[Chimera-users] COX inhibitor demo discrepancy
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.
> There is a ViewDock tutorial that includes sample input from DOCK:
> 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 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>
> > 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
> > 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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