Re: [ccp4bb] sftools

I have found I usually need to run an mtz through "CAD" in order to sanitize it after doing things in sftools and other programs that . CAD is kind of my "make it a cannonical mtz again" program. HTH -James Holton MAD Scientist On 4/5/2022 6:47 AM, Eleanor Dodson wrote: Does ANYONE know

Re: [ccp4bb] sftools

That looks simpler! On Tue, 5 Apr 2022 at 15:37, Paul Bond wrote: > Hi Eleanor, > > This is how you would do something similar in gemmi with ccp4-python: > > import gemmi > > mtz = gemmi.read_mtz_file("input.mtz") > dataset = mtz.add_dataset("mydataset") > dataset.crystal_name = "mycrystal" >

Re: [ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide crystallization?

Hi Mark, I also use dis.embl and IUPred in Jalview when trying to come up with construct boundaries. In the specific case I was referring to, we had a secreted human protein with a long and atypical secretion tag, which made it difficult to place the N-terminus of the mature protein within

Re: [ccp4bb] sftools

Hi Eleanor, This is how you would do something similar in gemmi with ccp4-python: import gemmi mtz = gemmi.read_mtz_file("input.mtz") dataset = mtz.add_dataset("mydataset") dataset.crystal_name = "mycrystal" dataset.project_name = "myproject" dataset.wavelength = 1.44555 for column in

Re: [ccp4bb] sftools

Thank you Robbie.. And good old CAD fixed it from ccp4i too Data line--- labin file_number 1 E1 = I_detw E2 = SIGI_detw Data line--- xname file_number 1 E1 = Petr E2 = Petr Data line--- dname file_number 1 E1 = detw1 E2 = detw1 Data line--- dpname file_number 1 Petr

Re: [ccp4bb] sftools

Hi Eleanor, I actually add the wavelength to an mtz file with CAD: cad \ HKLIN1 $WORKDIR/raw_nowavel.mtz \ HKLOUT $WORKDIR/raw.mtz \ <> $WORKDIR/mtz_creation.log LABIN FILE 1 ALLIN DWAVELENGTH FILE_NUMBER 1 1 $WAVELENGTH END eof I have no experience adding dataset names as

Re: [ccp4bb] sftools

It should be easy to do with gemmi And there was a program for editing datasets can’t remember what it was called Phil Sent from my iPhone > On 5 Apr 2022, at 14:47, Eleanor Dodson > <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > >  > > > Does ANYONE know how to use this useful

Re: [ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide crystallization?

Hi David, do you think that alphafold2 dis/order prediction is better than specific disorder predictors? i.e. http://dis.embl.de , which we've used for construct design https://prdos.hgc.jp , which I haven't really tried yet https://iupred2a.elte.hu

[ccp4bb] sftools

Does ANYONE know how to use this useful but ultra-frustrating program?? I have an mtz file which lacks WAVElength AND Dataset name. I try to follow the sftools documentation, and get an output file which - lacks WAVElength AND Dataset name. G sftools

[ccp4bb] Postdoc position at Rice Unversity, Houston

Dear All, A postdoctoral position is available in Dr. Yang Gao’s Lab (http://yanggaolab.blogs.rice.edu/) at Rice University, Houston, TX. Our lab studies enzymes and motors in DNA replication and repair (Science 363 (6429), eaav7003; Science 352 (6291), 1334). We combined biochemical, and

Re: [ccp4bb] off topic -- pymol error message

This means that you have an O-umlaut in your PDB file. That should never happen! PDB files should only have basic ASCII characters, not UTF-8. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board On Behalf Of 陈成 > Sent: Tuesday, April 5, 2022 13:12 > To:

[ccp4bb] off topic -- pymol error message

Hi all, What does this message means when loading a pdb file in pymol: 'utf-8' codec can't decode byte 0xd6 in position 37: invalid continuation byte Thank you! Chen -- Cheng Chen, Associate ProfessorSchool of Life Sciences, Building 15, Tianjin University No.92 Weijin Road, Nankai

[ccp4bb] EMBO Practical Course on High throughput protein production and crystallization - deadline 10th of April

Dear colleagues, deadline for registration for the "EMBO Practical Course on High throughput protein production and crystallization", Marseille,  is approaching: 10th of April More information below, with best wishes, Gerlind - I am glad to announce the "EMBO Practical Course on High

[ccp4bb] Position in drug discovery structural biology/biophysics in Newcastle

Dear all, Could I draw your attention to a great position that we have available to join a two year, MRC DPFS-funded project to provide structural and biophysical input to a drug discovery project in the CRUK Newcastle Drug Discovery Unit. The project is pursuing an exciting structural