[ccp4bb] Postdoc opportuniy in cryo-ET at IFSC/USP , Brazil

-partir-de-01082024>) and a research contingency fund, equivalent to 10% of the annual value of the fellowship, allocated for research-related expenses. *Ref: FAPESP Fellowship Opportunity 7194 (POR/EN)*: link 3 <https://fapesp.br/oportunidades/7194/> Thank you, and enjoy your week. -- A

[ccp4bb] FAPESP Postdoctoral Position on in situ Cryo-Electron Tomography

N)*: link 3 <https://fapesp.br/oportunidades/metabolismo_no_microambiente_e_o_papel_das_trocas_metabolicas_na_progressao_tumoral/6788/> Thank you, and enjoy your week. -- Andre LB Ambrosio Associate Professor, IFSC/USP - Bra

Re: [ccp4bb] Labeling centric and acentric reflections

ar but only outputs > centric reflections without additional labeling. > > Many thanks for your attention. > > -- > Andre LB Ambrosio > Associate Professor, IFSC/USP - Brazil > www.ifsc.usp.br/alba > > -- > > To unsubscribe from the C

[ccp4bb] Labeling centric and acentric reflections

thout additional labeling. Many thanks for your attention. -- Andre LB Ambrosio Associate Professor, IFSC/USP - Brazil www.ifsc.usp.br/alba To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.

[ccp4bb] Postdoctoral position at LNBio/CNPEM, Brazil

details at https://fapesp.br/oportunidades/5522/en or send inquiries to sandra.d...@lnbio.cnpem.br Best wishes, -- Andre LB Ambrosio Associate Professor, IFSC/USP - Brazil www.ifsc.usp.br/alba To unsubscribe from the

[ccp4bb] Standalone version of Ecalc

Dear all, I am trying to run a standalone version of the Ecalc program in a Google Colab notebook linked to my Google Drive. The executable returns the following error message: /content/gdrive/Shareddrives/programs/ecalc: error while loading shared libraries: libccp4f.so.8.0: cannot open shared ob

Re: [ccp4bb] Energy minimization and explicit solvent model

f ions, pH)? >> >> I want to observe the solvent effects on the conformational space around >> a starting model, all-atom, while preserving its geometry (I guess it can >> be better expressed as relaxation). >> >> Thank you in advance. >> >> -- >

[ccp4bb] Energy minimization and explicit solvent model

, while preserving its geometry (I guess it can be better expressed as relaxation). Thank you in advance. -- Andre LB Ambrosio To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi

Re: [ccp4bb] Change map handedness

e map will also > reverse the image of the structure which may not be what you want. In that > case Eleanor's solution which results in only reversing the image of the > map is probably the right one. > > Oh and happy April 1st to all! > > Cheers > > -- Ian >

[ccp4bb] Change map handedness

Dear all, is it possible to generate a mirror image of an existing .ccp4 map file? Many thanks in advance. -- Andre LB Ambrosio To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi

Re: [ccp4bb] Figure of merit in refinement

ommend this one: > > https://doi.org/10.1107/S0108767386099622 > > and Main, P. (1979) Acta Cryst. A35, 779-85 - the maths in this one are a > bit easier! > > > > On Wednesday, 2 October 2019, 22:47:56 BST, Andre LB Ambrosio < > an...@ifsc.usp.br> wrote: > >

[ccp4bb] Figure of merit in refinement

Dear all, How is the phase error estimated for any given reflection, specifically in the context of model refinement? In terms of math I mean. How useful is FOM in assessing the phase quality, when not for initial experimental phases? Many thank in advance, Andre. #

Re: [ccp4bb] R values from an .mtz file containing Fobs and Fcalc

ues, >> > > >> > > Can a CCP4 program calculate r_work and r_free directly from a .mtz >> > > file containing FP and FC_ALL (from PDB_REDO)? this without inputing >> > > the matching .pdb file and ideally using a commando line. >> > > >> >

[ccp4bb] R values from an .mtz file containing Fobs and Fcalc

Dear colleagues, Can a CCP4 program calculate r_work and r_free directly from a .mtz file containing FP and FC_ALL (from PDB_REDO)? this without inputing the matching .pdb file and ideally using a commando line. Many thanks in advance, -- Andre LB Ambrosio

Re: [ccp4bb] On estimating Unit Structure Factor distribution

pe it exemplifies enough > for you to pick up from there and modify it the way you wish. The only test > I did is I made sure it runs and outputs and MTZ file! > > Good luck, > Pavel > > On Wed, May 15, 2019 at 3:20 PM Andre LB Ambrosio > wrote: > >> Dear all, &

Re: [ccp4bb] On estimating Unit Structure Factor distribution

s in the bulk solvent. Add up all the atomic numbers in > your PDB file (including hydrogen) and you have the rest of the electrons > in your unit cell. The sum of all electrons in one unit cell is F000. > > HTH > > -James Holton > MAD Scientist > > On 5/15/2019 5:52 AM,

Re: [ccp4bb] On estimating Unit Structure Factor distribution

> together the number of electrons for all the atoms refined in the >> asymmetric unit (protein + ligands + solvent)? >> > > See my previous email. > > Pavel > > -- Andre LB Ambrosio To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

Re: [ccp4bb] On estimating Unit Structure Factor distribution

At the title, please read Unitary, not Unit. Apologies. Em qua, 15 de mai de 2019 às 09:09, Andre LB Ambrosio escreveu: > Dear all, > > We seek to calculate the distribution of Unitary Structure Factors, Uhkl, > from a few datasets (at different maximum resolutions) f

[ccp4bb] On estimating Unit Structure Factor distribution

) be best estimated from the final model, which is not necessarily always the most complete or best refined? Should we simply add together the number of electrons for all the atoms refined in the asymmetric unit (protein + ligands + solvent)? Many thanks in advance and best wishes, -- Andre LB