[ccp4bb] FAPESP Postdoctoral Position on in situ Cryo-Electron Tomography
Dear Colleagues, With the Aquilos 2 cryo-FIB soon available at our Institute (link 1 <https://www.ifsc.usp.br/alba/frontier-cryo-em-microscopes-delivered/>), allow me to advertise a fellowship opportunity in my lab briefly: *Overview*: This project to be developed at the São Carlos Institute of Physics (IFSC), University of São Paulo (USP) in Brazil, aims to study the in situ structure of mitochondrial filamentous enzymes involved in the metabolic adaptation of tumors and their effects on organelle ultrastructure and morphology upon filamentation. This research will be an extension of Adamoski et al., NSMB 2024 (doi: 10.1038/s41594-023-01118-0 <https://doi.org/10.1038/s41594-023-01118-0>), focusing on more profound questions with cutting-edge methodologies, such as correlative light-electron microscopy (CLEM), cryo-electron tomography in lamella (cryo-ET) and expansion microscopy (ExM), that can also be applied to other proteins in the lab. *Methodological Responsibilities*: 1) Sample Preparation: Engage in cell culturing, vitrification, and lamellae preparation in our lab at the IFSC/USP; 2) Data Collection and Processing: Perform high-resolution tomographic data collection using top-tier microscopy facilities in Brazil and internationally. Data processing will be done in-house. *Requirements*: 1) PhD in Chemistry, Biochemistry, Molecular Biology, or related; 2) Experience in Cell Biology; proficiency in cryo-FIB and cryo-ET, or single-particle cryo-EM is a big plus; 3) Strong analytical, collaboration, and English language skills. *Details and how to apply*: link 2 <https://www.ifsc.usp.br/alba/fapesp-postdoctoral-position-on-in-situ-cryo-electron-tomography/> This opportunity is open to candidates of any nationality. The selected candidate will receive a Postdoctoral fellowship from the São Paulo Research Foundation (FAPESP) for *R$ 9,047.40 monthly* and a research contingency fund, equivalent to 10% of the annual value of the fellowship, allocated for research-related expenses. *Ref: FAPESP Fellowship Opportunity 6788 (POR/EN)*: 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 - Brazil www.ifsc.usp.br/alba To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Labeling centric and acentric reflections
Thank you for the perfect answer, Alejandro. I have been Googling the subject since this morning and missed the CALC documentation entirely. The keyword "CALC COL centric = 1 c -" did the job! All the best. Em qua., 21 de dez. de 2022 às 16:40, Alejandro Buschiazzo < ale...@pasteur.edu.uy> escreveu: > Hi Andre > > I think you can use SFTOOLS. > Check it with the documentation (cause not sure exactly), but after > reading your mtz, you can use the command CALC. This calculates lots of > stuff, and even has some builtin functions, including the one you want > (which I think can be called with a “c”). > > something like > > READ my.mtz > CALC COL my_new_column = 1 c - > WRITE new.mtz > > Will add that new column with the name you choose, and put 1’s for > centrics and 0’s for acentrics. > > Best , Alejandro > > > > Hi, > > Is there a way to label centric and acentric reflections in the .mtz file > and output an additional column, let's say, with values 0 (acentric) and 1 > (centric), similar to R_free flagging? > > With the keyword CENTRIC_ONLY, CAD does something similar 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 CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > -- 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.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Labeling centric and acentric reflections
Hi, Is there a way to label centric and acentric reflections in the .mtz file and output an additional column, let's say, with values 0 (acentric) and 1 (centric), similar to R_free flagging? With the keyword CENTRIC_ONLY, CAD does something similar 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 CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Postdoctoral position at LNBio/CNPEM, Brazil
