Port details |
- pymol Free and Open-Source molecular modeling system
- 1.5.0.1.3978_3 biology
=2 1.5.0.1.3978_3Version of this port present on the latest quarterly branch. DEPRECATED: Not staged. See http://lists.freebsd.org/pipermail/freebsd-ports-announce/2014-May/000080.html
This port expired on: 2014-08-31
- There is no maintainer for this port.
- Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org
 - Port Added: 2002-08-13 11:53:54
- Last Update: 2014-09-01 11:37:14
- SVN Revision: 366862
- People watching this port, also watch:: zip, python, py39-tkinter
- Also Listed In: python
- License: not specified in port
- WWW:
- http://pymol.sourceforge.net/
- Description:
- PyMOL is a molecular graphics system with an embedded Python interpreter
designed for real-time visualization and rapid generation of
high-quality molecular graphics images and animations. It is fully extensible
and available free to everyone via the "Python" license.
PyMOL can be used to create images and animations with unprecedented ease.
It can also perform many other valuable tasks (such as editing PDB files)
to assist you in your research.
WWW: http://pymol.sourceforge.net/
cgit ¦ GitHub ¦ GitHub ¦ GitLab ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - There is no configure plist information for this port.
- Dependency lines:
-
- No installation instructions:
- This port has been deleted.
- PKGNAME: pymol
- Flavors: there is no flavor information for this port.
- distinfo:
- There is no distinfo for this port.
No package information for this port in our database- Sometimes this happens. Not all ports have packages. Perhaps there is a build error. Check the fallout link:

- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- Numeric.py : math/py-numeric
- python2.7 : lang/python27
- gmake : devel/gmake
- Runtime dependencies:
-
- Numeric.py : math/py-numeric
- Pmw : x11-toolkits/py-Pmw
- python2.7 : lang/python27
- Library dependencies:
-
- libpng15.so : graphics/png
- libfreetype.so : print/freetype2
- libglut.so : graphics/freeglut
- libGLEW.so : graphics/glew
- There are no ports dependent upon this port
Configuration Options:
- No options to configure
- Options name:
- N/A
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
Commit | Credits | Log message |
1.5.0.1.3978_3 01 Sep 2014 11:37:14
  |
bapt  |
Remove non staged ports without pending PR from b* |
1.5.0.1.3978_3 29 Jul 2014 18:41:17
  |
adamw  |
Convert a bunch of USE_BZIP2 to USES=tar:bzip2
Approved by: portmgr (not really, but touches unstaged ports) |
1.5.0.1.3978_3 23 Jul 2014 16:44:28
  |
bapt  |
Reset maintainership for ports not staged with no pending PR
With hat: portmgr |
1.5.0.1.3978_3 16 Apr 2014 18:28:50
  |
zeising  |
The FreeBSD x11@ and graphics team proudly presents
a zeising, kwm production, with help from dumbbell, bdrewery:
NEW XORG ON FREEBSD 9-STABLE AND 10-STABLE
This update switches over to use the new xorg stack by default on FreeBSD 9
and 10 stable, on osversions where vt(9) is available.
It is still possible to use the old stack by specifying WITHOUT_NEW_XORG in
/etc/make.conf .
FreeBSD 8-STABLE and released versions of FreeBSD still use
the old version.
A package repository with binary packages for new xorg will
be available soon.
This patch also contains updates of libxcb and related ports, pixman, as well (Only the first 15 lines of the commit message are shown above ) |
1.5.0.1.3978_2 13 Mar 2014 07:41:34
  |
miwi  |
- Convert USE_GMAKE to USES |
1.5.0.1.3978_2 11 Dec 2013 14:43:51
  |
bapt  |
In preparation for making libtool generate libraries with a sane name, fix all
LIB_DEPENDS in biology |
1.5.0.1.3978_2 20 Sep 2013 15:55:44
  |
bapt  |
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology) |
1.5.0.1.3978_2 04 Aug 2012 22:52:04
 |
kwm  |
Switch from libglut to freeglut and retire libglut. Libglut hasn't been
developed in years and has been dropped from the MESA 8.0 distribution.
Freeglut is a rewrite of glut and is actively developed and is used by
many linux distributions instead of libglut.
Bump all ports that directly depend on libglut because of the shlib version
change.
There are some extra items in this patch.
*) Because freeglut doesn't have the same dependancies as libglut, some ports
need extra dependencies added to USE_XORG to make them build.
