<font face="verdana, sans-serif">Hi Conrad,<br><br>first you have to convert the mentioned angles to degree. They are represented as rad here. (first 3 values in the translation file)<br>The formula for this would be rad*180/pi. We don't know why, but for the y angle you have to switch the algebraic sign. Simply multiplied by -1.</font><div>
<font face="verdana, sans-serif">We just did the conversions in Excel.</font></div><div><font face="verdana, sans-serif"><br>The rotation in PatchDock is in XYZ notation, first rotation, than translation (this would be the order you also have to use by appling the coordinates)<br>
Then we just loaded the receptor as well as the ligand, apply the changes you want (e.g. color active sites etc.) save it into a session file and wrote a little chimera command file containing the following:<br><br>close session<br>
open Z:\Sebastian\2013\Liganden\ohne Liganden\PatchDock\2+3\reference.py <br>cofr 0.0,0.0,0.0<br>cofr fixed<br>turn x -28.32 models 1 <br>turn y -42.12 models 1 <br>turn z 128.78 models 1<br>move x 33.96 models 1 <br>move y 68.95 models 1 <br>
move z 212.57 models 1<br><br>now you can just edit the turn and move values, open the command file and Chimera will perform the orientation.<br><br>Greets<br>Sebastian</font><br><div><br><div class="gmail_quote">2013/2/12 Conrad Huang <span dir="ltr"><<a href="mailto:conrad@cgl.ucsf.edu" target="_blank">conrad@cgl.ucsf.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi, Sebastian.<br>
<br>
Just out of curiosity, what is your solution? Thanks.<br>
<br>
Conrad<div><br>
<br>
On 2/12/2013 6:00 AM, Sebastian Mock wrote:<br>
</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>
Hi again,<br>
<br>
we figured it out by ourselves. No need to investigate this further!<br>
<br>
Thanks anyway! :-)<br>
<br>
Sebastian<br>
<br></div>
2013/2/11 Conrad Huang <<a href="mailto:conrad@cgl.ucsf.edu" target="_blank">conrad@cgl.ucsf.edu</a> <mailto:<a href="mailto:conrad@cgl.ucsf.edu" target="_blank">conrad@cgl.ucsf.edu</a>>><div><br>
<br>
Can you please send me the receptor and ligand PDB files as well?<br>
Perhaps we can cobble together something.<br>
<br>
Conrad<br>
<br>
<br>
On 2/7/13 1:13 AM, Sebastian Mock wrote:<br>
<br>
Hi,<br>
<br>
I am using Patchdock Algorithm to dock two Enzymes.<br>
<br>
I get the pdb's and can load them into Chimera without having<br>
problems.<br>
<br>
Because Patchdock only performs a jigsaw puzzle with the two<br>
molecules,<br>
I have to look at all the solutions it gave me and judge them by<br>
some<br>
criteria.<br>
This is very time consuming, as I have to match every single<br>
solution<br>
with the appropriate molecules in chimera and I get tons of<br>
solutions.<br>
I found the following two lists with imo coordinates of the<br>
dockings. Is<br>
it possible to load these into Chimera or at least to enter the<br>
coordinates, so that chimera moves the<br>
docking partner and I can just look at it and discard or accept?<br>
<br>
These are the example lists<br></div>
<a href="http://bioinfo3d.cs.tau.ac.il/__PatchDock/runs/1_Hexokinase___combined.pdb_2_G6PIsomerase___combined.pdb_37_58_16_6_1_113/__trans.txt" target="_blank">http://bioinfo3d.cs.tau.ac.il/<u></u>__PatchDock/runs/1_Hexokinase_<u></u>__combined.pdb_2_G6PIsomerase_<u></u>__combined.pdb_37_58_16_6_1_<u></u>113/__trans.txt</a><br>
<<a href="http://bioinfo3d.cs.tau.ac.il/PatchDock/runs/1_Hexokinase_combined.pdb_2_G6PIsomerase_combined.pdb_37_58_16_6_1_113/trans.txt" target="_blank">http://bioinfo3d.cs.tau.ac.<u></u>il/PatchDock/runs/1_<u></u>Hexokinase_combined.pdb_2_<u></u>G6PIsomerase_combined.pdb_37_<u></u>58_16_6_1_113/trans.txt</a>><br>
<a href="http://bioinfo3d.cs.tau.ac.il/__PatchDock/runs/1_Hexokinase___combined.pdb_2_G6PIsomerase___combined.pdb_37_58_16_6_1_113/__docking.res" target="_blank">http://bioinfo3d.cs.tau.ac.il/<u></u>__PatchDock/runs/1_Hexokinase_<u></u>__combined.pdb_2_G6PIsomerase_<u></u>__combined.pdb_37_58_16_6_1_<u></u>113/__docking.res</a><div>
<br>
<<a href="http://bioinfo3d.cs.tau.ac.il/PatchDock/runs/1_Hexokinase_combined.pdb_2_G6PIsomerase_combined.pdb_37_58_16_6_1_113/docking.res" target="_blank">http://bioinfo3d.cs.tau.ac.<u></u>il/PatchDock/runs/1_<u></u>Hexokinase_combined.pdb_2_<u></u>G6PIsomerase_combined.pdb_37_<u></u>58_16_6_1_113/docking.res</a>><br>
<br>
Thanks in advance<br>
Sebastian<br>
<br>
<br></div>
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