Re: [ccp4bb] Se SAD phasing map becomes worse after refinement

When something like this happens I always go back to the data. What do the mages look like - are the spots ugly streaky ones, or quite tidy. Then is the spacegroup right ? Did you integrate assuming C/mmm symmetry? If so go back and do it again in P1! Look carefully at the pointless analysis; I h

Re: [ccp4bb] Se SAD phasing map becomes worse after refinement

Dear Zhu, Questions specific to Phenix should really go to the Phenix-BB, so I am cross-posting my reply there. Here I’ll focus more on generic issues. There are also CCP4 tools that you could consider and presumably other people will offer advice on those. One point you raise comes up so mu

[ccp4bb] Se SAD phasing map becomes worse after refinement

Dear All I am sorry for the long context. I have one protein (252 AAs, 2 Met) bound to double-stranded DNA (24 bp) crystalized. I collected the Se-Met data of the crystal in C222 up to 2.8 angstrom. the space group is confirmed by running the pointless. I used the Phenix.Autosol to find the

[ccp4bb] Se-SAD phasing - SOLVED!

@JISCMAIL.AC.UK Assunto: Re: [ccp4bb] RES: [ccp4bb] Se-SAD phasing It would not surprise me at all if pseudotranslation (aka tNCS) were holding you back. It is like kryptonite to all phasing techniques, MR, MAD, SAD, MIR, you name it. I recently did an analysis of old, never-solved data sets from

Re: [ccp4bb] RES: [ccp4bb] Se-SAD phasing

;mailto:mario.murak...@lnbr.cnpem.br> Cc: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Assunto: Re: [ccp4bb] Se-SAD phasing Good advice above.. Someting extra - I would look at information about how the molecules might be arranged. Is there any non-crystallographic translation? ( On

Re: [ccp4bb] RES: [ccp4bb] Se-SAD phasing

t; IDXREF.LP from xds. > -Mensagem original- > De: Tim Grüne > Enviada em: quinta-feira, 18 de julho de 2019 13:06 > Para: Mario Tyago Murakami > Cc: CCP4BB@jiscmail.ac.uk > Assunto: Re: [ccp4bb] Se-SAD phasing > > Dear Mario, > > you may want to post the shelxc log

[ccp4bb] RES: [ccp4bb] Se-SAD phasing

lho de 2019 12:34 Para: Mario Tyago Murakami Cc: CCP4BB@JISCMAIL.AC.UK Assunto: Re: [ccp4bb] Se-SAD phasing Good advice above.. Someting extra - I would look at information about how the molecules might be arranged. Is there any non-crystallographic translation? ( One with a coordinate 0f say z= 0.5

[ccp4bb] RES: [ccp4bb] Se-SAD phasing

Sure, it follows attached. I am also attaching the pointless log and IDXREF.LP from xds. -Mensagem original- De: Tim Grüne Enviada em: quinta-feira, 18 de julho de 2019 13:06 Para: Mario Tyago Murakami Cc: CCP4BB@jiscmail.ac.uk Assunto: Re: [ccp4bb] Se-SAD phasing Dear Mario, you

Re: [ccp4bb] Se-SAD phasing

Great point Jeff. Unfortunately I have “been there and got the T-shirt”, so I can sympathize with this situation! From: CCP4 bulletin board On Behalf Of Jeffrey B Bonanno Sent: Thursday, July 18, 2019 11:39 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Se-SAD phasing EXTERNAL EMAIL – Use

Re: [ccp4bb] Se-SAD phasing

board [mailto:CCP4BB@JISCMAIL.AC.UK] De la part de Mario Tyago Murakami Envoyé : jeudi 18 juillet 2019 16:19 À : CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Objet : [ccp4bb] Se-SAD phasing Dear all, I am trying to solve the phases of the following SeMet data, but so far unsuccessfully. S

Re: [ccp4bb] Se-SAD phasing

: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Mario Tyago Murakami Sent: Thursday, July 18, 2019 11:28 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Se-SAD phasing Dear Andy, Clemens and Michal The solution for orthrombic SG is very clear. P1 indexing results in a very

Re: [ccp4bb] Se-SAD phasing

ller additional > improvement in thehit ratio than when PATS is absent. For small > substructures (<10 sites), WEED and SKIP cando more harm than good by > eliminating too many correct sites at once. > > > > *De :* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *De la part de*

Re: [ccp4bb] Se-SAD phasing

small substructures (<10 sites), WEED and SKIP cando more harm than good by eliminating too many correct sites at once. De : CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] De la part de Mario Tyago Murakami Envoyé : jeudi 18 juillet 2019 16:19 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Se-SA

Re: [ccp4bb] Se-SAD phasing

t once. De : CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] De la part de Mario Tyago Murakami Envoyé : jeudi 18 juillet 2019 16:19 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Se-SAD phasing Dear all, I am trying to solve the phases of the following SeMet data, but so far unsuccessfully. Sugg

[ccp4bb] Se-SAD phasing

Dear all, I am trying to solve the phases of the following SeMet data, but so far unsuccessfully. Suggestions are very welcome. Please see below some details about the case. The statistics below is from a merged data from different kappas of the same crystal to increase redundancy. We used th