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    Science Tools for GNU-Darwin

    Dr. Michael L. Love,
    updated Tue Aug 26 13:27:53 EDT 2008

    Updates:

    The PyMOL Molecular Graphics System has been ported to GNU-Darwin and Mac OSX.
    PyMOL is a powerful molecular graphics package for structural biology and other sciences. This interactive system is fully scriptable using the Python computing language, and it is free software! PyMOL is in CVS, and it will be added to the ports system.

    Pymol is an effective molecular builder, but it can also produce stunningly beautiful and realistic 3D graphics. Be sure to see the GNU-Darwin Art page for an example.

    The GNU-Darwin build of PyMOL-0.60 is available now for distribution, along with the required dependent packages, tcl-8.3.2, tk-8.3.2, python-2.0.1, py-tkinter, and py-pmw. In addition, these packages also require XFree86-4.1 (see XonX). Be sure to read the package installation instructions.

    Incidentally, IDLE is a good editor/debugger for python scripts. IDLE is also available from GNU-Darwin.

    Other Key Crystallographic and Molecular Graphics Programs Ported *

    CCP4-4.1 including PROTIN, Refmac, AMoRe, DM, MLPHARE, CAD, ARP_WARP, PLTDEV, FFT, OASIS, SCALEIT, SFALL, XDLMAPMAN, HKLVIEW, and RasMol

    Here is a link to our CCP4 porting tips page.

    CNS: no package available due to license restrictions.

      "YOU SHALL NOT DISCLOSE IN ANY FORM EITHER THE DELIVERED SOFTWARE OR DOCUMENTATION OR ANY MODIFICATIONS OR DERIVATIVE WORKS BASED ON THE SOFTWARE OR DOCUMENTATION TO THIRD PARTIES WITHOUT PRIOR WRITTEN AUTHORIZATION."

    POV-ray: with package available POV-ray builds automatically with the ports system.

    PovScript: no package available due to license restrictions (see Molscript).

    Molscript with GL: no package available due to license restrictions.

      "The LICENSEE shall not disclose in any form either the delivered SOFTWARE or any modifications or derivative works based on the SOFTWARE to third parties without prior written authorization from the LICENSOR."

      Tip: There are compiled molscript sources available from the Tenon third party apps page.

    Raster3D: We now have a package available, and the Darwin modifications are in CVS

    Mosflm: Here is a screen shot. Mosflm is now part of CCP4.

      Mosflm has been ported, but not yet tested to our knowledge.

    DPS should be ready soon as well!

    * The code will be optimized for the parallel architecture of an Apple G4 dual processor super cluster.

    More Biology and Chemistry programs for GNU-Darwin

    William Van Etten of Blackstone Technology Group has kindly provided the building instructions for EMBOSS, the sequence analysis suite.

    babel: Molecular Coordinate Conversion Utility

    clustalw: Multiple Sequence Alignment

    fastdnaml: Maximum Likelihood Phylogenetic Tree Generation

    gperiodic: GTK Periodic Table

    hmmer: Markoff Analysis of Biological Sequences

    molden: Molecular Graphics and Density Display

    mopac: Calculation of Molecular Orbitals

    nab: Nucleic Acid Building

    ortep3: Thermal Ellipsoid Plotter for Crystal Structures

    p5-bioperl: Perl Modules for Bioinformatics and Genomics

    phylip: Package for the study of Phylogeny

    povchem: PDB rendering for POVray

    psi88: 3D Waveform Plotter

    sim4: Alignment of Expressed and Genomic Sequences

    xmolwt: Molecular Weight Calculator for Elemental Analysis

    Astronomy Tools for GNU-Darwin

    dgpsip: Internet DGPS corrections

    luna: console moon phase calculator

    p5-GPS: perl interface to a GPS receiver with Garmin protocol

    rmap: Earth image generation

    saoimage: Astonomical image display

    sattrack: Satellite Tracking and Orbit Prediction Software

    wmmoonclock: Moon Phase WindowMaker applet

    wmspaceweather: WindowMaker space weather dockapp

    wmsun: Sun rising and setting times WM dockapp

    xearth: Earth imaging clock

    xplanet: Planet rendering tool

    Misc. Tools for GNU-Darwin

    fftw: Discrete Fourier Transform calculation library


    Scientific Consulting

    I do crystallographic consulting for data collection, refinement, and molecular graphics; with much synchrotron experience and particular expertise in the Supper Mirror System. I'm also a Physical Chemistry consultant specializing in water vapor equilibria in medical devices. Please feel free to contact me, if you want my help in porting these programs to your Mac, cheap laptops, or anything else. Here are links to my cv and NIH Biosketch.

