Re: [ccp4bb] statistics from a structure factors file
These days I always ask people to send me the XDS_ASCII.HKL file if they used XDS, then I can be sure that it is really UNMERGED, which has many advantages (and I can read it into hkl2map, shelxc or xprep directly). George On 01/17/2013 10:37 AM, Graeme Winter wrote: > Hi Sebastiano, > > If they hand you an *unmerged* mtz file containing scaled data you can > do this, by remerging the data with Scala or Aimless. Equivalently the > unmerged output of scalepack or XSCALE (or XDS CORRECT) > > If however you have merged data then you have lost this information, > though completeness and Mn(I/sig) are available, but not Rsym / Rpim / > multiplicity etc. Unmerged files are good :o) > > Cheerio, > > Graeme > > > > On 17 January 2013 09:18, Sebastiano Pasqualato > wrote: >> >> Hi all, >> maybe a silly question, but I can't figure this out. >> >> Is there a piece of software to calculate "Table I statistics" such as Rsym, >> Mn(I/sigI), Multiplicity, Completeness, from a structure factors file >> already containing merged structure factors? >> >> That is, if somebody hands me an mtz file he used to solve a structure, how >> can I determine the overall quality of the collected data, without having >> access to the processing logs? >> >> Thanks in advance, >> ciao, >> Sebastiano >> >> -- >> Sebastiano Pasqualato, PhD >> Crystallography Unit >> Department of Experimental Oncology >> European Institute of Oncology >> IFOM-IEO Campus >> via Adamello, 16 >> 20139 - Milano >> Italy >> >> tel +39 02 9437 5167 >> fax +39 02 9437 5990 >> >> please note the change in email address! >> sebastiano.pasqual...@ieo.eu >> >> >> >> >> >> > -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582
Re: [ccp4bb] statistics from a structure factors file
Thanks Graeme. Long live and prosper to the unmerged files, then. ciao, s On Jan 17, 2013, at 10:37 AM, Graeme Winter wrote: > Hi Sebastiano, > > If they hand you an *unmerged* mtz file containing scaled data you can > do this, by remerging the data with Scala or Aimless. Equivalently the > unmerged output of scalepack or XSCALE (or XDS CORRECT) > > If however you have merged data then you have lost this information, > though completeness and Mn(I/sig) are available, but not Rsym / Rpim / > multiplicity etc. Unmerged files are good :o) > > Cheerio, > > Graeme > > > > On 17 January 2013 09:18, Sebastiano Pasqualato > wrote: >> >> Hi all, >> maybe a silly question, but I can't figure this out. >> >> Is there a piece of software to calculate "Table I statistics" such as Rsym, >> Mn(I/sigI), Multiplicity, Completeness, from a structure factors file >> already containing merged structure factors? >> >> That is, if somebody hands me an mtz file he used to solve a structure, how >> can I determine the overall quality of the collected data, without having >> access to the processing logs? >> >> Thanks in advance, >> ciao, >> Sebastiano >> >> -- >> Sebastiano Pasqualato, PhD >> Crystallography Unit >> Department of Experimental Oncology >> European Institute of Oncology >> IFOM-IEO Campus >> via Adamello, 16 >> 20139 - Milano >> Italy >> >> tel +39 02 9437 5167 >> fax +39 02 9437 5990 >> >> please note the change in email address! >> sebastiano.pasqual...@ieo.eu >> >> >> >> >> >> -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 please note the change in email address! sebastiano.pasqual...@ieo.eu
Re: [ccp4bb] statistics from a structure factors file
Hi Sebastiano, If they hand you an *unmerged* mtz file containing scaled data you can do this, by remerging the data with Scala or Aimless. Equivalently the unmerged output of scalepack or XSCALE (or XDS CORRECT) If however you have merged data then you have lost this information, though completeness and Mn(I/sig) are available, but not Rsym / Rpim / multiplicity etc. Unmerged files are good :o) Cheerio, Graeme On 17 January 2013 09:18, Sebastiano Pasqualato wrote: > > Hi all, > maybe a silly question, but I can't figure this out. > > Is there a piece of software to calculate "Table I statistics" such as Rsym, > Mn(I/sigI), Multiplicity, Completeness, from a structure factors file > already containing merged structure factors? > > That is, if somebody hands me an mtz file he used to solve a structure, how > can I determine the overall quality of the collected data, without having > access to the processing logs? > > Thanks in advance, > ciao, > Sebastiano > > -- > Sebastiano Pasqualato, PhD > Crystallography Unit > Department of Experimental Oncology > European Institute of Oncology > IFOM-IEO Campus > via Adamello, 16 > 20139 - Milano > Italy > > tel +39 02 9437 5167 > fax +39 02 9437 5990 > > please note the change in email address! > sebastiano.pasqual...@ieo.eu > > > > > >
[ccp4bb] statistics from a structure factors file
Hi all, maybe a silly question, but I can't figure this out. Is there a piece of software to calculate "Table I statistics" such as Rsym, Mn(I/sigI), Multiplicity, Completeness, from a structure factors file already containing merged structure factors? That is, if somebody hands me an mtz file he used to solve a structure, how can I determine the overall quality of the collected data, without having access to the processing logs? Thanks in advance, ciao, Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 please note the change in email address! sebastiano.pasqual...@ieo.eu
Re: [ccp4bb] statistics of A/B
how about Delta method? see examples here: http://www.math.umt.edu/patterson/549/Delta.pdf = = = = = = = = On 2011-06-07 08:47:04 You wrote = = = = = = = = Thank you for the reply. Hypothesis: A and B are independent and normal distribution. Could you please explain more? Thanks. --- On Mon, 6/6/11, chris.mor...@stfc.ac.uk wrote: From: chris.mor...@stfc.ac.uk Subject: statistics of A/B To: capri...@yahoo.com Date: Monday, June 6, 2011, 4:00 AM HI, Do you have a hypothesis about the distributions of A and B? If so, there might be an analytic answer to your question, and certainly you can answer it by monte carlo simulation. Without a know distribution, it does not have an answer. From the mean and variance of A and B, you can work out the mean and variance of: A - B But not of: Log A Note that the answer you are looking for will be ill conditioned if the distribution of B includes points near 0. regards, Chris Chris Morris chris.mor...@stfc.ac.uk Tel: +44 (0)1925 603689 Fax: +44 (0)1925 603634 Mobile: 07921-717915 https://www.pims-lims.org/ Daresbury Lab, Daresbury, Warrington, UK, WA4 4AD If means and standard deviations of A and B are known, how to estimate the variance of A/B? Thanks. -- Scanned by iCritical.
