Re: [ccp4bb] 3D Structure Search

Also, TopSearch https://topsearch.services.came.sbg.ac.at/ CAME - TopSearch :: Structure Search topsearch.services.came.sbg.ac.at Sequence Analysis Highlight identical residues Jmol Mode HTML5 Java. Cite TopSearch © Dave == Dr David C

Re: [ccp4bb] question regarding sequence numbering

Hi Tony, When I've had similar issues, I've numbered them sequentially (i.e. 7,8,9) and remarked in the PDB header that they are vector-derived sequence. I believe that is what the PDB ask you to do in situations like this (maybe they can comment?). If they are not numbered sequentially,

Re: [ccp4bb] NMR or Homology Model as a MR model

Dear Nishant, You can use anything you want as a molecular replacement search model including NMR models/ensembles or homology models. Whether or not it will be successful is another matter! For borderline cases, some have reported success using Phaser in combination with the Rosetta

Re: [ccp4bb] Protein rapidly precipitates when off ice

Hi Chris, What is the theoretical pI of your protein? If it is around pH 7.5, you might try gel filtering your protein into a different buffer/pH combination. Try changing by at least 1 pH unit in either direction. If the pI isn't a problem, then you might try try solubility screening as

Re: [ccp4bb] weird diffraction pattern

Hi, I'd need to see more processing stats to figure out your data issues. Streaky spots in certain directions can be indicative of anisotropy and/or lattice disorders. However, if your Rfree is above 0.5, it is likely that your molecular replacement solution is poor/bad/wrong. HTH, Dave --

Re: [ccp4bb] long loop

I know that this might be considered heresy on a crystallography mailing list, but do you have any friendly NMRists at your institution? D Dr David C Briggs Hohenester Lab Department of Life Sciences Imperial College London UK http://about.me/david_briggs

Re: [ccp4bb] Correcting 3-letter codes based on protonation states in a PDB file

I believe the ProPka or Pdb2pqr webservers can do this. ProPka.org http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/ HTH, Dave -- Dr David C Briggs Hohenester Lab Department of

Re: [ccp4bb] mystery disappearance of CCP4 website(s)

http://www.ccp4.ac.uk/ works for me, (from Sunny London). Maybe it was just a glitch in the matrix? Dr David C Briggs Hohenester Lab Department of Life Sciences Imperial College London UK http://about.me/david_briggs From: CCP4 bulletin board

Re: [ccp4bb] Cys modification - deciding between CSS and SMC

Hi Mohamed, Did you try CSO or CSD? I've seen oxidation of Cys residues in the active site of Cysteine-dependent Phosphatases before. In addition, oxidation is more easily explainable than CSS and SMC, especially if reducing agents were omitted from final purification steps. HTH, Dave --

Re: [ccp4bb] BSA as additive

(Sorry... over-enthusiastic sending) As for an actual reference - I'm not sure. It's a bit like lab folk-lore. Dave Dr David C Briggs Hohenester Lab Department of Life Sciences Imperial College London UK http://about.me/david_briggs From: CCP4

Re: [ccp4bb] BSA as additive

Hello, I've seen BSA used to "block" membranes of centrifugal concentrators when proteins were sticking to them. It appeared to work (proteins could be concentrated with less loss), but I'm not sure how much BSA ends up in your sample. I can imagine the answer is "a bit" and therefore for