Dear all, My colleague Dr. Sandra Dias and I would like to bring to your attention a collaborative postdoctoral opportunity on the filamentous proteins involved in the metabolic adaptation process of tumors. The Sao Paulo Research Foundation (FAPESP) sponsors the fellowship. Please find all the 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 list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[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 object file: No such file or directory I already have the said library in a ./lib folder, but cannot point to it successfully. How can I set the appropriate environment variable within the Colab notebook? Many thanks in advance for your help! To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Energy minimization and explicit solvent model
Dear Sorin, many thanks for this. Very useful. By probing the conformational space around the model, I meant to try and predict how specific solvent conditions may (or may not) induce rearrangement, both intra and intermolecule, within an oligomeric multidomain protein compared to it in a crystalline state. I will have an immediate look at the software and documentation you recommended and may eventually reach out for extra help. With best wishes Andre. Em qua., 24 de jun. de 2020 às 16:18, Sorin Draga escreveu: > Dear Andre, > > I am not sure what you mean by conformational space around the model, but > to answer your question: short energy minimization can be done using, for > example, deep view/swiss pdb viewer. However, I think that you are most > likely looking for a short bout of molecular dynamics, in which you can use > explicit solvent and a proper ionic envelope. There you have a few options > - GROMACS, NAMD, AMBER etc. The first 2 are free for academia, but if you > have no prior knowledge of MD it can be a little bit tricky to set the > system up correctly. Let me know if I can help further. > > Best, > > Sorin > > On Wed, Jun 24, 2020 at 10:08 PM Andre LB Ambrosio > wrote: > >> Dear colleagues, >> >> could you please suggest a computational tool to perform energy >> minimization of a crystal structure under explicit solvent conditions (i.e, >> types and concentrations of 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. >> >> -- >> Andre LB Ambrosio >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 >> > -- Andre LB Ambrosio To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Energy minimization and explicit solvent model
Dear colleagues, could you please suggest a computational tool to perform energy minimization of a crystal structure under explicit solvent conditions (i.e, types and concentrations of 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. -- Andre LB Ambrosio To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Change map handedness
Thank you all very much for the responses! Yes, what I wanted to do was to
flip the volume of the map along the z-axis. Eleanor's solution worked
perfectly.
Best wishes and stay safe.
Em qua., 1 de abr. de 2020 às 10:56, Ian Tickle
escreveu:
>
> A file does not have a handedness, it's just a list of numbers. So the
> pedantic answer is that since it doesn't have a handedness you need do
> nothing to change it!
>
> I assume that what you mean is that you want to change the handedness of
> the _visual interpretation_ of the file. That's a different story
> altogether since it involves your own visual perception!
>
> Eleanor's trick with the phases will do it if you then view the map in the
> same way as you were doing before.
>
> Or you could keep the file the same and view a mirror image of the map.
> Eugene has already suggested using a mirror which reverses either the X or
> Y axis depending on where you place the mirror.
>
> The obvious and interesting alternative is to reverse the Z axis. In the
> days when we plotted maps on a stack of transparent sheets it was easy: you
> just reversed the order of the sheets! In fact you had to do exactly that
> since the plastic molecular model was viewed in a half-silvered mirror
> placed in front of the map ("Richard's box", a.k.a. "Fred's Folly":
> https://en.wikipedia.org/wiki/Frederic_M._Richards ).
>
> Now a computer screen being a 2-D object obviously doesn't have a Z axis
> so you can't reverse it! However we get the _impression_ of depth in our
> brain by using stereo or depth cueing, so you would need to reverse one of
> those (maybe a switch on the glasses controller?).
>
> Depth cueing is obtained by having objects that are supposed to be nearer
> to you brighter than ones that are supposed to be further away. So all
> need to do is convince your brain that the opposite is true!
