Local Informations

DBGS/CEBGS

Just some basic notes, I don't have enough time to write down many things, feel free to come and see me for help.

All major crystallographic programs (see main list) are installed locally on Stars cluster and also on CEBGS  machines.
Programs are only updated on Linux systems (surf, lameX, starvX , starX and all CEBGS graphic stations). SGI are no more updated.
If you think that a crucial program is missing, please contact me.

• Depending of  the data you have and what you want to do and how much you want to learn or know, several scenarios are possible.
• Data collection, especially at synchrotron sites, is the time where you may solve your structure in a few minutes or destroy months (or years) of work and waste a lot of money in a few seconds. Be prepared ! 
• Crystallographic programs are now very easy to use, require few parameters but are based on complicated algorithms. Try to understand what is going on and where crucial decisions need to be done. (read some articles)
• if you want an automated structure determination process, try Auto-Rickshaw Seb Server, at EMBL Hamburg, (HKL3000 is not yet distributed )
• It may be fast to build 90% of  a structure but it will take a longer time to finish the last 10%. 

Usually, but not always, to use a program named 'toto', type settoto and follows the instructions.  Few examples: 

• CCP4 programs
• setccp4 and then ccp4i
• solve, phenix,cns, coot : setphenix,  setcns, setcoot.
• Starting from phenix-1.5.2, use solve/resolve from phenix graphic interface
  
• for HKL2000, just type sethkl2000, and then  HKL2000
• HKL3000 (manga and FR-X computer)
  
• setautoproc

Many programs are now integrated in CCP4 and available through CCP4i. See "Programl list"  in CCP4i interface
The last available release of a given program is usually installed locally (this page may not be always updated).  

My favourite programs (a strong bias)

My selection of articles 

Notes for some specific programs. Just extra comments

Data Collection

• HKL2000 
• last available Linux running version is installed on:  manga, estrella, pegase, terra, surf, lame4, lame5, pabst, sidi
• autoproc (easy and automated use of XDS or Mosflm and more...)  (setautoproc, then process...)
  
• licence on manga, pegasse, estrella, surf, lame8
  
• mosflm
• Linux version, mosflm and imosflm  as integrated in CCP4
• XDS  (setxds).   I recommend the usage of xdsgui    (setxdsgui)
• d*TREK (off line on star3 and star4)
• start by setdtrek and them dtdisplay or dtprocess

Phasing and Refinement

• buster  
• See autoBuster for an easy and automated  use of Buster
  
• licence on  lame3, lame4, slame13, slame20, slame21, manga   ( also star3, starv4, surf)
• "Buster Wiki"
• "Buster tutorials"

• sharp
• sharp  is now intergrated in ccp4. use autosharp in ccp4i interface (only for machine having a valid licence for sharp)
  
• licence for sharp on surf, lame5, lame14, manga
  
• "AutoSharp/Sharp manual"
• "AutoSharp/Sharp wiki"
  
• Phenix
• setphenix, now include solve and resolve, MR-rosetta.
• sir2014
• setsir2014, licence on lame14

Molecular (re)placement

• start with Balbes, MrBUMP (see also CaspR)
• Balbes and MrBUMP are installed locally and accessible using CCP4i
• MrBUMP
• starting from scratch, do use the option "Run the FASTA search locally"
• Multiple alignment programs installed : T-COFFEE, ProbCons, Mafft, clustalw
• If sequence analysis fails, do not forget use fold prediction servers (FFAS, PHYRE) to guess starting models
• Phaser, Phenix

Model Building

• Coot

• coot is installed on our linux machines ( usually pre-release versions are installed)
• Type setcoot, and then coot
• you need a pdb file and an mtz file with your structure factors (or a map).
• More informations :  http://www.ysbl.york.ac.uk/~emsley/coot

• O

• Last installed version is o12, uses it by typing o12. more informations on this version
• Please read the release note before updating your database ( datablocks *ogl* should be killed…)
• before running o,
•  type setenv ODAT  /biolo/o12/data   (tcsh shell, tells O where to get some required files, can be included in the database)
• on Linux PCs, if you want to work with stereo, type setenv STEREO ON before typing o12 (then use F1 to start stereo)
  
• Local files, to be read when starting O from scratch :
• startup.odb, menu.odb
• access.odb
• stereo_chem.odb
• More informations from Alwyn and Uppsala

• Release Notes From A to Z How to Essential O Uppsala Software Factory
• MIFit
• linux and Windows version are available.

Validation

• Please use the servers : MolProbity, JCSG, Biotech
• The Validation software from RCSB has been locally installed on linux machines. Just type setvalid to use it

My favourite programs (a strong bias) :

• data processing : HKL2000. 
• data analysis : phenix tools, Pointless, Aimless, Truncate
• crystallographic calculus : ccp4 by ccp4i
• Phasing (and density modifications links) : sharp,solve (integrated in  PHENIX),crank
• molecular replacement : phaser, molrep, (integrated scripts:  BALBES, MrBUMP)
• refinement : phenix, buster, refmac
• automated model building :  resolve (integrated in PHENIX), Arp/wARP, Buccaneer
• model building : coot, o
• nice pictures : pymol, TexShade
• sequences analyses : pfaat, bioedit
• structure validation :  Molprobity, JCSG server, Biotech, Sfcheck(ccp4),
• fold prediction : FFAS, PHYRE.
• building by homology : JSCG-SCWRL 

Troubles ?  if needed, feel free to come and see me.

Links to

my teaching documents (request a moodle UNISTRA account, only available in French, english version is coming)

my selection of articles for students 

Bibliography