[ccp4bb] BBSRC-funded PDRA in CryoEM at University of Leeds

2017-09-20 Thread Chi Trinh
On behalf of Professor Neil Ranson (Director of EM, Astbury BioStructure Laboratory) Dear All, A new 3-year BBSRC-funded position in my lab is now available. The project is to work on high resolution structures of new plant viruses using the state of the art cryo-EM facilities with the

Re: [ccp4bb] AW: [ccp4bb] doubt regarding MR search model

2017-09-20 Thread Eleanor Dodson
Satvik - if you attach your data processing logs I can tell you what to look out for - too abstract to do without a concrete example to discuss. Eleanor On 20 September 2017 at 14:00, wrote: > Dear Satvik, > > > > An R/Rfree of 0.29/0.35 after one round of automatic

[ccp4bb] AW: [ccp4bb] doubt regarding MR search model

2017-09-20 Thread Herman . Schreuder
Dear Satvik, An R/Rfree of 0.29/0.35 after one round of automatic model building indicates that your solution is correct. You can proceed with refinement and rebuilding. You can take either the monomer-based or dimer-based solution, it does not matter. Personally I would take the monomer-based

Re: [ccp4bb] doubt regarding MR search model

2017-09-20 Thread Satvik Kumar
Hello, Thanks all for your valuable suggestions. Two things that stuck me were "one gets to know if the space group is correct only after solving the structure" and "to try all possible space groups until one lands up with the correct solution". I ran Phaser with "all alternative space groups".

Re: [ccp4bb] R free flag

2017-09-20 Thread Robbie Joosten
Hi Rashi, Rather than use the mtz file from EDS you should use he mmCIF reflection file from the PDB directly and convert it. If the authors deposited the test set, you can keep it this way. Otherwise you need to select a new test set. Note that if you want to optimize an existing PDB entry,

Re: [ccp4bb] AW: [ccp4bb] question regarding sequence numbering

2017-09-20 Thread John Berrisford
Dear Tony The only requirements we have for numbering is that every residue must be unique when using a combination of residue name (to handle microheterogeneity), residue number, insertion code and chain ID. During curation we will try to map your protein sequence to UniProt - please see

[ccp4bb] R free flag

2017-09-20 Thread Rashi Aggarwal
Hello, I am trying to refine a structure that is deposited in PDB. I have downloaded the _sigmaa.mtz file from the electron density server. Trying to run refmac using this mtz file gives me the popup free R label has not been set. How can I set free R label in an existing mtz file so that