
Frequently Asked Questions
Installation

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.
General Questions

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 300atom 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 812.

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.
Questions about Substructures

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 peakwavelength
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 datatype 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 structurefactor
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.