    Contact Info

    Michael L. Love Ph.D
    Department of Biophysics and Biophysical Chemistry
    School of Medicine
    Johns Hopkins University
    725 N. Wolfe Street
    Room 608B WBSB
    Baltimore MD 21205-2185

    Interoffice Mail: 608B WBSB, SoM

    office: 410-614-2267
    lab: 410-614-3179
    fax: 410-502-6910
    cell: 443-824-3451

    GNU-Darwin.org
    proclus@gnu-darwin.org

    Links
    Apple's SciTech Page

    Now you can do real science on your Mac! I have ported a variety of scientific computing programs to Darwin. In order to facilitate this work I have created a Package Distribution of Darwin and MacOSX software.
    The blog

    MOD

    Molecules@GNU-Darwin

    MOD

    xanthone-more
    Citric-acid-more
    apigenin-more
    naringenin-more
    hesperidin-more
    methyl-ethyl-more
    methyl-ethanol-more
    methyl-drene-more
    methyl-dopa-more
    methyl-cyclohexanone-more
    methyl-cyclohexanol-more
    methyl-cuprate-more
    methyl-carbamine-more
    methyl-borate-more
    methyl-beryllium-more
    methyl-benzyl-more
    methyl-benzilate-more
    methyl-benzene-more
    methyl-amyl-more
    methyl-alpha-d-glucopyranose-more

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    Apple's Darwin OS still unfree and unusable
    iPhone restricts users, GPLv3 frees them
    End the war, Impeach!
    Verizon Die!
    Current actions: Impeach Cheney, Tell Abbott
    Intel "open source fraud"?
    Yager's latest...
    Open-source Darwin? Not yet
    The kernel building fiasco
    GNU-Darwin: AMD Opteron support now
    Action item: war and energy
    U.S. Government Intervenes in EFF vs. ATT
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    kill micro$oft
    Bootstrapping your body
    The stupidest war

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    GNU-Darwin

    Jill Stein for President
    GNU-Darwin site blackout to protest #SOPA and #PIPA - #OpBlackout
    Concern about the 'Bill To Combat Online Infringement' - #eff #fsf #dmca #music #downloads #technology
    Spill onto Washington DC: Oil out of the U.S. Rally Labor Day Weekend
    GNU-Darwin: No More Oily Congress!
    BP Boycott
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    GNU-Darwin Action: multibanding
    Please help Dr. Love find ancient lore regarding parsley
    User@xi.nu email for all GNU-Darwin accounts
    Michael L. Love: addressing backlash pain
    GNU-Darwin Action: parsley and autism
    Current alpha darwin8+, plz report
    Thank you SourceForge!
    GNU-Darwin prehistory
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    Twitter, MySpace, redirection and short URLS
    GNU-Darwin Action: On value and money, molecules activism
    GNU-Darwin Action: iPhone boycott continues
    GNU-Darwin Action: winter bicycler
    GNU-Darwin Action: parsley an antidiarrheal
    The molecule of the day is: Apigenin
    GNU-Darwin Action: another health care reform message
    GNU-Darwin Action: Molecules activism revisited
    Michael L. Love: proclus blog
    Molecules activism
    GNU-Darwin Action: beta sitosterol
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    GNU-Darwin source code repository
    GNU-Darwin Program Documentation Project
    GNU-Darwin: blackout warning
    On the loss of US credibility: conscription, death penalty
    URGENT: Log a call against telecom immunity!
    GNU-Darwin: Shell access, AMD Phenom Quad CPU
    Apple Sued for iPhone Bricking
    GNU-Darwin to support Iraq moratorium
    GNU-Darwin OS on a Via CPU
    Apple's Darwin OS still unfree and unusable
    iPhone restricts users, GPLv3 frees them
    End the war, Impeach!
    Verizon Die!
    Current actions: Impeach Cheney, Tell Abbott
    Intel "open source fraud"?
    Yager's latest...
    Open-source Darwin? Not yet
    The kernel building fiasco
    GNU-Darwin: AMD Opteron support now
    Action item: war and energy
    U.S. Government Intervenes in EFF vs. ATT
    Nature's way: resveratrol supplement
    kill micro$oft
    Bootstrapping your body
    The stupidest war

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    The Radical Mormon

    Jill Stein for President
    GNU-Darwin site blackout to protest #SOPA and #PIPA - #OpBlackout
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    GNU-Darwin Action: parsley and autism
    Current alpha darwin8+, plz report
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    Michael L. Love/GNU-Darwin Twitter Feed
    GNU-Darwin Action: On value and money, molecules activism
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    GNU-Darwin Action: parsley an antidiarrheal
    The molecule of the day is: Apigenin
    GNU-Darwin Action: another health care reform message
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  • GNU-Darwin Posts about calorie restriction and the resveratrol
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