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It seems that Ubuntu left out the headers, so it cannot recompile with the nVidia driver correctly.

This is what worked for me, install headers & dpkg update.
https://bugs.launchpad.net/ubuntu/+s...s/+bug/1068942

sudo apt-get update
sudo apt-get upgrade
sudo apt-get install linux-headers-generic
# only reason to purge is there are several versions, if you know you have different nVidia use that:
sudp apt-get purge nvidia*
sudo apt-get install nvidia-current
sudo dpkg-reconfigure nvidia-current

Bug reports:
https://bugs.launchpad.net/ubuntu/+s...s/+bug/1068341

https://bugs.launchpad.net/fglrx/+bug/1068456
https://bugs.launchpad.net/ubuntu/+s...y/+bug/1068488
https://bugs.launchpad.net/fglrx/+bug/1068661

Validation reports are now available for all X-ray structures!

If you go to ftp://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports/ you can browse for your favourite crystal structure, and get a report on how good/bad it is. Presumably a good thing to do when creating an initial model.

This info was sent to the CCP-BIOSIM mailing list.

The Worldwide Protein Data Bank (wwPDB) partners are pleased to announce that validation reports for all X-ray crystal structures in the PDB archive are now publicly available. The new validation reports are set to become an indispensable resource for both crystallographers and the consumers of structural data who increasingly need to critically assess and compare PDB entries. The reports implement the recommendations of a large group of community experts on validation and include the results of geometric checks, structure-factor assessment and ligand validation. The reports include results from tried and tested software including MolProbity, Xtriage, Mogul, EDS and various CCP4 programs. They summarise the quality of the structure and highlight specific concerns by considering the coordinates of the model, the diffraction data and the fit between the two. Easily interpretable summary information that compares the quality of a structure with that of other structures in the archive is also provided. Validation reports for all X-ray structures archived in the PDB are accessible from the following FTP sites: * ftp://ftp.wwpdb.org/pub/pdb/validation_reports/ (wwPDB) * ftp://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports/ (PDBe) * ftp://ftp.pdbj.org/pub/pdb/validation_reports/ (PDBj) The new X-ray structure validation reports have been provided to depositors as part of the structure-annotation process since August 2013. More recently, a stand-alone wwPDB X-ray structure validation server was launched (http://wwpdb-validation.wwpdb.org/). The server allows crystallographers to check early, intermediate and near-final models on demand and helps identify any potential problems that need addressing prior to structure analysis, publication and deposition.

"The stand-alone validation server will run exactly the same validation tests that have recently been introduced for the annotation of new depositions," says Randy Read of Cambridge University. Read chairs the wwPDB X-ray Validation Task Force (VTF) that has produced detailed recommendations to the wwPDB about how macromolecular crystal structures should be validated [1]. "With the stand-alone server, crystallographers won't have any last-minute surprises when they deposit their structures just before submitting the paper," Read adds. The reports have been developed in the context of a larger initiative, the new wwPDB Deposition and Annotation system (http://wwpdb.org/system_info.html), which was created to unify the annotation tools and practices used across all wwPDB deposition centres and for all common structure-determination methods. About wwPDB wwPDB (http://wwpdb.org) is the international partnership that manages the PDB archive. It consists of: the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB; http://rcsb.org) and BioMagResBank (BMRB; http://bmrb.wisc.edu) in the USA, the Protein Data Bank in Europe (PDBe; http://pdbe.org) and the Protein Data Bank Japan (PDBj; http://pdbj.org). Together, the wwPDB partners are committed to ensuring high standards of quality, integrity and consistency of this uniquely important archive and to make it freely available for the benefit of scientists worldwide. [1] Read R. J., Adams P. D., Arendall III W. D., Brünger A. T., Emsley P., Joosten R. P., Kleywegt G. J., Krissinel E. B., Lütteke T., Otwinowski Z., Perrakis A., Richardson J. S., Sheffler W. H., Smith J. L., Tickle I. J., Vriend G., and Zwart P. H. A new generation of crystallographic validation tools for the Protein Data Bank. Structure, 19, 1395-1412, 2011. DOI: 10.1016/j.str.2011.08.006 -- Gary Battle Protein Data Bank in Europe (PDBe) EMBL-EBI http://www.facebook.com/proteindatabank http://twitter.com/PDBeurope --


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