[Chimera-users] COX inhibitor demo discrepancy

simon chapman rowanlodge19 at gmail.com
Thu Sep 7 02:17:45 PDT 2017


Very kind Elaine. Thank you. I'll follow up your comments. Hope I don't
have to bother you too much again, but there will probably be occasions
when I hit a brick wall...

It's all a part of the learning process!!

Best wishes    Simon

On 6 September 2017 at 17:59, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> HI Simon,
> We’re glad Chimera has been helpful in your studies!
>
> The COX inhibitors demo (under Tools… Demos in the menu) just uses some
> structures from RCSB PDB that already have the small molecules in the
> correct locations relative to the protein structures.  It’s not really a
> tutorial (it doesn’t tell you how to do anything) but a series of actions
> in Chimera that show you parts of these existing structures.  The Credits
> panel of that demo says which PDB entries were used:  1cqe (COX-1 with
> flurbiprofen) and 6cox (COX-2 with SC-558).  So if you just start Chimera
> and use command “open 1cqe” for example, it will show the COX-1 complex
> structure.  1cqe and 6cox each contain a homodimer (two copies of the
> protein+ligand), but for simplicity in the demos, only monomers were shown.
>
> I don’t know where you got the structures you opened, so the coordinates
> might be completely different.  I.e., maybe what you see is where DSV put
> the small molecules.  Also ViewDock will only display energies if what you
> read in to ViewDock is (1) a format that VIewDock knows, and (2) actually
> includes those energies.  Chimera doesn’t calculate them for you.  I have
> no idea what you opened in ViewDock.  Its manual page lists the types of
> docking outputs that it knows how to read, like from the programs DOCK,
> Glide, AutoDock, GOLD, etc.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/
> framevd.html>
>
> There is a ViewDock tutorial that includes sample input from DOCK:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html>
>
> If you meant you tried the Autodock Vina interface in Chimera and it
> didn’t put the small molecules in the right place, that is the way of
> docking calculations. There are a lot of docking parameters and setup
> options and sometimes adjusting those will get the right answer, or simply
> sampling more orientations.  Unfortunately the interface in Chimera uses a
> web service that doesn’t allow very much sampling.  To do a thorough
> docking study, you might have to obtain a docking program and run it
> separately from Chimera.
>
> However, no need to do docking for these particular molecules because the
> structures of the complexes are already known and publicly available from
> the PDB!
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > On Sep 6, 2017, at 4:17 AM, simon chapman <rowanlodge19 at gmail.com>
> wrote:
> >
> > Hi, I'm very impressed with Chimera as  a user of only 3 weeks so far
> >
> > Trying out the various facilities has been a very useful exercise for
> completing my Masters in MedChem.
> >
> > However, when I emulated  the tutorial covering COX 1 and 2 inhibition,
> inputting the molecules fluribrofen and SC558 I generated via DS Visualiser
> bind at the outside edge of  the enzymes. Not centrally as displayed in the
> video.
> >
> > I also noted the molecular data in  ViewDock, ie: energies etc, is
> missing. The table is blank other than the molecule number. Selecting
> 'Column' etc has no effect. The 'H-bonds' option does display however.
> >
> > I've probably done something  wrong, hey ho...but can you enlighten me?
> >
> > Best wishes   Simon
>
>
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