Bug 138061 – Scientific Gentoo reorg: crystallography herd/category?

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description George Shapovalov (RETIRED) 2006-06-26 08:28:00 UTC]

This one seems good too. 

Jan Marten Simons <[e-mail]> (to be trained) has submitted a few ebuilds. 

Anybody else?

What packages are in the tree already?

George

[Comment 1 Jan Marten Simons 2006-06-27 05:11:51 UTC]

List of packages, which are in tree so far and could be moved to a crystallographic herd (named xtal?):

sci-chemistry/ccp4
     Available versions:  ~6.0.1
     Installed:           none
     Homepage:            http://www.ccp4.ac.uk/
     Description:         Protein X-ray crystallography toolkit

* sci-chemistry/cns
     Available versions:  ~1.1
     Installed:           none
     Homepage:            http://cns.csb.yale.edu/
     Description:         Crystallography and NMR System

* sci-chemistry/coot
     Available versions:  ~0.1.2_pre1
     Installed:           none
     Homepage:            http://www.ysbl.york.ac.uk/~emsley/coot/
     Description:         Crystallographic Object-Oriented Toolkit for model building, completion and validation

* sci-chemistry/eden
     Available versions:  ~5.3
     Installed:           none
     Homepage:            http://www.edencrystallography.org/
     Description:         A crystallographic real-space electron-density refinement and optimization program

* sci-chemistry/maid
     Available versions:  ~20011112
     Installed:           none
     Homepage:            http://www.msi.umn.edu/~levitt/
     Description:         Automates the fitting of protein X-ray crystallographic electron density maps

* sci-chemistry/ortep3
     Available versions:  ~1.0.3
     Installed:           none
     Homepage:            http://www.ornl.gov/sci/ortep/
     Description:         Thermal ellipsoid plot program for crystal structure illustrations

* sci-chemistry/platon
     Available versions:  ~20060621
     Installed:           none
     Homepage:            http://www.cryst.chem.uu.nl/platon/
     Description:         Versatile, SHELX-97 compatible, multipurpose crystallographic tool

* sci-chemistry/shelx
     Available versions:  ~20060317
     Installed:           none
     Homepage:            http://shelx.uni-ac.gwdg.de/SHELX/
     Description:         Programs for crystal structure determination from single-crystal diffraction data

* sci-libs/coot-data
     Available versions:  ~1
     Installed:           none
     Homepage:            http://www.ysbl.york.ac.uk/~emsley/coot/
     Description:         Data for the Crystallographic Object-Oriented Toolkit

Maintainers of those would probably be interested in joining the new (sub-)herd, too.

[Comment 2 Donnie Berkholz (RETIRED) 2006-06-27 08:52:27 UTC]

(In reply to comment #1)
> Maintainers of those would probably be interested in joining the new
> (sub-)herd, too.

Heh. Maintainers? I wrote and added all of those myself, so that would be in the singular.

[Comment 3 Justin Lecher (RETIRED) 2009-04-30 19:21:02 UTC]

I would join you, but we should build a structure herd and include any kind of technique to obtain, manipulate and present those.

[Comment 4 Justin Lecher (RETIRED) 2010-06-22 12:29:37 UTC]

We should go for something like structural protein science, including nmr xray and em.

[Comment 5 George Shapovalov (RETIRED) 2016-02-12 09:44:59 UTC]

Heh, the bug us still open, many many years after the initial push to reorg sci and many years since the last comment. We gotta do something about it - either finally make that new category, given enough packages already, or close it.

Justin, Donnie: I guess I gotta give the honors of decision or eventual split to either of you, whoever feels more involved in this specific one ;).

[Comment 6 Justin Lecher (RETIRED) 2016-02-12 09:53:08 UTC]

(In reply to George Shapovalov from comment #5)
> Justin, Donnie: I guess I gotta give the honors of decision or eventual
> split to either of you, whoever feels more involved in this specific one ;).

Hi George,

both of us are probably drifting to far away from that topic.

I am not sure if it is worth the effort. If we do something, we could rather think about "structural biology", "protein science",... But I find it hard to structure the package in a meaningful way with a single CAT.

[Comment 7 George Shapovalov (RETIRED) 2016-02-12 10:46:51 UTC]

So, lets close this bug then? sci-chemistry has only 115 packages, which is far from being the largest, so it doesn't seem to need an urgent split..
I guess I'll just wait for Donnie's comment for a little and then close it in a week or so (hope I won't forget) if he doesn't comment or say something similar..