*) Mark graphics/f90gl broken, f90gl depends on a header that is only shipped
with libglut.
*) Remove option for libglut/freeglut selection in games/cake, only freeglut
remains now.
*) While here fix a png related build issue games/vegastrike.
Thanks to miwi for running the exp-run.
Approved by: portmgr (miwi)
Collaboration with: zeising@
Obtained from: xorg-dev staging area. |
1.5.0.1.3978_1 01 Jun 2012 05:26:28
 |
dinoex  |
- update png to 1.5.10 |
1.5.0.1.3978 16 Feb 2012 02:30:10
 |
maho  |
update to 1.5.0.1. |
1.4.1.3946 09 May 2011 04:36:54
 |
maho  |
update to 1.4.1
Notified by: Alvin Oga |
1.3r1.3913 19 Mar 2011 12:38:54
 |
miwi  |
- Get Rid MD5 support |
1.3r1.3913 16 Sep 2010 21:48:04
 |
maho  |
Update to 1.3r1.3913.
Actually the version number is from SVN, and maho@ manually
checked out from SVN.
The source archive is not distributed as tar ball. |
1.0r2_5 28 Mar 2010 06:47:48
 |
dinoex  |
- update to 1.4.1
Reviewed by: exp8 run on pointyhat
Supported by: miwi |
1.0r2_4 05 Feb 2010 11:46:55
 |
dinoex  |
- update to jpeg-8 |
1.0r2_3 08 Jun 2009 22:30:55
 |
miwi  |
- Update lang/python26 and make Python 2.6.2 to the default Python version
Tested by: 3 pointyhat runs
Thanks to: pav, gahr, lwhsu, mva, amdmi3 |
1.0r2_2 23 Jan 2009 16:28:36
 |
flz  |
- Update X.org ports to 7.4+ (few ports are more recent than the katamari).
- Bump PORTREVISION for all ports depending on libglut since the shlib
version number went from 4 to 3.
- Bump PORTREVISION for all ports depending on libXaw as libXaw.so.8 isn't
installed anymore.
- Couple of ports fixes (mostly missing xorg components added to USE_XORG). |
1.0r2_1 27 Mar 2008 11:20:18
 |
miwi  |
- Add missing dependens
- Bump PORTREVISION
Submitted by: pointyhat via pav |
1.0r2 10 Mar 2008 00:57:15
 |
maho  |
Fix pkg-plist
Submitted by: pav |
1.0r2 07 Mar 2008 02:38:09
 |
maho  |
Update to 1.0r2. |
0.99rc6_2 02 Sep 2007 07:16:05
 |
rafan  |
- Chase x11-toolkits/pmw renamed to x11-toolkits/py-Pmw
PR: 115302 |
0.99rc6_1 19 May 2007 20:32:57
 |
flz  |
- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}. |
0.99rc6 09 Feb 2007 00:11:55
 |
maho  |
Update to 0.99rc6.
PR: 108940
Submitted by: CHAO Shin |
0.99rc1 17 Sep 2006 11:51:56
 |
maho  |
Fix build on amd64
Submitted by: kris |
0.99rc1 17 Sep 2006 01:32:58
 |
kris  |
BROKEN on amd64 and ia64: Does not build |
0.99rc1 01 Jul 2006 05:06:21
 |
maho  |
o Update to 0.99rc1
o add data dir to have working port[1]
PR: 95121[1]
Submitted by: Sangwoo Shim <sangwoos at gmail.com>[1]
This commit is a result of hacks at the CodeFest Akihabara 2006 hosted by FSIJ. |
0.98_1 03 May 2006 23:26:35
 |
edwin  |
Remove USE_REINPLACE from all categories starting with B |
0.98_1 22 Jan 2006 08:20:34
 |
edwin  |
SHA256ify
Approved by: krion@ |
0.98_1 12 Jan 2006 12:54:32
 |
sem  |
- Update graphics/libglut to 6.4.1.
- Shared lib version and PORTREVISION bumb for all affected ports.
While I'm here:
- Remove USE_MESA knob where it was (35 ports).
It marked as depricated for 2 years.
