Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

Is it just me who is really impressed by it? Am I missing something? Get Outlook for Android From: CCP4 bulletin board on behalf of Rafael Marques Sent: Monday, May 13, 2024 3:13:16 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd:

[ccp4bb] Crystal screen for DNA binding proteins

Hi Can anyone recommend a good crystal screen to use to crystalise protein-NA complexes? Kind Regards Sylvia This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original messa

Re: [ccp4bb] Can nucleoprotein complex inhibit EtBr binding?

What is the charge on your protein? If it is a very positively charged protein it may not enter the gel. I have found this before in EMSAs but normally at low protein concentrations it still enters the gel only at the higher concs it does not. I had to change protein to DNA ratio and also the pe

Re: [ccp4bb] Strategies to bring out over-expressed protein from inclusion bodies to soluble fraction!!!

Have you tried adding a detergent such as SDS to your cells when you lyse them? This in my experience helps improve the soluble fraction significantly although it may lead to downstream problems with removal of the detergent. From: xaravich ivan [mailto:xaravich.i...@gmail.com] Sent: 17 October

Re: [ccp4bb] protein crystals or salt crystals

I didn't see the picture that you attached but if you have more than one crystal you could always run one on a gel to see if it runs the expected size of your protein From: Patrick Shaw Stewart [mailto:patr...@douglas.co.uk] Sent: Friday, February 08, 2013 11:47

[ccp4bb] Postdoctoral positions available

SARChI POSTDOCTORAL FELLOWSHIPS IN PROTEIN BIOCHEMISTRY AND STRUCTURAL BIOLOGY AT THE UNIVERSITY OF THE WITWATERSRAND SOUTH AFRICA Postdoctoral positions in protein biochemistry and structural biology are available for suitably qualified PhD graduates to pursue research into improving our u

Re: [ccp4bb] HKL-MTZ conversion

Use combat -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Dr. STEPHEN SIN-YIN, CHUI Sent: Friday, February 05, 2010 8:32 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] HKL-MTZ conversion Dear All, can anyone of you using Bruker PROTEUM X8? How ca

[ccp4bb] editing phi and psi angles in coot

by rotating either the peptide or the carbonyl, 2 dots appear. What do these 2 separate dots represent? I'm assuming they both should be in the allowed regions of the plot but I'm wondering how they relate specifically to the psi and phi angles of the peptide concerned? Best regards Sylvi

[ccp4bb] MR question

0. 0.050724.40 0.00 4.20 Best regards Sylvia Fanucchi Ph.D Protein Structure-Function Research Unit East Campus, Gate House Room 416 School of Molecular and Cell Biology University of the Witwatersrand Johannesburg 2050 South Africa Tel: +27 (11) 717-6348 Fax: +27 (11) 717-6351

[ccp4bb] creating mmcif file

Hi all I'm having some trouble creating a complete mmcif file for deposition using the harvesting manager. It does not appear to be able to read the files I would like to input (pdb files, mmcif, log files etc). It gives an error: "can't read "ext": no such variable". Should I change the exten

[ccp4bb] Adding ligand to model

Dear all I have a question regarding adding a ligand to my model. I'm not quite sure how to do it. I have obtained the ligand in two different ways, either in SMILES format from the drugbank or in PDB format. I have moved the ligand into the density in coot simply by using translate and rotate

[ccp4bb] how to improve Rfree?

rounds of refinement, the R-free actually starts to increase slightly although the R-factor continues to decrease. Does this mean that there is significant bias in my model? Does anybody know how I could go about addressing this problem? Thanks for any help :-) Sylvia Fanucchi Ph.D Protein Structure

[ccp4bb] Saint into Scala

Does anyone know how to convert data in Saint format into a format that is recognized by Scala? Best regards Sylvia Fanucchi Ph.D Protein Structure-Function Research Unit East Campus, Gate House Room 416 School of Molecular and Cell Biology University of the Witwatersrand Johannesburg

[ccp4bb] r-factor does not reduce

improve the refinement? Thanks for your suggestions Best regards Sylvia Fanucchi Ph.D Protein Structure-Function Research Unit East Campus, Gate House Room 416 School of Molecular and Cell Biology University of the Witwatersrand Johannesburg 2050 South Africa Tel: +27 (11) 717-6348 Fax: +27

[ccp4bb] Arpwarp not recognised by latest version of ccp4

Hi Does anyone know how to configure ArpWARP manually so that it will be recognized by the latest version of ccp4? Best regards Sylvia Fanucchi Ph.D Protein Structure-Function Research Unit East Campus, Gate House Room 416 School of Molecular and Cell Biology University of the

[ccp4bb] phaser troubles

Hi This is probably an obvious one but I'm having trouble getting Phaser to run. It simply says the status is "starting" and will not give me more information in the log file. I suspect the problem has to do with the F and Sigma F values but I am not sure what to assign them as? Any help woul