>
> Note that all the solutions that reverse the image of the 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
>
>
> On Wed, 1 Apr 2020 at 13:56, Andre LB Ambrosio wrote:
>
>> 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-bin/webadmin?SUBED1=CCP4BB=1
>>
>
--
Andre LB Ambrosio
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[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-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Figure of merit in refinement
Dear Jonathan, many thanks for this. I will have a look at it right away. With best wishes, Andre. On Wed, Oct 2, 2019, 7:51 PM Jonathan Cooper wrote: > This is a very good place to start: > > https://www-structmed.cimr.cam.ac.uk/Course/Statistics/statistics.html > > Also recommend 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: > > > 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. > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[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. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] R values from an .mtz file containing Fobs and Fcalc
Many thanks to all for the prompt and great inputs. Best regards, Andre. Em seg, 1 de jul de 2019 às 10:32, Eleanor Dodson < 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> escreveu: > Old program RSTATS would give r factor.. > > But easist to run 0 cycles of REFMAC - at least then you know what the > scaling algorithm might be > Eleanor > > On Mon, 1 Jul 2019 at 14:22, Robbie Joosten > wrote: > >> If you are using SFTOOLS you might as well use the CORREL function to >> calculate things. >> >> Datamining is easier though. Every PDB-REDO entry has a data.json file >> that has all the numbers you need. >> >> Cheers, >> Robbie >> >> > -Original Message- >> > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of >> > Tim Grüne >> > Sent: Monday, July 01, 2019 15:19 >> > To: CCP4BB@JISCMAIL.AC.UK >> > Subject: Re: [ccp4bb] R values from an .mtz file containing Fobs and >> Fcalc >> > >> > Dear Andre, >> > >> > easiest would be to select the FP and FC_ALL with sftools, write out the >> > values to a text file and calculate the R-value with a scripting >> language like >> > awk. >> > >> > Best, >> > Tim >> > >> > Am 01.07.2019 15:02, schrieb Andre LB Ambrosio: >> > > 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 >> > > >> > > - >> > > >> > > To unsubscribe from the CCP4BB list, click the following link: >> > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 >> > >> > -- >> > -- >> > Tim Gruene >> > Head of the Centre for X-ray Structure Analysis Faculty of Chemistry >> > University of Vienna >> > >> > Phone: +43-1-4277-70202 >> > >> > GPG Key ID = A46BEE1A >> > >> > ###### >> > ## >> > >> > To unsubscribe from the CCP4BB list, click the following link: >> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 >> >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 >> > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > -- Andre LB Ambrosio To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[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 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] On estimating Unit Structure Factor distribution
Dear Pavel, This is great, thank you so much! I shall try it ASAP. Thank you much for the very kind help. Best wishes, Em qua, 15 de mai de 2019 às 17:52, Pavel Afonine escreveu: > Hi Andre, > > here is the link to cctbx-based code that computes Uhkl according to your > formula below, using model mean B and F000 that accounts for atomic model > and bulk-solvent: > > https://www.dropbox.com/sh/g7sp7pqxst4ldj0/AAD1whlVD2mvAGoRa5jOF-fla?dl=0 > > I leave it up to you to read and understand the script, as well as > ensuring it works as you expect (bug-free!). I hope 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, >> >> We seek to calculate the distribution of Unitary Structure Factors, Uhkl, >> from a few datasets (at different maximum resolutions) for which the >> corresponding atomic models are already available at the PDB; this >> according to the formula (6.4), in the 2nd edition of Jan Drenth´s book: >> >> Uhkl = exp[B*(sin^2(theta)/lambda^2)] x FOBShkl / F(000) >> >> Hence, the following questions: >> >> - Is there any macromolecular crystallography software that can compute >> Uhkl as above, or equivalent? >> >> - If not, would it be more correct to use the Wilson-B or the mean B from >> the final model? >> >> - How can F(000) 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 Ambrosio >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 >> > -- Andre LB Ambrosio To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] On estimating Unit Structure Factor distribution
