">Everything is working fine.</span></span></font></div><div><font class="" face="Courier"><span class="" style="border-collapse:collapse"><span class="Apple-style-span" style="font-size:large"><br>
</span></span></font></div><div><font class="" face="Courier"><span class="" style="border-collapse:collapse"><span class="Apple-style-span" style="font-size:large">Now I am searching for the code which can give me the filled unit cell or matrix (3X3X3) of unit cell.</span></span></font></div>
<div><font class="" face="Courier"><span class="" style="border-collapse:collapse"><span class="Apple-style-span" style="font-size:large">I have checked the codes available for the pymol and cctbx working together (</span></span></font><span class="" style="color:rgb(51,51,51);font-family:Verdana,Arial,Verdana,Arial,Helvetica,Tahoma,Verdana,sans-serif;line-height:21px"><span class="Apple-style-span" style="font-size:large"><a href="http://pymolwiki.org/index.php/Supercell">http://pymolwiki.org/index.php/Supercell</a></span></span><span class="" style="font-family:Courier;border-collapse:collapse"><span class="Apple-style-span" style="font-size:large">) or (<a href="http://pymolwiki.org/index.php/SuperSym">http://pymolwiki.org/index.php/SuperSym</a>).</span></span></div>
<div><span class="" style="font-family:Courier;border-collapse:collapse"><span class="Apple-style-span" style="font-size:large">It will be better, if I can get the code which does not use Pymol.</span></span></div><div><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="border-collapse:collapse;font-size:large">Especially I am concentrating on SuperSym, but when I ran using command line, it gives segmentation fault (I think I need to remove everything which is for displaying in Pymol window, not sure though).</span></font></div>
<div><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="border-collapse:collapse;font-size:large"><br></span></font></div><div><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="border-collapse:collapse;font-size:large">Thanx in advance</span></font></div>
<div><font class="Apple-style-span" face="Courier"><span class="Apple-style-span" style="border-collapse:collapse;font-size:large">Prasun Kumar</span></font></div><meta http-equiv="content-type" content="text/html; charset=utf-8"></div>
<div class="gmail_extra"><br clear="all"><div>PRASUN (ASHOKA)<br>Desire + stability = Resolution<br>Resolution + Hard work = Success</div>
<br><br><div class="gmail_quote">On Wed, Mar 20, 2013 at 2:44 AM, Luc Bourhis <span dir="ltr"><<a href="mailto:luc_j_bourhis@mac.com" target="_blank">luc_j_bourhis@mac.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word"><font face="Courier">Dear Prasun,<br></font><div class="im"><div><font face="Courier"><br></font><blockquote type="cite"><div dir="ltr"><div><font face="Courier">My main program is in PERL and I am calling OPENBABEL by installing it on my PC and using the system command on UNIX. e.g. system("babel -i pdb input file -o cif output file");</font></div>
<div><font face="Courier"><br></font></div><div><font face="Courier">Same thing I wanted for cctbx. Since it does alot of other things along with unitcell generation, I wanted to have the relevant part of cctbx.</font></div>
<div><font face="Courier"><br></font></div><div><font face="Courier">I wanted to make binary of that part, so that I can call it from the main program.</font></div></div></blockquote><font face="Courier"><br></font></div>
</div><div><font face="Courier">I got it this time, sorry for being rather thick on that one!</font></div><div><font face="Courier"><br></font></div><div><font face="Courier">The easiest is definitively to follow Graeme's excellent advice. </font></div>
<div><font face="Courier"><br></font></div><div><font face="Courier">Let me spell it out with more details:</font></div><div><font face="Courier"><br></font></div><div><font face="Courier">1. Grab a distro of the cctbx that works on the machine you target </font></div>
<div><font face="Courier"> at <a href="http://cci.lbl.gov/cctbx_build" target="_blank">http://cci.lbl.gov/cctbx_build</a> and install it.</font></div><div><font face="Courier"> Actually, since your main program is written in Perl, it would be rather </font></div>
<div><font face="Courier"> </font><span style="font-family:Courier">easy</span> <font face="Courier">to figure out which OS it is running on, </font><font face="Courier">and then to deduce </font></div><div><font face="Courier"> which </font><span style="font-family:Courier">installer to download, </span><span style="font-family:Courier">and finally to install the cctbx on-the-fly </span></div>
<div><span style="font-family:Courier"> as the program launches for the first time. That way the same Perl code</span></div><div><span style="font-family:Courier"> would run on a wide range of Linuxes and versions of MacOS, and even</span></div>
<div><span style="font-family:Courier"> on Windows if you bundle Perl with your program (you would not need</span></div><div><span style="font-family:Courier"> to bundle Python as the cctbx installer does that for you on Windows).</span></div>
<div><span style="font-family:Courier"><br></span></div><div><font face="Courier">2. system "/path/to/cctbx_build/bin/cctbx.python", "script_of_yours.py";</font></div><div><font face="Courier"> * cctbx_build is one of the directory created by the cctbx installer;</font></div>
<div><font face="Courier"> again rather easy to have your Perl program find it if it installed</font></div><div><font face="Courier"> the cctbx in the first place!</font></div><div><font face="Courier"> * script_of_yours.py would be a Python script you would devise </font></div>
<div><font face="Courier"> to generate unit cells: you would be much more productive writing that </font></div><div><font face="Courier"> in Python than </font><span style="font-family:Courier">targeting the cctbx C++ interface, as Graeme and I have</span></div>
<div><span style="font-family:Courier"> already pointed out.</span></div><div><font face="Courier"><br></font></div><div><font face="Courier">HtH,</font></div><div><font face="Courier"><br></font></div><div><font face="Courier">Luc</font></div>
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