Re: [ccp4bb] How to include in refinement high resolution shells with VERY low completeness ?

Dear Ivan, one thing I forgot to mention: I think the difference maps should not show model bias due to "fill-in". This is because the term D*Fcalc that is filled in as a replacement for m*Fobs is just compensated by the term D*Fc that is subtracted when forming the m*Fobs - D*Fcalc difference

Re: [ccp4bb] Extra density close to phosphate bound to Zn2+

One thing to remember is that Li+ only has two electrons. It should be a little more than twice the density of an hydrogen (because the charge pulls in the electron cloud). If you are seeing lithium at 8 "sigma" you should be seeing the well located hydrogen atoms at 4 "sigma". Are you? I

Re: [ccp4bb] How to include in refinement high resolution shells with VERY low completeness ?

Dear Kay, Thanks a lot for your answers! To my best understanding, REFMAC does not have an option of for restoring reflections only in certain resolution shells. But, it should not be a problem for datasets with good completeness in low resolution shells. Also, refinement against intensities

Re: [ccp4bb] How to include in refinement high resolution shells with VERY low completeness ?

Hi Robbie, Thanks! Then, using STARANISO sounds like a good option to me (only if low resolution completeness is good). But, im curios if there are other feasible ways. Do you have any other practical approach on how to shape the MTZ file accordingly? Thanks, Ivan With best regards, I

[ccp4bb] Fwd: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Extra density close to phosphate bound to Zn2+

-- Forwarded message - From: Daniel M. Himmel, Ph. D. Date: Mon, Aug 5, 2019 at 12:45 PM Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Extra density close to phosphate bound to Zn2+ To: Pentagonal phosphate geometry would be a transition state, except that three oxygens woul

[ccp4bb] Cif deposition from CCP4i2

I am not quite sure if this is a bug report, or advice for other people or what. Essentially I wanted an mmCIF of a refmac refined structure for deposition.  The CCp4i2 "prepare files for deposition" gives an mmcif with a Rfree several % higher than my best refinement. Essentially this appear

[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Extra density close to phosphate bound to Zn2+

PS, you also have to define an alternative conformation, but that you probably already did. Von: Schreuder, Herman /DE Gesendet: Montag, 5. August 2019 17:55 An: 'Maria Håkansson'; CCP4BB@JISCMAIL.AC.UK Betreff: AW: [EXTERNAL] Re: [ccp4bb] Extra density close to phosphate bound to Zn2+ Hi Maria

[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Extra density close to phosphate bound to Zn2+

Hi Maria, Did you rotate the phosphate, or invert it? If you invert the phosphate, you may get into trouble with the parameters. Although a phosphate is symmetric, its oxygens have different names and inverting it leads to all kind of problems, especially in a high resolution map which does not

Re: [ccp4bb] Extra density close to phosphate bound to Zn2+

I always say this, but is there any feature in the anomalous map? You can sometimes see S atoms. Eleanor And do the temperatre factors suggest anything about multiple occupancies etc.. E On Mon, 5 Aug 2019 at 16:32, Maria Håkansson wrote: > Hi, > > Thanks for your suggestions but I have tried

Re: [ccp4bb] Extra density close to phosphate bound to Zn2+

Hi, Thanks for your suggestions but I have tried to invert the phosphate and it is not fitting the map. The geometry is not correct that way and it is too good data to ignore and to my knowledge a pentacoordinated phosphate is a non existent species. That leaves me with ions. Best regards, Mar

[ccp4bb] Listserv problem

Dear Guardians of the List: I have been banned from the ccp4bb due to some temporary delivery problems and I cannot subscribe anymore - can someone please contact me off board please? Thx, BR -- Bernhard Rupp

[ccp4bb] Postdoc position at IBS, Grenoble, France

Dear all, A postdoc position is available in our lab at the Institute for Structural Biology (IBS) in Grenoble to study the structure of post-meiotic chromatin. The work involves biochemistry, crystallography and cryo-EM and will take place at the IBS in close collaboration with the lab of Sa

[ccp4bb] Postdoc position on E3 Ubiquitin Ligase Structural Cell Biology: Dundee, UK

A postdoctoral position is available immediately to join my group at Dundee’s School of Life Sciences to investigate the structure, mechanism and druggability of novel E3 ubiquitin ligases using structural biology and cell biology. The project is in collaboration with one of the pharmaceutical

Re: [ccp4bb] Improve your previously released coordinates with OneDep

Dear Jonathan, As you have correctly identified from the policy documentation at wwPDB, if a structure factor file was never initially deposited for an entry (i.e. before 2018 when this was not mandatory), this can be provided at a later date. Please contact the wwPDB site where this was origi