Dear James, Many thanks for this! I will follow all the suggestions described above. With best wishes, Andre. Em qua, 15 de mai de 2019 às 14:59, Holton, James M < jmhol...@slac.stanford.edu> escreveu: > The CCP4 program you are looking for is "cad". Using the "SCALE" keyword > you can apply an overall positive or negative B factor to any mtz data > set. Negative B factors are sharpening, which is what you are trying to do. > > There is also another program called "ecalc", which is specifically > designed for computing normalized structure factors like "U", which is > closely related to "E". > > As for which B factor to apply? Ostensibly the Wilson B factor and the > average atomic B factor should be the same number. The Wilson B, however, > is prone to systematic errors arising from how you decide which resolution > range to fit. There are also details about the distribution of B factors > in the model and the relative abundance of different atomic numbers. > However, I've always found these considerations dwarfed by the errors in > estimating the Wilson B. Depending on what you are trying to accomplish, > you might want to raise your B factor a bit anyway to reduce the overall > noise. > > > As for F000, another article describing its estimation is here: > https://doi.org/10.1073/pnas.1302823110 > > Script from that publication for calculating F000 is here: > https://bl831.als.lbl.gov/END/RAPID/scripts/find_F000.com > > This script requires the CCP4 Suite and the Phenix Suite version 1.6 or > lower. This was the last version of phenix.refine that reported k_sol and > B_sol for the bulk solvent. Without these, you cannot calculate the number > of electrons in the bulk solvent. > > Alternately, if you have run refmac you can look through the log for the > string: "Partial structure1: scale = " > The "scale =" and "B =" numbers that follow are the k_sol and B_sol for > the bulk solvent. You can then provide these numbers on the command line > of the find_F000.com script above. Then again, if you have already run > refmac it might be simpler to provide the MSKOUT command-line parameter to > refmac. This will output the bulk solvent as a CCP4 map file. Once you > have that, all you need to do is run "mapdump" to report the average value > of the electron density in this map. You multiply this by the k_sol value > from the log and then multiply by the unit cell volume and you now have the > number of electrons 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, Andre LB Ambrosio wrote: > > Dear Pavel, thank you so very much for the prompt feedback. > That would be extremely useful if you could script the Uhkl calculation in > CCTBX. > With best regards, > Andre. > > Em qua, 15 de mai de 2019 às 09:47, Pavel Afonine > escreveu: > >> Hi Andre, >> >> >>> - Is there any macromolecular crystallography software that can compute >>> Uhkl as above, or equivalent? >>> >> >> I estimate this can take about 10 minutes to script in CCTBX. I can write >> a script for you, if interested, and send off list. >> >> >>> - If not, would it be more correct to use the Wilson-B or the mean B >>> from the final model? >>> >> >> I'd guess mean B from the model is a better estimate. >> >> - How can F(000) 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)? >>> >> >> 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=1 > > > -- Andre LB Ambrosio To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] On estimating Unit Structure Factor distribution
Dear Pavel, thank you so very much for the prompt feedback. That would be extremely useful if you could script the Uhkl calculation in CCTBX. With best regards, Andre. Em qua, 15 de mai de 2019 às 09:47, Pavel Afonine escreveu: > Hi Andre, > > >> - Is there any macromolecular crystallography software that can compute >> Uhkl as above, or equivalent? >> > > I estimate this can take about 10 minutes to script in CCTBX. I can write > a script for you, if interested, and send off list. > > >> - If not, would it be more correct to use the Wilson-B or the mean B from >> the final model? >> > > I'd guess mean B from the model is a better estimate. > > - How can F(000) 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)? >> > > 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=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) for which the > corresponding atomic models are already available at the PDB; this > according to the formula (6.4), in the 2nd edition of Jan Drenth´s book: > > Uhkl = exp[B*(sin^2(theta)/lambda^2)] x FOBShkl / F(000) > > Hence, the following questions: > > - Is there any macromolecular crystallography software that can compute > Uhkl as above, or equivalent? > > - If not, would it be more correct to use the Wilson-B or the mean B from > the final model? > > - How can F(000) 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 Ambrosio > -- Andre LB Ambrosio To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] On estimating Unit Structure Factor distribution
Dear all, We seek to calculate the distribution of Unitary Structure Factors, Uhkl, from a few datasets (at different maximum resolutions) for which the corresponding atomic models are already available at the PDB; this according to the formula (6.4), in the 2nd edition of Jan Drenth´s book: Uhkl = exp[B*(sin^2(theta)/lambda^2)] x FOBShkl / F(000) Hence, the following questions: - Is there any macromolecular crystallography software that can compute Uhkl as above, or equivalent? - If not, would it be more correct to use the Wilson-B or the mean B from the final model? - How can F(000) 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 Ambrosio To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
