Macs in Chemistry

Insanely Great Science

PyMOLProbity

 

Just heard of a new PYMOL plugin, created by Jared Sampson, called PyMOLProbity which allows a PyMOL user to visualize MolProbity-style structural validation data directly in a PyMOL session. PyMOLProbity is a plugin allows the user to produce MolProbity-style visualization of atomic interactions within a structure (e.g. H-bonds, van der Waals interactions and clashes) directly within a PyMOL session.

The plugin runs local copies of several executable programs from the Richardson Lab at Duke University, authors of the MolProbity software, parses the output, and displays the results in the PyMOL viewport. There are both a graphical user interface (GUI) for general point-and-click use, and a command-line interface (CLI) suitable for scripting.

1600px-pymolprobity_gui.png

Chen et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica D66:12-21 DOI.

Full installation instructions are here

The Reduce, Probe, and Prekin executables are only available for Linux and MacOS, PYMOL is available from Schrödinger and also available via Homebrew, you will need to install XQuartz first.

There are detailed instructions on how to install a variety of chemistry/cheminfomatics/biology packages on a Mac here.


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XQuartz update

 

XQuartz 2.7.11 is available for download.

Changes in 2.7.11

All changes in 2.7.10 plus:

lib:

  • fontconfig
  • Fix font caching (#97546)

libpng 1.6.26

libX11

  • Plug a memory leak

libXi 1.7.8

  • Plus fixes for a memory leak and improved error handling

mesa 12.0.1


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XQuartz 2.7.10 released

 

XQuartz 2.7.10 has been released. OS X 10.6.3 or later is required to install this package.

I did some very limited (MOE and PYMOL) testing under Mac OSX 10.12 (Sierra) and didn’t find any issues. Changes in 2.7.10 All changes in 2.7.9 plus

app

  • mkfontdir
  • Fix a buffer underrun crash (#96905) quartz-wm
  • Properly handle updates to WM_PROTOCOLS property changes (#92652)
  • xinit
  • Fixed support for enabling TCP server connections (#95379)
  • Added support for enabling IGLX (#96260)
  • defaults write org.macosforge.xquartz.X11 enable_iglx -bool true
  • xterm 326

proto:

  • xcb-proto 1.12
  • xproto 7.0.31

lib:

  • fontconfig 2.12.1
  • CVE-2016-5384
  • freetype 2.7
  • libpng 1.5.27
  • libpng 1.6.25
  • libxcb 1.12
  • libX11 1.6.4
  • libXfixes 5.0.3
  • libXfont 1.5.2
  • Fix a buffer overrun (#83224)
  • libXfont2
  • Fix a buffer overrun (#83224)
  • libXi 1.7.7
  • libXrandr 1.5.1
  • libXrender 0.9.10
  • libXt
  • libXt.6.dylib is now a two-level-namespace dylib
  • libXt.7.dylib is now a stub dylib that re-exports libXt.6.dylib (for binary compatibility with anything built against XQuartz 2.7.9)
  • A flatnamespace version of libXt is available in /opt/X11/lib/flatnamespace to help ease the transition (#96292)
  • Set DYLDLIBRARYPATH=/opt/X11/lib/flat_namespace when executing older non-compliant software (eg: Motif-based applications)
  • Motif users are encouraged to file bugs against Motif to encourage them to fix that library.
  • libXtst 1.2.3
  • libXv 1.0.11
  • CVE-2016-5407
  • libXvMC 1.0.10
  • mesa 11.2.2
  • xcb-util-cursor 0.1.3

server:

  • xorg-server 1.18.4 plus other patches
  • Fix the issue where the h key could be come “stuck” after hiding XQuartz with cmd-h (#92648)

Comments

Support of indirect GLX (iGLX) in XQuartz.

 

An update from X11.org

On Thu, 2016-05-26 at 16:34 +0000, Cook, Rich wrote:

Hello, I recently heard on the Apple x11-users mailing list that remote OpenGL rendering (IGLX) is being phased out of XOrg and not being replaced. Is this really the case or am I misunderstanding?

You have heard incorrectly. It is disabled by default for security reasons, as it's been a repeated source of exploitable bugs, but the feature itself isn't going away.

One caveat is there's no easy way to enable it other than the command line, and not all display managers give you a mechanism to pass arbitrary options in (which is reasonable enough). I've added an xorg.conf option to enable IGLX in master, and I'll be backporting that to the various stable branches as well.


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Support of indirect GLX (iGLX) in XQuartz.

 

There is an important discussion taking place on the X11 users list regarding the support of indirect GLX (iGLX) in XQuartz.

Indirect GLX is an extension offered by X11 that enables the transmission of OpenGL commands from an X11 client on a remote machine to an X11 server on your desktop over the network. For example, when your OpenGL science application running on a remote host tries to draw images using OpenGL and display on your local XOrg (XQuartz) desktop, IGLX (red line below) is used to send the commands to your local X server, which then uses OpenGL locally to draw the commands.

siggraph-2012-nvidia-opengl-for-2012-78-728

In seems in the latest version of XQuartz (2.7.9) this is turned off by default and there appears to be a move to deprecate this protocol. This seems to have been prompted by security concerns but I know nothing of the details.

However many scientific applications use this capability and it seems there is no alternative. If this is likely to be an issue for you I suggest you subscribe to the X11 list and make your views known.


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