PyMOL Molecular Graphics System

Hi Warren,
	When will PyMol 0.92 be available via fink?
Thanks,
Scott

On Oct 26, 2003, at 11:06 PM, Warren L. DeLano wrote:

> PyMOL version 0.92 can be obtained from http://pymol.sf.net at your
> convenience.
>
> Though this is mostly an "under the hood" improvements release, there
> are some developments worth noting:
>
>   Significant changes
>
>    - New "dss" command assigns secondary structure quickly.
>    - PyMOL can now read O/BRIX maps and some Biosym GRiDs maps.
>    - Improved ray tracing quality and speed.
>    - Long lists of residues in selections are now allowed.
>
>   Other changes
>
>    - New "import pymol" support for RPM & Win32 builds that use system
> Python.
>        [Don't forget to call pymol.finish_launching() afterwards
> though!]
>    - Improved alpha-channel support for transparent surfaces and
> backgrounds.
>    - API's "cmd.do" can now take multi-line strings and lists.
>    - New "split_states" command for separating NMR ensembles.
>    - New "cartoon_transparency" setting.
>    - Can display bond valences while in stick mode.
>    - New "stick_ball", "stick_ball_ratio" settings for ball & stick
> models.
>    - Gaussian map generation from model coordinates.
>    - Can preserve original PDB atom IDs (pdb_retain_ids) & order
> (retain_order).
>    - Much much faster loading of multi-model PDB files and 
> trajectories.
>    - Deuterium and Calcium handling improved.
>    - New "set_symmetry" & "get_symmetry" commands.
>    - Mutagenesis wizard preserves cartoons.
>    - New "get_pdbstr" API function.
>    - New "movie_loop" setting can disable looping.
>    - Sculpting engine now aware of simple sp3-sp3 torsions.
>    - Finer Z-scaling/movement control.
>    - Upgrade facility for secure enterprises running Windows.
>
> PyMOL 0.92 also includes various bugs fixes with cartoons, rendering,
> CGOs, sessions, endianness, multithreading, raytracing, OS X, and
> isosurfaces.
>
> As always, upgrade with caution.  Don't update right before an 
> important
> presentation, and be sure to test your existing session files. Please
> report any trouble.
>
> Probably the most problematic aspect of the new version will be the
> increased WYSIWYG behavior of the ray-tracer with respect to line
> widths.  If the bonds in your figure just got thinner, that's the
> culprit.  You can manually adjust the various *_width or *_radius
> settings to achieve the desired results.
>
> Cheers,
> Warren
>
>
> --
> mailto:warren@...
> Warren L. DeLano, Ph.D.
> Principal Scientist
> DeLano Scientific LLC
> Voice (650)-346-1154
> Fax   (650)-593-4020
>
>
>
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>
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   Scott Classen, Ph.D.
   ACS Postdoctoral Fellow
   Department of Molecular & Cell Biology
   University of California, Berkeley
   237 Hildebrand Hall #3206
   Berkeley, CA 94720-3206
   LAB 510.643.9491
   FAX 510.643.9290
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Hi,

I'm having some trouble with PyMOL on my SGI's.  When we upgraded from (I
think) 6.5.11 to 6.5.20m, things stopped working for me.  Here's what we
have right now:

<oregano> mlerner: uname -aR
IRIX64 oregano 6.5 6.5.20m 04091957 IP30

We also upgraded the compilers, and we're now using this:

<oregano> mlerner: cc -version
MIPSpro Compilers: Version 7.3.1.3m

<oregano> mlerner: /usr/freeware/bin/gcc -v
Reading specs from /usr/freeware/lib/gcc-lib/mips-sgi-irix6.5/3.3/specs
Configured with: ../configure --prefix=/usr/freeware
--enable-version-specific-runtime-libs
--disable-shared --enable-threads --enable-haifa --enable-libgcj
--disable-c-mbchar
Thread model: single
gcc version 3.3

In case this is relevant, here's the hardware setup:

<oregano> mlerner: hinv
2 360 MHZ IP30 Processors
CPU: MIPS R12000 Processor Chip Revision: 3.5
FPU: MIPS R12010 Floating Point Chip Revision: 0.0
Main memory size: 512 Mbytes
Xbow ASIC: Revision 1.4
Instruction cache size: 32 Kbytes
Data cache size: 32 Kbytes
Secondary unified instruction/data cache size: 2 Mbytes
Integral SCSI controller 0: Version QL1040B (rev. 2), single ended
  Disk drive: unit 1 on SCSI controller 0
Integral SCSI controller 1: Version QL1040B (rev. 2), single ended
IOC3/IOC4 serial port: tty1
IOC3/IOC4 serial port: tty2
IOC3 parallel port: plp1
Graphics board: V6
Integral Fast Ethernet: ef0, version 1, pci 2
Iris Audio Processor: version RAD revision 12.0, number 1


I downloaded pymol-0_92-bin-irix65-r10k.tar today, and when I run
pymol.com, both windows (the Viewer window and the Tk window) show up and
look good.  The Tk window seems to work (I can use the menus to load a pdb
file, etc.), but the Viewer window is completely unresponsive.  The
display never updates, and it doesn't seem to notice any key presses or
mouse clicks.

If I recall correctly, this breakage happened when we upgraded.  We were
using PyMOL 0.86 at the time, and it just stopped working.  I downloaded
0.90 and it didn't work either.  I tried compiling 0.90 from source and
had the same result (i.e. I was able to compile everything, but the Viewer
window was unresponsive).

Clearly, I should have asked about this earlier, but I was pretty busy,
and I hoped that things would magically fix themselves with the next
release :).

Anyway, does anyone have any idea what could be wrong?  I'll be glad to
recompile things and try out various fixes, but I don't quite know where
to start.  It's possible that I used an older gcc (2.8.1) when I tried to
compile PyMOL before, so maybe I should just try recompiling, but I'm not
sure that's the problem.

Thanks,

-michael

--
Michael Lerner