Hello Cristian-- > I am trying to use SAXS data to refine a structure which has potassium ion > bound to it. When I try to run the script I get the following error: > > File "/usr/software/xplor-nih/python/solnXRayPotTools.py", line 558, in calc_f > > (a,b) = atomicFormFactor[ name ] > > KeyError: 'K' > > What I understand is that the program can not find the form factor data for > potassium ion. From the documentation of “create_SolnXRayPot” it seems it is > possible to add that data directly when initializing the class, but also there > are other methods that suggest the same, so I’m a little confused about how to > use them and the input as well. I would appreciate any suggestion about what > the best way to add the missing data. I’m currently using Xplor-Nih version > 2.51 that runs in NMRBox. >
I *think* the following will work: First define your form factors with a function, by copying the function use5GaussianFormFactors from python/solnXRayPotTools.py and adding it to your script- then add the potassium form factors. Then, before calling create_SolnXRayPot, do this: import solnXRayPotTools solnXRayPotTools.use5GaussianFormFactors = use5GaussianFormFactors > Also, if you have any idea where to find the form factor data for potassium > ion that will help a lot, I know part of the information was taken from the > CRYSOL paper but potassium is not there. > Apparently, crysol does currently have the numbers for potassium- it may be easiest if you query those folk for the values. They can also be determined by fitting a curve, but there should be no need to redo that effort. best regards-- Charles ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