Re: [ccp4bb] statistics of A/B
Thank you for the reply. Hypothesis: A and B are independent and normal distribution. Could you please explain more? Thanks. --- On Mon, 6/6/11, chris.mor...@stfc.ac.uk wrote: From: chris.mor...@stfc.ac.uk Subject: statistics of A/B To: capri...@yahoo.com Date: Monday, June 6, 2011, 4:00 AM HI, Do you have a hypothesis about the distributions of A and B? If so, there might be an analytic answer to your question, and certainly you can answer it by monte carlo simulation. Without a know distribution, it does not have an answer. From the mean and variance of A and B, you can work out the mean and variance of: A - B But not of: Log A Note that the answer you are looking for will be ill conditioned if the distribution of B includes points near 0. regards, Chris Chris Morris chris.mor...@stfc.ac.uk Tel: +44 (0)1925 603689 Fax: +44 (0)1925 603634 Mobile: 07921-717915 https://www.pims-lims.org/ Daresbury Lab, Daresbury, Warrington, UK, WA4 4AD If means and standard deviations of A and B are known, how to estimate the variance of A/B? Thanks. -- Scanned by iCritical.
[ccp4bb] statistics
Dear everybody! I recently tried out the anisotropy server at http://www.doe-mbi.ucla.edu/~sawaya/anisoscale/ I also see that there is much discussion going on about the correctness of this method. In any case, does anyone know a tool that gives me the datacollection statistics that I normally record from the SCALA log file? I am talking about multiplicity, completeness, I/sI etc all _AFTER_ ellipsoidal truncation and anisotropic scaling. My crystal diffracts in one direction to at least 1.8A whereas in the other directions it is rather 2.0 to 2.1. The spacegroup is C2. Thank you a lot, Matthias
Re: [ccp4bb] Statistics differences
Hi all, here is very incomplete list of why the statistics is different: - different bulk solvent models (flat mask based, Babinet, etc.); - different parameters for mask calculation (shrink and solvent radii, grid step) if flat bulk solvent model is used; - different scattering factor tables (International tables, W&K, n-gaussian); - different structure factor calculation algorithms: FFT or direct; - different parameters for FFT based structure factor calculations (grid step, atom truncation radius, Badd); - different stereo-chemistry dictionaries; - silent (implicit or explicit) use of hydrogens; - different minimizers; - different X-ray refinement target functions: ML (CNS, REFMAC, PHENIX), LS (SHELXL); - different ways of parameterizations of ML target (sigmaa (CNS, REFMAC), alpha&beta (PHENIX)); - different algorithms for estimation of parameters for ML; - different algorithms for calculation of relative weights "wxc" in Etotal = wxc*Exray+Egeom and "wxu" in Etot = wxu*Exray+Eadp; - different ways of handling unobserved Fobs for maps calculations; - different parameterizations for geometry restraints targets (not the same as different dictionaries); - different functions for ADP restraints (TNT-like, PHENIX-like, CNS-like); - different binning schemes; - different random seeds for SA ... oh, tired from typing, but I can easily double or triple the list above. Yes, I agree with Garib: hopefully all these technicalities do not affect significantly the maps. Cheers, Pavel. 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
Re: [ccp4bb] Statistics differences
Dear Jacob The main reason why different programs produce different resutls is that methods used in these programs are different. For example refinement programs use different methods for scaling. Some include bulk solvent a Babinet, some use mask bulk slvent and some use anisotropic scaling others do not use. Even for each parameterisation there are variations. Fortunately for most of the cases the results are mathematically equivalent and maps do not change too much. Regards Garib On 7 Sep 2007, at 16:27, 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] ***
Re: [ccp4bb] Statistics differences
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 PR
[ccp4bb] Statistics differences
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] ***
