Hi Folmer,
Sadly we do not have a UI version without the Silverlight of SiteBInder ready
yet. The reason is that SiteBinder is the first tool from our WebChemistry
platform and back at the time of its development, we had expected that
Microsoft will support it also on other platforms rather than shut it down
completely J. I think that you can use a cross-platform implementation on linux
– moonlight (not tested). In Mac, Silverlight is available directly from
Microsoft and it runs just fine (tested). But, we are planning to port the
whole application to the JavaScript/HTML5 in the next version.
Anyway, I have compiled for you a binary file of SiteBinder in .NET (for
linux/mac use you can use mono http://mono-project.com). You can reach it from
http://is.muni.cz/de/256262/MotiveMatch.zip There are also some test data and
expected results included. If you execute the application without any
parameters (MotiveMatch.exe | mono MotiveMatch.exe) you will get a hint what
the parameters are and how you can use it.
And just to add to that: <Advertisement> For the ligands selection you can use
our molecular language selection framework (paper in the process of writing) as
well - webchem.ncbr.muni.cz/Platform/MotiveQuery/Index </Advertisement>
If you would have further questions, just let me know.
Lukas
From: Folmer Fredslund [mailto:folm...@gmail.com]
Sent: Monday, February 9, 2015 4:21 PM
To: Lukáš Pravda
Subject: Re: [PyMOL] ligand superimpose (multiple structures) and RMSD value
Hi Lukes,
That sounds interesting.
Is there a version that does not requires Microsoft Silverlight?
Best regards,
Folmer
2015-02-09 11:31 GMT+01:00 Lukáš Pravda <xpra...@ncbr.muni.cz>:
HI Abdul,
Not sure if this is the solution you would like to, but there are several tools
which are tailored specifically for this purpose (i.e. superimposition of small
molecules). One of them is SiteBinder
(http://webchem.ncbr.muni.cz/Platform/App/SiteBinder), it allows you to do
variety of superimpositions and the results can be loaded back to PyMOl. If you
need further assistance with SiteBInder, just let me know.
Cheers
Lukas
From: Abdul Ajees [mailto:a_abdul_aj...@yahoo.com]
Sent: Saturday, February 7, 2015 7:46 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] ligand superimpose (multiple structures) and RMSD value
Dear Pymol users and developers,
I need to superimpose more than 200 ligands (same ligand with different
conformations) to one target ligand and obtain the RMSD value.
for example
align 1RGS.pdb 1KMS.pdb
align 1VKS.pdb 1KMS.pdb
align 1CHC.pdb 1KMS.pdb
.......
......
I can manually do this action but it take long time. Is there a way to do this
action quick and automatic using pymol ? For your kind information, I have
pymol windows and linux version.
My idea is to group the 200 ligands into various groups based on their
conformation. I found some scripts at
"http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/";. But it is not working
for me.
It will be highly beneficial to me, if you could kindly suggest any idea.
Thank you,
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