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A kind person that compiled pymol for windows and for us

Two years ago, I was really  pissed off when i realized that pymol was not completly free any more. It was some kind of "Ok guys thanks to help me and make pymol what it is, but now if you want it, you have to pay it."
So was still using pymol the last compiled accessible. A while ago now, I discovered this site http://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol. Where they kindly proposed to anyone to download the last (or almost the last) compiled version of pymol for windows.
So thanks a lot to Christoph Gohlke from Laboratory for Fluorescence Dynamics from all guys that didn't know like me how compiled pymol from the svn.....

Some fun

From there: http://xkcd.com/26/

Karmix and xorg.conf

To my big surprise Vmware 7 and Karmix are working together perfectly.
For now CPP4, arp warp, phenix are install easly without any trouble.
I just got some difficulties with imosflm.
It appears when the X11 is not well setup that imosflm display extremely big and ugly fonts.
The only way to fix that is to configure properly the X11.
Only trouble no more xorg.conf in the karmix. BOUH!!!!!

However after some tricks, you can create one which by default will not work, but gives the framework.

You have to stop the x server
sudo service gdm stop

Note: replace gdm by kdm depending of your Ubuntu version.

Login

And now we will create a default xorg.conf

sudo Xorg -configure

this will create in your home directory a file call:

xorg.conf.new

Which looks like:

# Section "ServerLayout"
# Identifier "X.org Configured"
# Screen 0 "Screen0" 0 0
# InputDevice "Mouse0" "CorePointer"
# InputDevice "Keyboard0" "CoreKeyboard"
# EndSection
# Section "Files"
# ModulePath "/usr/lib/xorg/modules"
# FontPath "/usr/share/fonts/X11/misc"
# FontPath "/usr/share/fonts/X11/cyrillic"
# FontPath "/usr/share/fonts/X11/100dpi/:unscaled"
# FontPath "/usr/share/fonts/X11/75dpi/:unscaled"
# FontPath "/usr/share/fonts/X11/Type1"
# FontPath "/usr/share/fonts/X11/100dpi"
# FontPath "/usr/share/fonts/X11/75dpi"
# FontPath "/var/lib/defoma/x-ttcidfont-conf.d/dirs/TrueType"
# FontPath "built-ins"
# EndSection
#Section "Module"
# Load "record"
# Load "dbe"
# Load "dri"
# Load "dri2"
# Load "glx"
# Load "extmod"
#EndSection
#Section "InputDevice"
# Identifier "Keyboard0"
# Driver "kbd"
#EndSection
#Section "InputDevice"
# Identifier "Mouse0"
# Driver "mouse"
# Option "Protocol" "auto"
# Option "Device" "/dev/input/mice"
# Option "ZAxisMapping" "4 5 6 7"
# EndSection
#Section "Monitor"
# Identifier "Monitor0"
# VendorName "Monitor Vendor"
# ModelName "Monitor Model"
#EndSection
# Section "Device"
# ### Available Driver options are:-
# ### Values: : integer, : float, : "True"/"False",
# ### : "String", : " Hz/kHz/MHz"
# ### [arg]: arg optional
# #Option "HWcursor" # []
# #Option "Xinerama" # []
# #Option "StaticXinerama" #
# Identifier "Card0"
# Driver "vmware"
# VendorName "VMware"
# BoardName "SVGA II Adapter"
# BusID "PCI:0:15:0"
# EndSection
#Section "Screen"
# Identifier "Screen0"
# Device "Card0"
# Monitor "Monitor0"
# SubSection "Display"
# Viewport 0 0
# Depth 1
# EndSubSection
# SubSection "Display"
# Viewport 0 0
# Depth 4
# EndSubSection
# SubSection "Display"
# Viewport 0 0
# Depth 8
# EndSubSection
# SubSection "Display"
# Viewport 0 0
# Depth 15
# EndSubSection
# SubSection "Display"
# Viewport 0 0
# Depth 16
# EndSubSection
# SubSection "Display"
# Viewport 0 0
# Depth 24
# EndSubSection
#EndSection

So now you have to make some modifications about the Screen section and the Monitor section, which are controlled by vmware.

for the monitor replace the section by:

Section "Monitor"
Identifier "vmware"
VendorName "VMware, Inc"
HorizSync 1-10000
VertRefresh 1-10000
EndSection

And for the display (for me a laptop 15” screen)

