Re: [ccp4bb] alternating strong/weak intensities in reciprocal planes - P622

2007-08-27 Thread jjwarren
You said: > 8) Processed in P6, P312 and P321, all of course suggest twinning. These will all suggest partial twinning, but not necessarily perfect twinning. I would start to consider twinning a possibility if the statistics for these lower symmetry space groups suggest a partial twin fraction of

Re: [ccp4bb] Probelm in creating topology files for CNS refinement

2007-08-23 Thread jjwarren
The sizes of several arrays (such as the ones that store atomic positions) are defined at compile time, and your structure appears to have run up against one such limit. Here's what the CNS website says: "Changing array dimensions The array dimensions for several arrays which may need to be cha

Re: [ccp4bb] SelenoMet protein?

2007-06-14 Thread jjwarren
2 methionines in 63 amino acids might work. However, if I'm reading your message correctly, the methionines are likely to be located in disordered loops, which makes them less of a good bet. One alternative to consider is using modified DNA oligos, e.g. with 5-iodo-deoxyuracil or 5-bromo-deoxyur

Re: [ccp4bb] (bigger) fragment identification of limited proteolysis w/ mass-spec

2007-03-31 Thread jjwarren
Yong- There is a program called PAWS that does exactly what you're talking about, and I think there is a freeware version (unfortunately for PC only, it appears): http://bioinformatics.genomicsolutions.com/paws.html Josh Quoting Artem Evdokimov <[EMAIL PROTECTED]>: Dear Yong, There are se

Re: [ccp4bb] : misbound ligand examples?

2007-01-29 Thread jjwarren
Here's another late addition to the discussion, which Chad's comment reminded me of: We just deposited a similar-sounding structure of a DNA polymerase (2HVI). The protein is in the closed conformation, with ddCTP pairing with G in the active site of the two monomers in the ASU. A third ddCT