Re: [ccp4bb] am I doing this right?

?usp=sharing Best wishes, Gergely Gergely Katona, Professor, Chairman of the Chemistry Program Council Department of Chemistry and Molecular Biology, University of Gothenburg Box 462, 40530 Göteborg, Sweden Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 Web: http://katonalab.eu

Re: [ccp4bb] am I doing this right?

construct a modified Multinomial likelihood function that includes 0 trials, because I am that stubborn. Best wishes, Gergely Gergely Katona, Professor, Chairman of the Chemistry Program Council Department of Chemistry and Molecular Biology, University of Gothenburg Box 462, 40530 Göteborg

Re: [ccp4bb] am I doing this right?

I am sorry, this was a dead-end idea multinomial distribution with 0 trials is not defined. Gergely From: CCP4 bulletin board On Behalf Of Gergely Katona Sent: 21 October, 2021 15:29 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] am I doing this right? Dear Randy and Kay, My solution would

Re: [ccp4bb] am I doing this right?

Dear Randy and Kay, My solution would involve a multinomial distribution for assigning the counts to pixels. Something like this: rate ≈ Gamma(1,1) total_counts ≈ Poisson(rate) probs ≈ Dirichlet (alpha=1, for all pixels) pixel_counts ≈ Multinomial (total_counts, probs of the different pixels

Re: [ccp4bb] am I doing this right?

the belief about what the rate may be independent of time is quite irrelevant and so are the predictions they may make. And I guess you would not intend to deposit images that were generated by the predictions of these posterior models and the "new and improved data". Best wishes, Gerge

Re: [ccp4bb] am I doing this right?

trap of frequentist thinking and reduce data one step at the time. Best wishes, Gergely -Original Message- From: James Holton Sent: 17 October, 2021 19:25 To: Gergely Katona ; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] am I doing this right? Thank you Gergely.  That is interestin

Re: [ccp4bb] am I doing this right?

On 10/16/2021 12:47 AM, Kay Diederichs wrote: > Dear Gergely, > > with " 10 x 10 patch of pixels ", I believe James means that he observes 100 > neighbouring pixels each with 0 counts. Thus the frequentist view can be > taken, and results in 0 as the variance, right

Re: [ccp4bb] am I doing this right?

interpretation of the error based on 0 counts then I am not sure how useful it is. Best wishes, Gergely -Original Message- From: Kay Diederichs Sent: den 16 oktober 2021 09:48 To: CCP4BB@JISCMAIL.AC.UK; Gergely Katona Subject: Re: am I doing this right? Dear Gergely, with " 10

Re: [ccp4bb] am I doing this right?

of k and strength of belief with its location and scale parameter, respectively. Best wishes, Gergely Gergely Katona, Professor, Chairman of the Chemistry Program Council Department of Chemistry and Molecular Biology, University of Gothenburg Box 462, 40530 Göteborg, Sweden Tel: +46-31-786-3959

Re: [ccp4bb] Meaning of a pdb entry

Message- > From: CCP4 bulletin board On Behalf Of Ethan A > Merritt > Sent: 29 May, 2021 19:16 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] (R)MS > > On Saturday, 29 May 2021 02:12:16 PDT Gergely Katona wrote: > [...snip...] > I think the

Re: [ccp4bb] Meaning of a pdb entry

23 To: Gergely Katona Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] Meaning of a pdb entry Dear Gergely, For authoritative advice you'd need to ask the PDB. Below is my take. > I am not sure if it is possible to use MODEL-ENDMDL loops in pdb or mmcif > format for storing multiple crystal

[ccp4bb] Meaning of a pdb entry

reduction and refinement protocols and most of the metadata. I am afraid I do know how the PDB and associated services work internally, but I hope someone here can provide guidance. Best wishes, Gergely Gergely Katona, Professor, Chairman of the Chemistry Program Council Department of Chemistry

Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] (R)MS

matrices, analogously how MD trajectories can be described as average structures and covariance matrices. I think the assumption of independent variations per atoms is too strong in many cases and does not give an accurate picture of uncertainty. Best wishes, Gergely Gergely Katona, Professor

Re: [ccp4bb] (R)MS

Dear Jonathan, In 1D sd may be intuitive, but in 3D it is not so much. The square root of a symmetric covariance matrix is not universally defined and it is not intuitive to me. Best wishes, Gergely Gergely Katona, Professor, Chairman of the Chemistry Program Council Department of Chemistry

Re: [ccp4bb] Anomalous signal to noise details

Hi, I am not sure about the 1.2-1.3 limit, but 0.8 probably comes from sqrt(2/pi), which is the ratio of the mean of a half-normal and its sigma when the mean parameter is 0. Best wishes, Gergely From: CCP4 bulletin board On Behalf Of David Waterman Sent: 18 December, 2020 12:53 To: CCP4BB@

Re: [ccp4bb] [3dem] Which resolution?

Hi, I think through bond and through space B factor (+ sphericity) restraints primarily exist for pragmatic reasons: they are needed to maintain the numerical stability of the refinement. That is a separate issue from making physical sense. If one finds consistent B-factor similarity in atoms c

[ccp4bb] Fwd: Post-Doctoral Position in Biophysics at the University of Gothenburg, Sweden

*Post-Doctoral Position in Biophysics at the University of Gothenburg, Sweden *A postdoctoral research positions is available from the beginning of 2014 in the biomolecular dynamics group of Dr. Gergely Katona at the Department of Chemistry and Molecular Biology, University of Gothenburg, Sweden

Re: [ccp4bb] Comparing two proteins

ege > > -- > -- > Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > phone: +49 (0)551 39 22149 > > GPG Key ID = A46BEE1A > > > -BEGIN PGP SIGNATURE- > Version: GnuPG v1.4.10 (GNU/Linux) > > iD8DBQFNpqOSUxl