[Chimera-users] COX inhibitor demo discrepancy

simon chapman rowanlodge19 at gmail.com
Sat Sep 16 14:04:58 PDT 2017


Thank you Elaine...that did it! Couldn't save as Plaintext, but it still
worked as Notepad.

I am very pleased with the MD Movie tutorial...it worked for me without too
many changes, and is suitably impressive. Did the authors supplying the
data derive them from AMBER?  How can I supply data relevant to the
molecules I'm studying to produce the appropriate MD Movie?

Also, and I hope it's OK to bother you again, the attached screenshots show
the result of trying to download 1plx.pdb. I've tried several formats, but
the message "no pdb structures found" appears every time.  Clicking "
1plx.pdb" in the tutorial leads to the page shown. Selecting "save as..."
 leads to  the other two pop-ups in screenshot 1. Downloads lists the file
as Tutorial FrameSet, and contains the four files shown in screenshot 2.
Feel like I'm going round in circles with this one.

Thanks in advance...despite the challenges, Chimera is very impressive, and
should enhance my MSc thesis which commences next month

Best wishes   Simon



On 10 September 2017 at 01:49, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Simon,
> I see in the screenshot image you sent in the earlier e-mail (yesterday)
> that your ViewDock dialog with the “ras.mol2” data opened in it says
> “Created by: Discovery Studio”.  Thus I can only guess that you’d saved the
> “ras.mol2” file from that program, and that it either removed or
> reformatted the energy information so that Chimera could not read it.  Try
> downloading the ras.mol2 file again from the link in the tutorial, saving
> it as plain text and using it in Chimera WITHOUT opening it in DIscovery
> Studio first and it should work.
>
> Kudos on making your own demo!  By the way, all of the User Guide is
> included with your download, and you can search it from the Help menu.
> Best,
> Elaine
>
>
> > On Sep 9, 2017, at 6:42 AM, simon chapman <rowanlodge19 at gmail.com>
> wrote:
> >
> > Hello Elaine, apologies for another email..!
> >
> > I selected 'Columns' on the first occasion I followed the tutorial. It
> only selects Show, Hide ,Read and Display. clicking the first two just
> shows 'Number' . Selecting that does nothing at all. 'Display' shows 2D
> structures as expected. I get the same result every time I've tried since.
>   I've left- and right-clicked all the options several times,but it seems
> the energy data simply isn't available...
> >
> > Got the rotate speed sorted immediately along all 3 axes, so thanks for
> that.
> >
> > I have also made a (shaky) demo from the instruction link you provided.
> >
> > Best wishes   Simon
> >
> >
> > On 8 September 2017 at 17:16, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Hi Simon,
> > You missed a step or two in the ViewDock tutorial.  You have to use the
> Columns menu to control what the dialog is showing.  See the paragraph in
> the tutorial starting “The docked compounds are enumerated…”
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html>
> >
> > There are several options to the “roll” command including number of
> degrees per frame.  For a slower roll, you can set this to a low number,
> e.g. “roll y 0.1”.  Use command “help roll” to see the manual page, or view
> the copy at our website:
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/roll.html>
> > … it says the default is 1.5 degrees per frame.
> >
> > If you already started a roll with inifinite frames, you can use
> “freeze” to halt it.
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/freeze.html>
> >
> > If you mean the COX demo credits, yes, I created that demo.  It is
> really a series of  Chimera commands to execute for each “panel."   Users
> can create their own demos, but it requires some familiarity with the
> commands.
> > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/demos/
> demos.html>
> >
> > Best,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> >
> > > On Sep 8, 2017, at 6:57 AM, simon chapman <rowanlodge19 at gmail.com>
> wrote:
> > >
> > > Hello again Elaine. I understand now about the COX demo... I used DSV
> and PDB to generate the structures. Obviously had incorrect co-ordinates.
> Will watch out for that next time.
> > >
> > > However, following the tutorial exactly for ViewDock still doesn't
> quite match. Attached screenshot shows tutorial pic and the version  that I
> get... the onscreen background molecular structure is identical with the
> 'official' one. So, not sure why the energy data isn't showing up??
> > >
> > > Also, is there a way to slow down rotation of a molecule after
> command 'roll'?
> > >
> > > I  notice your name is at the top of the data slide...is the video
> your production?
> > >
> > > Best wishes   Simon
> > >
> >
> >
> > _______________________________________________
> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > Manage subscription: http://plato.cgl.ucsf.edu/
> mailman/listinfo/chimera-users
>
>
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