Re: [ccp4bb] exclude water from anisotropic refinement in PDB_REDO

Hi Abhishek, At the moment, there isn't. However, the decision to use anisotropic B-factors is based on comparing the refinement a fully isotropic model with that of a fully anisotropic model using the Hamilton test. So it should be safe to use anisotropic B-factors for all atoms. Cheers, Robb

Re: [ccp4bb] High R/Rfree after MR

I sent this on Friday to Gianluca but forgot to also send it to the bulletin board, so I’m posting it now, as it relates to Eleanor’s response. __ It would also be worthwhile to consider the possibility of out-of-register errors in the sequence as

[ccp4bb] exclude water from anisotropic refinement in PDB_REDO

Hi all, Is there a way to exclude water from anisotropic refinement in PDB_REDO? Best regards, Abhishek

Re: [ccp4bb] AW: Another troublesome dataset (High Rfree after MR)

Rarely do I disagree with the wit and wisdom of James Holton, but R1 is not a property that Macromolecular World is unaware of. R1 is just Rwork. It's just R1 = Σ | |Fo| – |Fc| | / Σ |Fo| However e.g. George Sheldrick's SHELXL reports it based on a 4 sig(F) cutoff as well as on all data. Exam

Re: [ccp4bb] AW: Another troublesome dataset (High Rfree after MR)

Discarding weak data was not the way macromolecular refinement was done prior to 1990. Discarding data to lower your R-value is a bad practice now and was a bad practice back then. It is my recollection that some people using X-plor adopted this practice, along with discarding all low resoluti

Re: [ccp4bb] AW: Another troublesome dataset (High Rfree after MR)

Dear James. What small molecule programs report often looks like: R1 = 0.1550 for 17413 Fo > 4sig(Fo) and 0.2058 for all 23715 data R1(Free) = 0.2208 for 1938 Fo > 4sig(Fo) and 0.2766 for all 2635 data from a well-known small molecule program being (mis)used to refine a protein. T

Re: [ccp4bb] AW: Another troublesome dataset (High Rfree after MR)

If you suspect that weak data (such as all the spot-free hkls beyond your anisotropic resoluiton limits) are driving up your Rwork/Rfree, then a good sanity check is to compute "R1".  Most macromolecular crystallographers don't know what "R1" is, but it is not only commonplace but required in

Re: [ccp4bb] TYC not linked to previoys amino-acid

But it is not L-peptide. And I would not like to make it L-peptide in the standard ccp4 dictionary. You can add trans link between GLY and TYC. But it would not be nice. The best solution is to use TYR and amilate C terminus. Garib On 16 Oct 2017, at 07:40, Eleanor Dodson wrote: > Thank you

[ccp4bb] AW: Re: [ccp4bb] TYC not linked to previoys amino-acid

Dear Eleanor, The method I proposed works for any amino acid, not just tyrosine. Having an amide as a separate residue may sound strange, but is it exactly how our chemists treat it as well. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Eleanor Dodson Gesen

Re: [ccp4bb] TYC not linked to previoys amino-acid

Thank you Garib.. So you have to copy the $CLIBD/monomers/t/TYC.cif to your own directory and change the string "non-polymer" to "L-peptide" Then use that as a dictionary entry and indeed that behaves as expected - ie forms the peptide link GLY-TYC Eleanor On 16 October 2017 at 12:32, Garib Mur

[ccp4bb] Experiences with Simplex

Hi Fellows, we are dabbling with membrane proteins and thus are wondering if any of you have experiences with this wunder-method: Making water-soluble integral membrane proteins in vivo using an amphipathic protein fusion strategy. Mizrachi

Re: [ccp4bb] Problem with *.ref format (from Rigaku)

Dear Gottfried, I think you should take this up with Rigaku. They might have a re-formatting program for .ref files, and/or they may be able to tell you how to process the Saturn92 data with XDS (I can hardly imagine that they changed the format in a XDS-incompatible way). But you paid for the

[ccp4bb] AW: Another troublesome dataset (High Rfree after MR)

Dear Michael, Did you ask Phaser to check for all possible space groups? There are still I422 and I4 you did not mention. If the space group that came out of Phaser is different from the space group used for processing, subsequent refinement programs may use the wrong space group from the proce