PR: ports/90247
Submitted by: Ermal Lu?i <eri--@albabsd.org> |
0.98 10 Oct 2005 09:08:23
 |
maho  |
Update to 0.9.8 |
0.97 26 Mar 2005 22:20:19
 |
kris  |
Try to unbreak on amd64 and ia64
Approved by: portmgr (self) |
0.97 24 Mar 2005 01:06:40
 |
maho  |
Fix build on amd64
Submitted by: kris via pointy hat
Approved by: portmgr (marcus) |
0.97 07 Feb 2005 08:39:51
 |
maho  |
update to 0.97 |
0.93 24 Oct 2004 03:40:23
 |
maho  |
Forced commit
Actually this report was submitted by mharo,
and eik kindly told me how to fix.
PR: 71095
Submitted by: mharo |
0.93 24 Oct 2004 03:37:02
 |
maho  |
Avoid the use of != statements in ports Makefile
PR: 71095
Submitted by: eik |
0.93 06 May 2004 19:49:54
 |
maho  |
Make portlint happy by replacing space to tab
PR: 65409
Submitted by: trevor |
0.93 10 Apr 2004 16:07:10
 |
trevor  |
Trim whitespace. |
0.93 20 Mar 2004 05:20:47
 |
maho  |
Do not hardcord PICFLAG
Submitted by: ru |
0.93 19 Mar 2004 04:20:12
 |
maho  |
Backout previous change of PICFLAG, since
behaviour of -fPIC and -fpic are different.
Here is the comment form obrien:
--
"-fpic" is a [minor?] optimization for machines that can handle it:
-fpic
Generate position-independent code (PIC) suitable for use in a shared
library, if supported for the target machine. Such code accesses all
constant addresses through a global offset table (GOT). The dynamic
loader resolves the GOT entries when the program starts (the dynamic
loader is not part of GCC; it is part of the operating system). If
the GOT size for the linked executable exceeds a machine-specific
maximum size, you get an error message from the linker indicating (Only the first 15 lines of the commit message are shown above ) |
0.93 18 Mar 2004 23:06:12
 |
maho  |
-fPIC is appropreate on all architectures.
Submitted by: kris |
0.93 17 Mar 2004 10:47:29
 |
maho  |
1) update to 0.9.3
2) honor PREFIX & LOCALBASE
3) SIZEify
4) possible fix for amd64 and ia64 |
0.90_1 04 Feb 2004 05:21:48
 |
marcus  |
Bump PORTREVISION on all ports that depend on gettext to aid with upgrading.
(Part 2) |
0.90 07 Nov 2003 20:40:50
 |
anholt  |
LIB_DEPENDS on libglut for libglut rather than soon-to-disappear Mesa3. |
0.90 20 Aug 2003 10:40:37
 |
perky  |
Fix build on python2.3 |
0.90 24 Jul 2003 07:06:17
 |
maho  |
Update to 0.90 |
0.86 03 May 2003 03:45:31
 |
maho  |
Updated to 0.8.6.
Submitted by: M. L. Dodson <bdodson@scms.utmb.EDU>
Pkg-plist by: maho |
0.82_3 07 Mar 2003 05:56:43
 |
ade  |
Clear moonlight beckons.
Requiem mors pacem pkg-comment,
And be calm ports tree.
E Nomini Patri, E Fili, E Spiritu Sancti. |
0.82_3 19 Nov 2002 23:01:49
 |
maho  |
1. add a missing dependency on png and unbreak.
2. change e-mail address of maho. |
0.82_3 26 Aug 2002 05:13:29
 |
perky  |
o Fix examples directory path which is changed in last revision.
Submitted by: Glenn Johnson <glennpj@charter.net> |
0.82_2 25 Aug 2002 08:37:53
 |
perky  |
o Fix RUN_DEPENDS path (PMW -> Pmw)
o Fix DISTNAME which was broken by previous commit.
o Install example files
PR: 41977
Submitted by: Glenn Johnson <glennpj@charter.net>
Approved by: maintainer |
0.82_1 22 Aug 2002 04:20:19
 |
perky  |
o Remove redundant dependency on py-tkinter.
o Bump PORTREVISION that I've missed on last commit.
Submitted by: Glenn Johnson <glennpj@charter.net> |
0.82 22 Aug 2002 03:35:32
 |
perky  |
Add a dependecy to x11-toolkits/pmw
PR: 41857
Submitted by: Glenn Johnson <gjohnson@srrc.ars.usda.gov>
Approved by: maintainer |
0.82 13 Aug 2002 11:53:44
 |
perky  |
Add pymol 0.82, Free and Open-Source molecular modeling system.
PR: 40694
Submitted by: Nakata Maho <chat95@mbox.kyoto-inet.or.jp> |