Re: [ccp4bb] Off-topic structural genomics related question.

Hi, "Question posed in a different way - One experienced crystallographer is being supplied with crystals of proteins - how many can one solve in a year (40 hour weeks, with 5 week holidays)." Under your assumptions with slight modifications (median length ~365 aa, all Se-Met-mostly MAD, s

[ccp4bb] Off-topic structural genomics related question.

Hello all, I apologize for this slightly off topic structural genomics kind of question(s). The number of structures deposited in the PDB is increasing, the number of groups doing structural work is also increasing. Given these two scenarios - how much has efficiency increased? W

Re: [ccp4bb] 3D mouse?

Diagnosis: Looks too good to be true. Prognosis: Never widely adopted or supported because it fails too good to be true test. James p.s. Of course I was wrong about the internet for this reason too when I first saw mosaic, so there may be hope. On Mar 18, 2008, at 8:59 AM, Daniel Schlie

Re: [ccp4bb] Broken Masks

Could it be that NCSMASK folded the mask back into an asymmetric unit? My NCSMASK input file contains explicit xyzlim boundaries and "notrim" keyword. On Tue, 18 Mar 2008, Laurence Pearl wrote: I'm trying to generate a mask around a molecule using NCSMASK under the CCP4i interface, for ultima

[ccp4bb] STFC submission, deadline this friday

Those of you still meaning to send something in to the STFC consultation exercise might find it useful if I let you know the points I intend to include, of course this is not exhaustive! Protein Crystallography: Diamond & ESRF Protein crystallography in the UK needs access to high-quality, state

[ccp4bb] 3D mouse?

Hi, has anybody tried 3dconnexion's space mouse with O, coot or ccp4mg? How does it compare to a normal mouse or to a 6 knob rotary encoder? http://www.3dconnexion.com/ Best regards, Daniel -- Daniel Schlieper email: [EMAIL PROTECTED] Molecular Motors Group

Re: [ccp4bb] Summary: Calculating R-factor and maps from a Refmac model containing TLS downloaded from the PDB

Hi Martyn, When the rcsb processes files, that line is stripped form the PDB file. We have taken an effort in the last few years to copy it into the REMARK 3 OTHER REFINEMENT REMARKS: field so that it is retained in the PDB file. Sometimes you can find out if that line was in the original PD

[ccp4bb] Early registration deadline extended for Quo Vadis Structural Biology?

Pardon the interruption: We have extended the early registration deadline for the SBGrid user summit 'Quo Vadis Structural Biology?' Information from the initial mailing is below. Come on by and see us now, ya hear? -ben -- Ben Eisenbraun Structural Biology Grid http://sbgrid.org/ == The fi

[ccp4bb] Broken Masks

I'm trying to generate a mask around a molecule using NCSMASK under the CCP4i interface, for ultimate use in NCS averaging and density modification in dm. Being a little old-fashioned I wanted to check that it covered the required molecule. However when displayed in COOT, there seem to be arbit

Re: [ccp4bb] Summary: Calculating R-factor and maps from a Refmac model containing TLS downloaded from the PDB

Refmac (at least 5.2) and TLSANL write a line into the PDB header specifying what is in the B column: REMARK 3 ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY Looking at 2qua which used Refmac 5.3, that line isn't there. I don't know at what stage it has been lost. Of course, it would be nice

Re: [ccp4bb] Summary: Calculating R-factor and maps from a Refmac model containing TLS downloaded from the PDB

Hi Dale, as I've mentioned before, another source of discrepancy in reproducing R-factors could be a different treatment of the bulk solvent correction in the refinement program and in sfcheck. The sfchelc manual says: SFCHECK applies the "soft" low resolution cut-off to structure