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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.

Pymol in action

First post

The objective of this blog is to put some of the fun features produced during my work as a structural biologist (at least trying to be). With the idea to share them and most impotrtant to show how I made them. These hopefully will help some people and in return I could get some good ideas or suggestions.

So the first post is a video made with pymol (http://pymol.sourceforge.net/) on the pro-collagen maturation, my actual post doctoral study at IBCP LYON FRANCE, in the team of David Hulmes. This movie is just in between Sci-Fi and a real proposed mechanism of action of Tolloïdes proteases BMP-1 with its natural subtract, the Procollagen type III. The maturation of procollagen III is crucial in the case of the formation of scar. Very very very basically if you have breach at the surface of your skin, the organism should as quick as possible close it, to prevent infection for exemple. One way used is the quick synthesis and maturation of procollagen III in the extracellular matrix, that will be process to form fiber in order to fill the hole.

This movie is based on the recently publication of the team “Strong cooperativity and loose geometry between CUB domains are the basis for procollagen C-proteinase enhancer activity. » (PMID: 19801683). It has been realized for a French local television.

In windows there is no way to make a direct movie from pymol. It will do a set of images that you will have to assemble yourself like a cartoon to make the movie. What seems to be a limitation is fact quiet good because this gives you more flexibility. You can make several set of images depending of your story board and at the end assemble everything.

How it has been done

With two good features of Pymol

1- Scene recording (in the upper panel Scene->store->Fx), and the fact that pymol is able to go by itself from one scene to the other and calculate each step. So you made your structure with one orientation store in F1 and display your molecule in a second orientation store in F2. Pymol will make the transiton in between.

2- The possibility to load states. States contains several pdb files that can be display in a chronological way (pdb -1,pdb-2…).So if you want to move one pdb file from one position to another you can used the morphing approach.

For the scene the applied script was:

#to flush he memory

mclear

#to define the number of images (steps) of the movie

mset 1x100

#recall the scene

scene F1,

#image where it the scene F1 will be display start

mview store, 1

#image where it will start the transition

mview store, 10

#recall the scene

scene F2,

# image where it will stop the transition

mview store, 11

#image where it will stop to display F2

mview store, 100

#to tell to pymol to calculate each step between the 2 scenes

mview interpolate

#to tell to pymol to make smooth transition

mview smooth

#optional to see the result.

mplay

script end

The morphing allows to move a structure across the screen. There are several web site which can do it for you (maybe on a next post). However in this case I think the best is to use Lsqman (from http://xray.bmc.uu.se/usf/).

It is only under Linux or Mac osX . I have windows with a Linux virtual machine under VMware which will make the trick. So you need two pdb files, one outside of the screen (action) and one at the final position. Lsqman will calculate all the missing pdb files in between. And these will be load by pymol as one pdb file containing several states.

The script for Lsqman is something like:

#Read in the two files

re m1 lsq-a.pdb

re m2 lsq-b.pdb

#Tell LSQMAN to use all atoms

ATom_types ALl

#Fix silly nomenclature problems of your bad pdbs

nomen m1

nomen m2

fix

m1

A1-999

m2

A1-999

s

s

t

#Morph between the two structures

morph

m1

A1-999

m2

A1-999

#number of steps

100

#name of the intermediate pdb file

morphy

#type of morphing

c

m

A1-999

999.

Quit

script end

So in this case, lsqman will generate 100 pdb files from the first one to the last one you just have to load them inside pymol as state

Script:

from glob import glob

lst = glob("morphy*.pdb")

lst.sort()

for fil in lst: cmd.load(fil,"mov")

script END


!!!!not available temporarly!!!!!
the video will be re-post soonn!!!!



So what are we seeing?

First the procollagen (known structure PDB code 3DMW) represented by sphere with three colors for each chain and electronic density for the C-terminal part (blue). This part of the movie is only done by scene representation and pymol is going through them. You can see that you can do a lot of funny camera movement and some zoom in and out depending of the choice of your scene.

After that we have a pause and we can see the arrival of the Co-factor of BMP-1 named PCPE. PCPE is represented in cartoon. This is a mixture of high homology modeling (>40%) and real structure (PDB code 1UAP). This is the first morph of the movie. The first pdb have been place out of the screen and the last is in contact with the procollagen.

For the science there is no indication of the interaction area so it’s just a "artistic" guess. Lsqman has made several pdb that are going from outside of the screen to the contact with the procollagen. All this pdb files have been load in one state in pymol and I just display the states.

After that scene again we see just a movement of camera to get to the front of the complex pro-collagen/PCPE. Next is the arrival of the catalytic domain of BMP1 (PDB code 3EDG) using the morphing made by Lsqman.

Zoom out with the scene feature and movement of the mature collagen to form fiber with the morphing.

that all folks!!!