[ccp4bb] contrast missing issue

Dear CCP4 development team, I meet an issue when I use the latest version ccp4 8.0 in the Centos 7 system, there is no contrast output item when I try to construct a protein model by molecular replacement with Run Molre-autoMR method, but it works in the win10 system according to the same meth

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Re: [ccp4bb] extra Fo-Fc density in two Cysteines

Hi Liliana, May be it would be good to know if this adduct was formed during crystallization or protein was modified prior to crystallization. One could consider performing a protease digestion, followed by LC-MS/MS to determine the molecular weight of the adduct and then work backwards to account

Re: [ccp4bb] extra Fo-Fc density in two Cysteines

Difficult to be sure from a single angle pic but I would suggest Cys oxidation. There is an important 20 years old paper (see below) on Cys oxidation in a tyrosine phosphatase (like yours) Best Roberti] Nature *

Re: [ccp4bb] extra Fo-Fc density in two Cysteines

Hello, this looks like beta-mercaptoethanol adduct through a S-S bond. See [ https://pubmed-ncbi-nlm-nih-gov.insb.bib.cnrs.fr/12421561/ | The crystal structure of the Epstein-Barr virus protease shows rearrangement of the processed C terminus. ] Buisson M, Hernandez JF, Lascoux D, Schoehn G,

Re: [ccp4bb] extra Fo-Fc density in two Cysteines

Hello, you seem to have positive difference density for the Cys sulphur/sulfur atom. It would be worth checking it's occupancy. Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail mobile Original Message On 18 Dec 2023, 17:03, Liliana Margent wrote: > H

Re: [ccp4bb] contrast missing issue

Dear Zhihong Xin, am I understanding correctly that you get very different output, using CentOS7 versus using Windows10, for the exact same calculation? In that case, it seems surprising (to me at least) that it is only the contrast value that is affected. There is not much to work on, from your

Re: [ccp4bb] solvent mask for partial ligands, addendum

Hi Gottfried, I was wondering what happens if you make a Polder omit map for the HEPES? I am also curious, if the extra positive density is for missing bulk solvent with ligand of occupany 0.5, do you observe the density with ligand present at 0.5 occupancy to be more diffuse than with no liga

Re: [ccp4bb] contrast missing issue

Dear Kay, Thank you for your responses. Please find the window10 and Centos7 logfiles in the attachment. Your Best, Zhihong xin From: Kay Diederichs Date: 2023-12-19 02:35:50 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] contrast missing issue>Dear Zhihong Xin, > >am I understanding cor

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