[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,

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 ).

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

l the best, 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] Historic books [Was: Fun Question ...]

evelopment 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 Molecul

[ccp4bb] Bug in sftools 'write' command ?

FILE STATISTICS10737 .. .. .. __ 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 Alexandrou

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

pecially low resolution overloaded reflections) and putative outliers (for difference Patterson maps), 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

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

t; looked at do require sigma values. > > I wanted 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 e

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

cholas -- 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] Refmac executables - win vs linux in RHEL VM

rating-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.7762

Re: [ccp4bb] Refining Against Reflections?

cents, 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] Movements of domains

gt; 'significant' in a 10A map? If it is, how do we quantify the significance? > > If anybody has a great reference or just an individual opinion, I'd like to > hear about it. > > Regards, > > Filip Van Petegem > > -- Nicholas M. Gl

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

es, significantly less than 1000. In one case the _total_ 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

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

-- 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] Linux vs MacOS for crystallographic software

ong ... All the best, 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

;convincing' remains to be seen ... ;-) My 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

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

epare a map with the projection down the sectioning axis. 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,

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

f the program used for the final > > refinement. > > That would be true if the refinement is conducted in real space. > However, it is nearly universal to do the final refinement in > reciprocal space. The emphasis of what I said was clearly on model building, and not on the

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

e deposited models dependant on their intended usage, would possibly qualify as 'fraud' ;-) -- 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

rtion of what you 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://u

Re: [ccp4bb] Understanding Conformational Differences

wocents, 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] Why Do Phases Dominate?

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

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

are that neurosis ;-)) -- 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] FW: pdb-l: Retraction of 12 Structures...

can not (and should 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, Dra

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

f detailed understanding of the physical world encoded in these models. 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, Ni

Re: [ccp4bb] Blast from the past

me the opportunity 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 a

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

equations, but I have my doubts whether 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 --

Re: [ccp4bb] Patterson Map missing a peak?

TOM2 Ano 0.4686 0.5000 0.04658.99 0.0 BFAC 20.0 > ATOM3 Ano 0.5000 0.5000 0.94044.92 0.0 BFAC 20.0 > 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.

Re: [ccp4bb] Molecular Replacement of a small peptide

is great 1.1 A, ~35% > solvent, 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, Dep

Re: [ccp4bb] Computer hardware and OS "survey"

100.0 % ___ 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, 681

Re: [ccp4bb] Computer hardware and OS "survey"

e line of code, 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, Draga

Re: [ccp4bb] Computer hardware and OS "survey"

to my 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

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

). What you 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

Re: [ccp4bb] brute force molecular replacement

duce correct information that was not part of the initial model (as you said). > Can I run Qs when a partial structure is available? No. Sorry. Nicholas -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, U

Re: [ccp4bb] brute force molecular replacement

ant for a stochastic search, 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 +

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 Mol