Re: [ccp4bb] mmCIF files from PDB format for AlphaFill

Hi Harry, You can do this using the MAXIT tool [https://sw-tools.rcsb.org/apps/MAXIT/index.html] which can be installed locally. Best wishes, Avinash To unsubscribe from the CCP4BB list, click the following link:

Re: [ccp4bb] How to rotate subunits

Hi, There is a tool InterfaceAnalyzer in the Rosetta software suite that can probably do this. More details here (https://www.rosettacommons.org/docs/latest/application_documentation/analysis/interface-analyzer) Best wishes, Avinash

Re: [ccp4bb] normalization of B-factor values from different crystal structures

Hi Asmita, Try running your different crystal structures through PDB_REDO. That should normalize the B-factors to some meaningful values for comparison. Best wishes, Avinash

Re: [ccp4bb] Shape similarity of ligand binding sites

Hi Steve, Have you tried CASTp server (http://sts.bioe.uic.edu/castp/). That should help you to compare the shape of the ligand-binding sites. Best wishes, Avinash

Re: [ccp4bb] mystery feature near a PLP substrate

DMSO may fit nicely there.

Re: [ccp4bb] BSA as additive

Dear H.Sin, These references may help you: Meireles, M., Aimar, P., and Sanchez, V. (2004) Albumin denaturation during ultrafiltration: effects of operating conditions and consequences on membrane fouling, Biotech. Bioeng. 38, 528-534. Schratter, P., (2004) Purification and concentration by

Re: [ccp4bb] Chains view

Dear Remie, PyMol considers both chain identifier (chainID, column 22 in a PDB file) as well as the Residue sequence number (resSeq, columns 23-26 in a PDB file) to show the order of arrangement. So, simply renaming chainID’s will not work. In addition to that you will also have to renumber

Re: [ccp4bb] Chains view

Dear Remie, May be you have saved the coordinates as A.pdb? In that case the first /A/ will be the file name followed by the second /A/ for the protein chain. Else, somewhere in the pdb you may have an empty atom record, which is very unlikely. Best regards, Avinash

Re: [ccp4bb] Non-catalytic Rossmann fold domain

Saccharomyces cerevisiae (http://www.ncbi.nlm.nih.gov/pubmed/11684083). Best wishes, Avinash Punekar Uppsala University

Re: [ccp4bb] density near Histidine

Dear SDY, It looks like ethylene glycol to me. Try EDO (http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-searchoperation=ccidtarget=EDO) Avinash -- Avinash S. Punekar Uppsala University

Re: [ccp4bb] Large Conformational Change Upon Binding Ligand...

Dear Jacob, We recently solved crystal structures of apo and ligand bound forms of a cofactor S-adenosyl-methionine (SAM) dependent methyltransferase RlmJ (http://nar.oxfordjournals.org/content/41/20/9537.long). Comparison of the structures revealed that binding of the cofactor and a substrate

Re: [ccp4bb] Fitting of a trigonal bipyrimidal phosphorus

, Avinash Punekar

Re: [ccp4bb] residuewise rmsd for multiple chain superposition

Dear Sreetama, ProFit (http://www.bioinf.org.uk/software/profit/) does the RMS-by-residue calculation for multiple chain superposition. Avinash Punekar

[ccp4bb] Uppsala Crystallization Symposium, 12 May 2011

/terese/symposium -- Avinash Punekar PhD Student Department of Cell and Molecular Biology (Structural Biology) BMC, Uppsala University Uppsala, Sweden Phone : +46-736169636 Email: avinash.pune...@icm.uu.se