Re: [ccp4bb] Superpose

of a strand. Just a guess. Best, Tim On 05/09/2014 08:05 PM, Horacio Botti wrote: Dear all, Why does (if it is suppossed to do so) Superpose output results for a subset of atoms only? See a summary of log file below (just the top lines, data on atoms, and final data and message). In the example, results

[ccp4bb] Superpose

Dear all, Why does (if it is suppossed to do so) Superpose output results for a subset of atoms only? See a summary of log file below (just the top lines, data on atoms, and final data and message). In the example, results for residues 69-76 are absent, other atoms are absent as well,

Re: [ccp4bb] Superpose

I should have said that this is the comparison of two crystaline states of the same molecule, the sequences are identical. Best H hbo...@pasteur.edu.uy ha escrito: Dear all, Why does (if it is suppossed to do so) Superpose output results for a subset of atoms only? See a summary of log

[ccp4bb] Not to refine B factors, not to refine coordinates

Dear all, hi!! I need help in order to use Refmac in two particular ways. On one hand I would like to ask the program not to refine B factor values (whichever the selected refinement mode was) and in the other I would like to ask it not to refine coordinates (whichever the selected refinement

Re: [ccp4bb] Extra positive density seen after TLS refinement?

Dear Naveed A Nadvi I think that your results highlight the fact that modelling the disorder/complex ordering of your crystal is relevant and in general, that we should take care in optimizing B factor refinement as a strong factor for model improvement. In this sense I would not relay

Re: [ccp4bb] On pKa of Aspartic acid

the pKa is 3.8 or 6.44; isn’t that true? d) Have similar increase in pKa values observed for aspartic acids before? I would be grateful if anybody could explain or comment on the above queries. Deepak Oswal -- Horacio Botti PhD MD Protein Crystallography Unit Institut Pasteur of Montevideo

Re: [ccp4bb] Reasoning for Rmeas or Rpim as Cutoff

Dear all Perhaps a bit off of theme, just an example about resolution cut-off mean I/sigma(I) = 2 for dmin = 3.35 A (please have a look at the attached pdf) I would trust in I/s(I) = 2 (in this case it worked), but why not to determine what is information after the model has been refined to

[ccp4bb] Crystallization robot and trypsin

will be appreciated. Thks!! Horacio Botti Unit of Protein Crystallography, Institut Pasteur of Montevideo, Uruguay. PS: below you have an old short CCP4 discussion: [ccp4bb]: Crystallization robots and protease. * /To/: ccp

Re: [ccp4bb] Dehydration treatments

Hi Israel! The phenomena you describe seems to be related to cryoprotection, but you don't say anything about collection temperature or cryoprotection used. Controlled-slow dehydration is one way of achieving optimized cryocooling of specially fragile crystals. I would recommend you to

Re: [ccp4bb] OT: Covalent modification of Cys by reducing agents?

Dear Mike BME readily autooxidizes (need for metal traces and dissolved O2). Is yours a metalloprotein? Is your buffer contaminated with metals? Those situations would make the case a bit different. If not, unless your BME stock is already oxidized, blocking of the accesible thiols with