Re: [ccp4bb] How long does it take crank 2 (refmac step) to run?
Hi Gabriel, My datasize is very small with a very low resolution. Was there an error output when your refmac process didn't converge? I started a SAD process along as you suggested and will see what is going to happen. Thanks NIck >>>>>> Hi Nick, In my experience, this is too long and there is probably an error. That said, the SAD dataset I used for crank 2 with a partial model was small (~18,000 reflections and no NCS at 3Å). Interestingly, though I had a partial model (built with phenix.mr_rosetta), crank 2 failed to converge when I gave it this model (took ~3-4 hours to finish on a dual core 2.5Ghz iMac). When I ran crank 2 with my SAD dataset alone (no partial model input), I got a much better solution in ~2 hours and was able to solve the structure, so I suggest you try this as well. Depending on your computer and dataset size, it is possible that more than 24 hours are needed. I’d be happy to discuss further. Best of luck, Gabe Salzman On Sat, Jan 31, 2015 at 11:46 AM, Nick Huang wrote: > Hi all, > I started a crank 2 process to run a SAD model building with a partial > model input yesterday. From the log file, crank 2 was in the step of > "Starting > process of iterative refinement and (substructure) atom picking" and had > been running a whole night without any further output. Does anybody know if > it is normal or there is an error? > Thanks, > Nick Huang > > Hauptman-Woodward Institute > >
[ccp4bb] How long does it take crank 2 (refmac step) to run?
Hi all, I started a crank 2 process to run a SAD model building with a partial model input yesterday. From the log file, crank 2 was in the step of "Starting process of iterative refinement and (substructure) atom picking" and had been running a whole night without any further output. Does anybody know if it is normal or there is an error? Thanks, Nick Huang Hauptman-Woodward Institute
[ccp4bb] Autoscale in HKL2000
Dear all, I am trying to figure out what exactly Autoscale does in HKL2000 and decide what is the best practice. Autoscale definitely does more than adjusting error models for me. It seems that using the .sca file it generated dramatically improved my density modification map. However, Xtriage from phenix suggested that the data was truncated or scaled for its unisotropicity and data completeness suffered. As a result it suggested me to use a full dataset instead and let the refinement take care of the unisotropicity. Maybe I should use the autoscaled dataset to build the model because the density modification is better, but to run the final refinement with full dataset instead because refinement also treats unisotropicity? Best, Nick Huang
Re: [ccp4bb] About NCS and inhibitors
Yes, it is very common. I solved two of them at 2-3 A resolution and saw my colleague had one with 1.4 A resolution (can't remember the name of the protein). Please see references J Med Chem. 2010 Jul 22;53(14):5229-39. doi: 10.1021/jm100377f. Complexes of bacterial nicotinate mononucleotide adenylyltransferase with inhibitors: implication for structure-based drug design and improvement. Huang N, Kolhatkar R, Eyobo Y, Sorci L, Rodionova I, Osterman AL, Mackerell AD, Zhang H. Chem Biol. 2009 Aug 28;16(8):849-61. doi: 10.1016/j.chembiol.2009.07.006. Targeting NAD biosynthesis in bacterial pathogens: Structure-based development of inhibitors of nicotinate mononucleotide adenylyltransferase NadD. Best, Nian On Mon, Jan 7, 2013 at 4:28 AM, Xiaopeng Hu wrote: > > Dear All, > > We recently resolved an enzyme/inhibitor complex structure. The enzyme > contains two NCS related active site and we did find extra density in both of > them.However we observed that the two inhbitor moleculors are not NCS > related, but partly overlaped if make a NCS moleculor. Has anyone else > observed this before? Thanks for any help and suggestion! > > > Best, > > Xiaopeng Hu >