Section "Screen"
Identifier "Default Screen"
Device "VMware SVGA"
Monitor "vmware"
# Don't specify DefaultColorDepth unless you know what you're
# doing. It will override the driver's preferences which can
# cause the X server not to run if the host doesn't support the
# depth.
Subsection "Display"
# VGA mode: better left untouched
Depth 4
Modes "640x480"
ViewPort 0 0
EndSubsection
Subsection "Display"
Depth 8
Modes "1366x768"
ViewPort 0 0
EndSubsection
Subsection "Display"
Depth 15
Modes "1366x768"
ViewPort 0 0
EndSubsection
Subsection "Display"
Depth 16
Modes "1366x768"
ViewPort 0 0
EndSubsection
Subsection "Display"
Depth 24
Modes "1366x768"
ViewPort 0 0
EndSubsection
EndSection

Becarefull to change also the Section "ServerLayout"
by replacing
Screen0
by

Default Screen

Record your modified xorg.conf under
/etc/X11/
Restart
And it should work
Mosflm has a correct display
tata!!!!

CNS installation on Ubuntu Jaunty

Crystallography & NMR System (CNS)
http://cns.csb.yale.edu/v1.2/
CNS installation on Ubuntu Jaunty

I don’t if I’m the only one, but it appears tricky for me to compile properly cns under Ubuntu Jaunty.
It requires gfortran 4.1, which is not longer supported by ubuntu jaunty. I tried with more recent gfortan version but with no success.

So I had to build the gfortran-4.1 myself from this depository:
https://launchpad.net/ubuntu/hardy/i386/gfortran-4.1/4.1.2-21ubuntu1
After few downloads and installations, I succeed to build properly with all dependencies gfortran-4.1.
the command line is

sudo dpkg -i nom_du_package.deb

My next steps was to tell to cns to use the right gfortran. thus I created a specific makefile based on the one provide by cns.

To do so you have to go under

cns_solve_1.21/intel-i686-linux/

and create a makefile like this:

###############################################################################
# #
# Machine dependent Makefile header for CNSsolve #
# Paul Adams 20-10-98 #
# copyright Yale University #
# #
###############################################################################

# fortran options
F77 = gfortran-4.1
F77STD = -w
F77OPT = -O3 $(CNS_MALIGN_I86) -funroll-loops -ffast-math
F77FLAGS = $(F77STD) $(F77OPT) $(EXT_F77FLAGS) $(F77BUG)

# C options
CC = gcc
CCFLAGS = -O -DCNS_ARCH_TYPE_$(CNS_ARCH_TYPE) $(EXT_CCFLAGS)

# link options
LD = gfortran-4.1
LDFLAGS = -w $(EXT_LDFLAGS)

# utility programs
compile-utils:
@ cd $(CNS_INST)/utils; \
make utils F77="$(F77)" CC="$(CC)" \
F77FLAGS="-w -O" CCFLAGS="-O" \
F77LINK="" CCLINK="-lm"

#==============================================================================

And name it

Makefile.header.2.gfortran-4.1

Note: that my gcc version is 4.3 but doesn’t seems to be a problem.

After that it’s straight forward:
You go in your cns installation folder and run

make install compiler=gfortran-4.1

It will peak the right Makefile from cns_solve_1.21/intel-i686-linux/
and it should work.

Alternatively you could also change the symlink for gfortran towards the 4.1 version. But I don’t like messing around with the symlink.
You have to be super user remove the previous one and make the new one under :

/usr/bin/

Something like “ln -s nom_pointé nom_du_symlink »

ln –s gfortran-4.1 gfortran

However i didn't tested so i don't know if it's working or not.....

The best, always leaves first

On Tuesday, Nov 3, 2009 Warren DeLano passed away suddenly at his home. He was 37 years old.

Warren DeLano was born in Philadelphia, raised in Palo Alto, and educated at Yale University. At Yale, he joined Axel Brunger's lab, where he made critical contributions to the computational tools and methods that made "CNS" a universal computational crystallography progam.

After Yale, Warren received his doctorate at the University of California, San Francisco under the mentorship of Jim Wells, PhD. He then became a founding scientist at Sunesis Pharmaceuticals, creator of PYMOL, and founder of DeLano Scientific.

Throughout his life and career, Warren made fundamental and highly valued contributions to science. His Open Source PyMOL software is widely used throughout the world, and nearly all publications that display macromolecular structures use PyMOL. He was a strong advocate of freely available software and the Open Source movement. He also encouraged all who came into his lab or office. His sunny, optimisitic outlook endeared him to all he knew; his brilliance awed and inspired many throughout the scientific and software worlds.

He is survived by his wife Beth Pehrson, mother Margaret DeLano, father James DeLano, Jr., step-mother Cathy Groves DeLano, step-father Tom Snouse, sister Jennifer DeLano and brother Brendan DeLano, as well as three aunts and eight cousins. Memorial service is pending.

The family greatly appreciates your memories of Warren and invites you to comment on our MEMORIES OF WARREN BLOG.