Hi. Perhaps people more familiar with the inner workings of the programs can comment better on this, but I believe the FOM is simply a measure of how unimodal and sharp your phase distribution is. If you're working with experimentally determined phases, you have phase distributions that might be very broad and noisy and the FOM will be low. If you do solvent flattening or other density modifications involving calculating structure factors, you'll end up with delta functions for your phase distributions (which you might broaden with Sim weighting or some other approximation), and the FOM will be very high.
You might think FOM is well defined, but you need to keep in mind what kinds of phase distributions are being handled by the different programs. As far as R and Rfree go, I'm unaware of anyone who can explain why different programs give different values. There are a lot of ways those values can be affected, in particular in the treatment of the scale factor. And it's been many years (and many program ago) since the scale factor was under the control of the user. Ron Stenkamp On Fri, 7 Sep 2007, Jacob Keller wrote:
Dear list, I have for some time now wondered why different programs output different statistics. A low FOM from program A might be much better than a high FOM from program B, and so on. I wonder why, then, considering that statistical measures are precisely, mathematically defined, how is there any discrepancy? I have also wondered whether people might prefer certain programs because they are statistically flattering. I think in my experience I have seen even statistics like Rfree to be different from different programs, I think even without any refinement--so should one use that program last, right before composing "Table I" for publication? That seems suspicious... Jacob Keller ==============Original message text=============== On Fri, 07 Sep 2007 3:39:27 am CDT Andreas Kohl wrote: Dear all, we have currently two open postdoctoral positions in our department. We would very much appreciate it if you could bring this announcement to the attention of suitable candidates. All inquiries and applications should be send to: Prof. Pär Nordlund ([EMAIL PROTECTED]) or Dr. Said Eshaghi ([EMAIL PROTECTED]) Andreas #################################################################################### Postdoctoral positions available at Karolinska Institutet, Sweden Two postdoctoral positions are available at the division of Biophysics in the department of Medical Biochemistry and Biophysics, at Karolinska Intitutet in Stockholm. The division is headed by Professor Pär Nordlund and is focused on functional characterization of proteins, primarily using X-ray crystallography. In addition, new technologies are being developed and improved as tools to enable high-throughput approaches within protein production. The group has a strong record in structure determination of soluble and membrane proteins. The laboratory is well-equipped with state-of-the-art instruments for protein production and crystallization. Currently, two postdoctoral positions are available in the membrane protein group, working with medically important proteins from different families, such as solute transporters, ion channels and enzymes: 1. Membrane protein chemistry/structural biology. The applicant should have strong background in recombinant membrane protein production in E. coli system, preferably with some experience in protein crystallization. The main topic is to develop new and improved methods for purification and crystallization of integral membrane proteins. Knowledge about X-ray crystallography is ideal but not a requirement. The successful candidate will be part of a dynamic team that is working on production, crystallization and structure determination of membrane proteins. The applicant must therefore have the ability to work as a team-player as well as independently. The position is initially announced for two years. 2. Membrane protein X-ray crystallography. The applicant should have a strong background in X-ray crystallography with a good track record. The main tasks are crystallization screening, crystal optimization, data collection and structure determination of integral membrane proteins. Previous experience with membrane proteins is ideal but not a requirement. The successful candidate will be part of a team that is working on production and crystallization of membrane proteins. The applicant must therefore have the ability to work as a team-player as well as independently. The position is initially announced for two years. Applicants should send a full CV, including a publication list, together with the name and contact details of three references to: Prof. Pär Nordlund ([EMAIL PROTECTED]) or Dr. Said Eshaghi ([EMAIL PROTECTED]) ------------------------------------------------------------------------------------------------------------------- Prof. Pär Nordlund [EMAIL PROTECTED] Institutionen för Medicinsk Biokemi och Biofysik (MBB) Karolinska Institutet, 171 77 Stockholm Biofysik ===========End of original message text=========== *********************************** Jacob Keller Northwestern University 6541 N. Francisco #3 Chicago IL 60645 (847)491-2438 [EMAIL PROTECTED] ***********************************
