[ccp4bb] Web service for the calculation of maximum entropy maps

this service. Kind regards, Nicholas -- Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620, Ext.77620, Tel (lab) +302551030615, http

[ccp4bb] Naturally occuring alpha-Methyl-L-Proline

, Nicholas -- Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620, Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/

Re: [ccp4bb] Naturally occuring alpha-Methyl-L-Proline

N-methyl-Pro is a known protein modification. This is not an N-methyl-Pro. This is a Ca-methyl-Pro (with loads of synonyms, see http://www.chemicalbook.com/ChemicalProductProperty_EN_CB9127522.htm ).

Re: [ccp4bb] Historic books [Was: Fun Question ...]

of crystallography. That generation of crystallographers is leaving this world and soon nobody will be able to say how the protein and non-protein structures were solved in those days. Alex -- Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus

[ccp4bb] Bug in sftools 'write' command ?

.. .. .. __ Regards, Nicholas ps. Please do keep my mail address in the CCs, I'm subscribed to daily digests. -- Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece, Tel/Fax

Re: [ccp4bb] Calculating ED Maps from structure factor files with no sigma

to calculate the electron density for PDB id: 1HFS but the structure file only lists the Fo's, Fc's and Phases, but no sigmas. Would such structure factor file be considered incomplete? Thank you for your kind explanation. Francisco -- Nicholas M. Glykos, Department of Molecular

Re: [ccp4bb] Calculating ED Maps from structure factor files with no sigma

), but in certain cases (with very accurate or inaccurate data) standard deviations do matter. All the best, Nicholas -- Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece

Re: [ccp4bb] Refmac executables - win vs linux in RHEL VM

-system-dependent and compiler-specific hypotheses. Nicholas -- Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620, Ext.77620, Tel (lab

Re: [ccp4bb] Refmac executables - win vs linux in RHEL VM

-- Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620, Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/

Re: [ccp4bb] Refining Against Reflections?

-- Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620, Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/

Re: [ccp4bb] Movements of domains

like to hear about it. Regards, Filip Van Petegem -- Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620, Ext.77620, Tel (lab

Re: [ccp4bb] should the final model be refined against full datset

from different sets reaching up to 4%. Ideally, and instead of PDBSET+REFMAC we should have been using simulated annealing (without positional refinement), but moving continuously between the CNS-XPLOR and CCP4 was too much for my laziness. All the best, Nicholas -- Dr Nicholas M

Re: [ccp4bb] should the final model be refined against full datset

number of reflections was 5132 reflections (which were, nevertheless, slowly and meticulously measured by a CAD4 one-by-one. These were the days ... :-)) ]. -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University

Re: [ccp4bb] Linux vs MacOS for crystallographic software

, Nicholas -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620, Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/

Re: [ccp4bb] How to evaluate Fourier transform ripples

twocents, Nicholas -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620, Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr

Re: [ccp4bb] contour map

executable appears to run flawlesly under ubuntu 10.04, but as always YMMV. Nicholas [1] http://utopia.duth.gr/~glykos/mcps_graph.html [2] http://utopia.duth.gr/~glykos/other.html [3] http://utopia.duth.gr/~glykos/mcps.html -- Dr Nicholas M. Glykos, Department of Molecular Biology

Re: [ccp4bb] generating 2D projections

. You can then directly compare your projections. Nicholas -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620, Ext.77620, Tel

Re: [ccp4bb] Deposition of riding H: R-factor is overrated

methodology. The reference to the refinement program was again model-centric (ranging from the treatment of hydrogens, to the bulk solvent model used). Best regards, Nicholas -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace

Re: [ccp4bb] Deposition of riding H: R-factor is overrated

' ;-) -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620, Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/

Re: [ccp4bb] software to represent raw reflections in hkl zones

are after. -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620, Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/

Re: [ccp4bb] Why Do Phases Dominate?

snip ... and on the other side, laws like Moore's law seem completely descriptive and not at all causal or essential. /snip http://dx.doi.org/10.1088/0143-0807/16/4/005 ;-) -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University

Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures...

not) be used as an excuse for converting validation tools to the sacred holders of scientific standards. My twocents, Nicholas -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis

Re: [ccp4bb] video that explains, very simply, what Structural Molecular Biology is about

. Lastly, may I add that a significant portion of the PDB (the NMR structures), are very heavily dependant on these same molecular mechanics forcefields that are used for molecular modeling and simulation. My twocents, Nicholas -- Dr Nicholas M. Glykos, Department of Molecular

Re: [ccp4bb] Blast from the past

to say printf(Increase MAX_NOF_REFL and recompile (if you can).\n); exit(1); Nicholas ps. I know it wasn't me. I never say 'Too many reflections to store' .-) -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University

Re: [ccp4bb] taming structural biology

) (for details start from http://www.ccp4.ac.uk/ccp4course.php ) Nicholas -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620

Re: [ccp4bb] attachments

we should aim to fit all possible communication media inside a good-old SMTP-based mailing list (when it comes to communicate legible equations we normally use other media, like pdf files produced from pdflatex). My twopence Nicholas -- Dr Nicholas M. Glykos, Department

Re: [ccp4bb] Patterson Map missing a peak?

ATOM4 Ano 0.3074 0. 0.24473.49 0.0 BFAC 20.0 ATOM5 Ano 0.1803 0.5000 0.77103.44 0.0 BFAC 20.0 ATOM6 Ano 0.0479 0. 0.90723.35 0.0 BFAC 20.0 -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics

Re: [ccp4bb] Molecular Replacement of a small peptide

, and two molecules in the ASU. I have tried all the standard stuff, changing resolution cut off etc. I may move to sulfur phasing at this resolution but I would like to get the MR to work. Allen -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics

Re: [ccp4bb] Computer hardware and OS survey

, or without having to modify sources (and recompile). Guess what: never happened (and, hopefully, never will ;-) Nicholas -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis

Re: [ccp4bb] Computer hardware and OS survey

% ___ Nicholas ² http://www.top500.org/stats/list/32/osfam -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece

Re: [ccp4bb] Computer hardware and OS survey

mind, largely irrelevant. My twopence, Nicholas -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620, Ext.77620, Tel (lab

Re: [ccp4bb] Rigid body refinement as last refinement?

think you see in the map is not what your data really 'say'. -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, 68100 Alexandroupolis, Greece, Fax +302551030613 Tel ++302551030620 (77620

Re: [ccp4bb] brute force molecular replacement

is available? No. Sorry. Nicholas -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, 68100 Alexandroupolis, Greece, Fax +302551030613 Tel ++302551030620 (77620), http://www.mbg.duth.gr

Re: [ccp4bb] brute force molecular replacement

, and so the program got baptised. Nicholas -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, 68100 Alexandroupolis, Greece, Fax +302551030613 Tel ++302551030620 (77620), http://www.mbg.duth.gr

Re: [ccp4bb] brute force molecular replacement

Dear Xie, What are the other brute force programs for molecular replacement out there? Qs (available via http://www.mbg.duth.gr/~glykos/Qs.html) can be as brutal with your CPU(s) as they can take. Nicholas -- Dr Nicholas M. Glykos, Department of Molecular Biology