Hi Dave and Marcus,
No problem - like I said it's great to see Avogadro2 getting underway and
I'm glad to be able to help.
The molecule I looked at earlier was just under 9000 atoms. Avogadro 1
crashes on reading it unless I import the molecule and turn off the bond
order perceiving functionality, and there is a noticeable lag when I rotate
the molecule. With Avogadro2, it whizzes round instantly.
Keep up the great work!
Jens
PS - having said that I just tried loading a pdb of a protein I'm working
on (3HAP) and I just get a big yellow blob, so there may still be the odd
niggle to iron out... ;) I'll file a bug report as soon as my account on
the tracker is activated.
On 12 April 2013 15:35, Marcus D. Hanwell <marcus.hanw...@kitware.com>wrote:
> On Fri, Apr 12, 2013 at 9:29 AM, David Lonie <david.lo...@kitware.com>
> wrote:
> > Hi Jens,
> >
> > On Fri, Apr 12, 2013 at 5:00 AM, Jens <linuck...@gmail.com> wrote:
> >> Really great to hear that avogadro2 is now on the scene and I'm excited
> to
> >> see how it develops in the future.
> >>
> >> It's already looking very impressive - I read in some pretty big
> molecules
> >> and the performance and responsiveness was incredibly snappy.
> >
> > Great to hear the positive feedback! Out of curiousity, just how big
> > were your molecules?
> >
> >> Where's the place to log bug reports while it's still in the initial
> testing
> >> phase? I found one (see below) but it wasn't immediately obvious on the
> >> openchemistry website where the tracker was.
> >
> > We have a bug tracker up here:
> >
> > http://projects.openchemistry.org/
> >
> > I'll add a link on the openchemistry wiki and see about adding one to
> > www.openchemistry.org.
>
> The main site already has a link (Resources, Bug Tracker), we can
> certainly get links on the wiki too. The Doxygen links there too, but
> let's work on making it as obvious as possible.
> >
> > As for the bug:
> >
> >> draw C atom, click Extensions -> Open Babel -> Add Hydrogens:
> >>
> >> Command-line output:
> >>
> >> OBProcess::executeObabel: Running
> >> "/Volumes/Avogadro2-0.5.0-Darwin/Avogadro2.app/Contents/MacOS/obabel"
> "-icml
> >> -ocml -h"
> >> "/Volumes/Avogadro2-0.5.0-Darwin/Avogadro2.app/Contents/MacOS/obabel"
> >> stderr:
> >> "==============================
> >> *** Open Babel Error in RegisterOptionParam
> >> The number of parameters needed by option "t" in The LPMD file format.
> >> differs from an earlier registration.
> >> 0 molecules converted
> >> "
> >> Bad CML: ""
> >
> > I noticed this odd behavior in obabel and brought it up on
> > openbabel-devel a little while ago, see
> >
> http://forums.openbabel.org/obabel-h-bug-while-adding-hydrogens-td4655976.html
> .
> > This is a feature, not a bug from their perspective.
> >
> > We plan to implement our own add-hydrogens routine (and maybe even our
> > own "remove-hydrogens", if I can figure that out ;-) ). I've filed a
> > bug for this here:
> >
> > http://projects.openchemistry.org/issues/169
> >
> There seem to be a few bugs on the Mac with obabel and CML too, so I
> am afraid geometry optimization looks a little dicey. I think there
> are some simple workarounds we can implement there to improve things
> in the next release.
>
> Thanks for the feedback Jens. I think ensuring anyone can have
> Avogadro 1 and 2 installed should make it easier to try out the new
> stuff without having to give up Avogadro 1.
>
> Marcus
>
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