Re: [ccp4bb] CSYMMATCH for help

As I am sure you know - if you generate experimental phases from isomorphous or anomalous scatterers the differences between the reflection pairs can be equally well described by sites at (x,y,z) or (-x,-y,-z) . In addition many spacegroups allow coordinates to be related to several alternative

Re: [ccp4bb] CSYMMATCH for help

The -origin-hand option is also useful for comparing molecular replacement solutions that may have different origins. I think the slides in Andrey Lebedev's presentation help to visualise this problem (specifically slides 49 & 50).

Re: [ccp4bb] CSYMMATCH for help

I don't know for sure, but I think the -origin-hand thing would be for heavy atom work where both enantiomers of the solution can fit the data. Cheers, Jon.C. Sent from ProtonMail mobile Original Message On 18 Mar 2022, 04:02, 付兴科_201928000807036 wrote: > Dear Colleagues, >

Re: [ccp4bb] Cysteine-S-Iodine interaction

Check the electron density (O, Cl, I ?) and the anomalous signal on your "iodine". Cysteine has an interesting chemistry and one is oxidation to the sulfenic acid, CSO, already mentioned. Probably, it is more common than we tend to expect and may be overlooked, because we don't look for it and

[ccp4bb] PostDoc in cellular structural biology

Hello everyone, I would like to draw your attention on a ERC-funded 4 years PostDoc position available in my group, focused on unravelling the molecular basis of thyroid function and disease, using a combination of cell biology,

[ccp4bb] PhD position in experimental research on neurodegenerative diseases

Dear colleagues, We are looking for a Ph.D candidate to explore the pathological mechanisms of neurodegenerative diseases by using X-ray phase-contrast tomography in structural neurobiology group at the Paul Scherrer Institute, Switzerland

Re: [ccp4bb] Cysteine-S-Iodine interaction

Dear Modh, I agree with Paul, this is covalente modification of Cys. I would try cysteine persulfide (CSS), and cysteine sulfenic acid (CSO). In COOT, center on this cysteine, and then do: Calculate -> Modelling -> Replace residue; write CSS (or CSO), save the coordinates and refine. HTH,

[ccp4bb] **CCP-EM Spring Symposium 2022 Early Bird Offer Closing Tomorrow - Saturday 19th March**

**Early Bird Offer Closes tomorrow - Saturday 19th March** *Registration increases by £75 after this date* Dear CCP-EM, CCP-EM are pleased to announce the eighth annual 'CCP-EM Spring Symposium', 3-5th May 2022. The conference aims to provide a forum to highlight state of the art developments

Re: [ccp4bb] Cysteine-S-Iodine interaction

Hi, it may be oxidized cysteine. Look here: https://www.researchgate.net/publication/44656220_Protein_S-thiolation_by_glutathionylspermidine_Gsp_The_role_of_Escherichia_coli_Gsp_synthetASEamidase_in_redox_regulation and here: Trundle D, Cunningham LW. Iodine oxidation of the sulfhydryl groups of

[ccp4bb] SHELXD - Limit Number of CPUs?

Hi Jessica, there is a flag -t, which you should give in the command line to set the number of threads. eg shelxd -t4 name Best wishes, Isabel -- ICREA Res. Prof. Isabel Usón Crystallographic Methods Department of Structural Biology (“Maria de Maeztu” 2014 Unit of Excellence), Molecular

Re: [ccp4bb] Cysteine-S-Iodine interaction

On 17/03/2022 17:37, Mohd Syed Ahangar wrote: I have been doing some protein crystal soaking with some covalently binding fragments and in one structure I have got an extra density on Cysteine but that density doesn't match with the expected fragment. The fragment was in the form of iodide