Re: [ccp4bb] Finding Homologs with Specific Residues Conserved

I am also not sure of what your goal is, but you can build a sequence profile for your sequence and use that profile as input instead of your sequence. You can do this by aligning a set of sequences homologous to your target sequence, and use that alignment as input for, for example, HMMER or

Re: [ccp4bb] cannot read h5 data file

Dear Shijun, it is always difficult to answer such questions without very specific information, like e.g. exact error messages, and exact description what was done. In addition to what others wrote, I see two general ways to solve the problem: a) talk to the beamline people. They should know

Re: [ccp4bb] Finding Homologs with Specific Residues Conserved

Not sure if I understand the question right, but wouldn't phi-blast do trick. You supply on too your conserved pattern and blast again. Christian Am 20.12.2017 19:37 schrieb "Keller, Jacob" : > Dear Crystallographer-Bioinformaticians, > > > > Is anyone aware of a way

[ccp4bb] Structural Biology Scientist position at Sanofi - Boston Area

We have an opening in our structural biology group in Waltham MA for a scientist to support small molecule drug discovery efforts. Experience with membrane proteins is desired. If interested, please apply through the Sanofi portal.

[ccp4bb] Finding Homologs with Specific Residues Conserved

Dear Crystallographer-Bioinformaticians, Is anyone aware of a way to tweak BLAST or similar software to be able to specify certain residues to be absolutely required, e.g., active site residues? I guess one can winnow broad-scale resuts with scripts, but it would seem to be a pretty common

Re: [ccp4bb] average B-factors

This is quite straightforward in any package with a reasonable scripting interface. In ChimeraX, for example: -load your model -make your selection (https://www.rbvi.ucsf.edu/chimerax/docs/user/selection.html) -open the shell (Tools/General/Shell), and in it, type: from chimerax.core.atomic

Re: [ccp4bb] cannot read h5 data file

Shijun, I have processed .h5 format data successfully that was collected at NSLS II AMX (this beamline has a Eiger 9M, not 16M, incidentally, but I don't think that this matters). I used XDSGUI without converting to .cbf format. To do so, and without knowing what the error messages are that you

Re: [ccp4bb] average B-factors

Easy with GUI2 Import coordinates and select the part you want Under validation and analysis Choose analysis Bs etc and you will get your answer BAVERAGE will give you Bs for main chain & side chain for each monomer but there is no selection option - you would have to do that in some other way

[ccp4bb] average B-factors

Dear all, Sorry for naive CCP4 question, is there a simple way to calculate average B-factors (side chain, backbone, all) for only part of a model, such as a domain, loop, etc… Thanks, Amir

Re: [ccp4bb] cannot read h5 data file

Hi Graeme and Shijun eiger2cbf was indeed used for the conversion - so the metadata should be in the CBF headers (unless the H5 files produced do not conform to what eiger2cbf expects). The most recent version of eiger2cbf should be used rather than the one on the Mosflm website! My guess is

Re: [ccp4bb] cannot read h5 data file

Dear Shijun How did you convert? If H5ToXDS it throws away all header information - this tool will preserve the metadata: https://github.com/biochem-fan/eiger2cbf which should allow XDSGUI to work. If DIALS can read the data but comes out with the wrong answer, please could you provide some

[ccp4bb] Dials

Dear all When I run dials.index it result me "Sorry: No suitable lattice could be found", but the other software can give me C2 space group. How could I DO with this situation Best Regards Shijun

[ccp4bb] cannot read h5 data file

Dear all I just collected some data with Eiger16M whose file format is *.h5. But I cannot read it with HKL2000, because I don't have the Eiger16M detector license now, while, I have *.cbf detector license. So I transfered the *.h5 to *.cbf files, but the problem is XDSGUI still cannot read