I am having trouble installing SnB on my Linux box. Where can I get help?

Reread the README. If you are still having problems go to http://www.ccp14.ac.uk/tutorial/snb/snb_linux.html.

I have never used SnB. How do I get started?

First take the SnB tutorial and then read the Overview of SnB Operation.

I have 1.7 Angstrom data for my 300-atom structure that contains one iron atom. Can SnB solve it?

Probably not. Please read the introduction.

Do I have to know exactly how many atoms are in my structure in order to run SnB?

No. Please read the comments about ASU contents for the General Info and Create Es screens.

How can I tell if I have a solution?

Follow the directions given in the Overview, sections 8-12.

I think I have found some of my atoms (or sites), and I want to use them to find more. How do I do this, and what format do I use for the coordinates?

Follow the directions given in the Overview, section 13.

 How can I get the coordinates for another trial (i.e. some trial other than the best trial)?

Follow the directions given in the Overview, section 14.

How can I rerun a trial and do Fourier refinement without repeating the whole job?

Same as question #6.

I used 5 processors to run 5000 trial structures, and I specified "job1" as the prefix for my output files. The histogram tells me that trial number 2748 is the best. Where do I find the coordinates?

In the file "job1_2.SnB_peak".

Is there an optimum number of processors to use for an SnB job?

No. If you use two processors, the job gets done in half the time. If you use three processors, the job is finished in one third of the time, etc.

If I use SAS data, my substructure sites will have the correct hand, right?

Wrong. The probability that you will have the correct hand is 50%.

I know that SnB can generally find sites from the peak-wavelength anomalous difference alone, but I would like to use the Fa values I calculated for my MAD data. Can I do this?

Yes. Follow the directions given under the Basic data-type option.

How can I tell which peaks actually correspond to the sites of my anomalous scatterers?

Please read the section on selecting correct sites in the discussion of substructures.

I get errors messages telling me that I don't have enough reflections (or invariants). What can I do?

Please read the section on reflection/invariant problems in the discussion of substructures. The discussion of the reflection & invariants screen.

My substructure is very large, and SnB takes a long time to run. Is there anything I can do?

You may be able to use a coarser grid for the Fourier maps.

I have native and SeMet data that I collected in the home lab, and I want to use the SIR option to find the Se substructure. Should I specify Se or A (i.e. the difference between S and Se) in the substructure formula?

SnB uses the atomic number as a weight in the structure-factor calculation for atoms bigger than oxygen (no attempt is made to distinguish C, N, and O), with the largest peaks being assumed to be the larger atoms if any are present. In this case, the atoms are all equal, so it really doesn't matter what you call them. However, you should give the proper formulas for the native and derivative ASUs.