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Re: BALLView - a molecular viewer and modeling tool

Hi Andreas:
I have seen your mail of Sunday, though I make my
remarks here because they concern present debian
package for i386.

I am not going to details, only basic features from my
personal viewpoint of potential user. Then, it is up
to you to average the various requests.

First, I must congratulate with you and your staff for
this beautiful work. Then, I would like to see in the
future a BAKMDL-type global conformational search in
molecular mechanics. The basic step in any
computational work with natural products, be that
semiempirical or quantum mechanical, is to get a
reliable list of low-lying conformers.

Second, I have not yet examined in full the
possibilities of your MD. I have seen on internet that
there is a python script for simulated annealing. I'll
try that (and I'll try also to learn python, which I
also need for nwchem). What I expect is that this
simulated annealing procedure offers the possibility
to sample conformers. The beautiful graphics of
ballview could aid grouping similar conformers
together and than subject them to BAKMDL exploration,
once this is implemented.

I have not yet checked if there is a debian amd64
package. The molecules I am interested in (no
polymers, though huge number of degrees of freedom,
require the power of a 64bit multiprocessor machine).
To this regard, is any plan to parallelize ballview
for dual-opteron?

There is a lot of meat in my eamil. Hope it is good


francesco pietra

--- Andreas Moll <amoll@bioinf.uni-sb.de> wrote:

> Hi,
> I have uploaded a new version of the package.
> > As BALLview is a new package, if it fails to build
> on one architecture,
> > its propagation to the testing distribution will
> not be impaired. This
> > lets you one year or two to either fix the problem
> or drop arch support
> > before inclusion in the next stable release of
> Debian 
> OK, you convinced me ;)
> > I will try to build your package overnight on
> powerpc, and tell you the
> > result tomorrow (japan time...). I hope that you
> can enble ppc support
> > in the meantime.
> I have changed the control file again, to support
> the ppc arch. In 
> addition I modified the configure files, but could
> not test the PPC 
> support, since I have no PPC available. It would be
> great, if you could 
> send me your output.
> > Looks interesting, but I can't play with it, as it
> requires python 2.3.
> > I have 2.4 installed for another app, and don't
> think I can downgrade
> > that (aptitude and apt-get refuse to install 2.3
> now).
> This issue is fixed in the new version, I have set
> the build dependency 
> to python-dev instead of python2.4-dev.
> >     1. I would repack the tarball and leave out
> the Mac OSX and Windows
> >        directory.  It is useless burden to the ftp
> archive
> I tried, but failed miserably ;)
> I deleted these folders in the extracted upstream
> package, but 
> build-package just printed some warnings that it
> will ignore the missing 
> directories.
> Do I have to manually create a new orig.tar.gz
> without the mentioned 
> folders?
> >     2. The debian-upstream directory is a really
> interesting
> >        alternative to something we do not really
> like if upstream
> >        provides a debian directory.  I have to
> clear up my mind
> >        whether I wil like it or not. ;-)
> *g* Well, I like the idea, since our upstream
> authors, can develop 
> install routines, that can be used by future
> downstream authors as well.
> > I am quite interested in trying BALLView, just
> because
> > I need tools in this category every day. However,
> it
> > would be easy for you (and probably very time
> > consuming for me) to provide in some way a debian
> > package (I use viewers on etch i386; computational
> on
> > amd64 etch, not set OpenGL at 64bit and no 32bit
> > chroot)
> The source package is available from
> The binary package for i386 Debian unstable/testing
> from
> >> retitle 407665 ITP: ballview -- Molecular viewer
> and modeling tool [med-bio]
> > Bug#407665: ITP: ballview -- Molecular viewer and
> modeling tool
> > Changed Bug title.
> I got this email from the  Debian bug tracking
> system and I am not 
> really sure what it means? Did someone tagged my
> package for usage in 
> the med-bio project?
> Best regards
> Andreas Moll

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