Hi Thanks for the help, it seems working fine. Regards Intekhab Alam On Mon, Mar 28, 2011 at 11:26 PM, Thomas C. Terwilliger < [email protected]> wrote:

Hi Intekhab,

Usually you should be able to open resolve_composite_map.mtz with coot using "open mtz" (not auto-open mtz). Then be sure to use FP PHIM FOMM (include weights, not just FP PHIM).

Also you can use

phenix.mtz.dump resolve_composite_map.mtz

to verify that the file is ok.

Let me know if that doesn't do it!

-Tom

...

...

Hi i generated an iterative build omit map using phenix and the output fule that i got is resolve_composite_map.mtz, but i cannot open this file in coot, what modifications do ineed to open this file in coot.

Regards

-- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

Hi, In the manual of phenix.refine, it mentioned the weighting of adp term wrt Exray: ******************* Etotal = wxu_scale * wxu * Exray + wu * Eadp ******************* I understand what is the geometry weighting, but for adp, could somebody explain more about what is Eadp (or references)? By the way, for curiosity, I want check into the source code for details. To save some time, can somebody direct where the source code part is located for this Eadp calculation? Thanks! Best Regards, Hailiang

Hi Pavel: Yes, the formula of Eadp (Tadp) is exactly in the paper you sent me (sorry I should have read it more carefully:-( By the way, since sometimes I may want to check into the python codes for details, are there any sources for the program archtecture description to make life easier (say to locate the Eadp formula in phenix code)? Thanks! Best Regards, Hailiang

Hi Hailiang,

I mentioned this paper to you yesterday:

"On atomic displacement parameters ..." ( http://www.phenix-online.org/newsletter/CCN_2010_07.pdf )

Sounds like you didn't have chance to have a look at it yet -:)

Both of your questions, this one below and yesterday's, are answered in the above article!

Actually, what's not explicitly written in that article is the formula you quoted (my mistake!, although it is in phenix.refine docs):

Etotal = wxu_scale * wxu * Exray + wu * Eadp

which is the refinement target for ADP optimization (similarly to refinement of coordinates).

All the best! Pavel.

On 4/1/11 12:18 PM, [email protected] wrote:

...

Hi,

In the manual of phenix.refine, it mentioned the weighting of adp term wrt Exray: ******************* Etotal = wxu_scale * wxu * Exray + wu * Eadp ******************* I understand what is the geometry weighting, but for adp, could somebody explain more about what is Eadp (or references)?

By the way, for curiosity, I want check into the source code for details. To save some time, can somebody direct where the source code part is located for this Eadp calculation?

Thanks!

Best Regards, Hailiang

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Hi Hailiang, phenix.model_vs_data handles input TLS exactly as described in the paper you mentioned below - I didn't change anything in the relevant code since publication of that paper. Essentially, there may be three types of input files: - containing total ADP, and - containing residual (or local or atom) ADP, - various weird mixtures of two above, so without trusting too much input REMARK 3 records, phenix.model_vs_data tries both possibilities and picks the one that yields a lower R-factor, which makes the program a bit slower but way more robust. Pavel.

In phenix.model_vs_data, a special handling of ANISOU records and TLS parameters were mentioned in "http://scripts.iucr.org/cgi-bin/paper?he5476". My understanding is the following and pls let me know if I am wrong:

************ (1) In TLS, some programs output a PDB with ANISOU including only TLS B-factor (case A), and other programs output a PDB with ANISOU including both TLS and residual B-factor (case B).

(2) In the former case (A), the ANISOU B will be added to the residual B; The later case (B) is straightforward. (Both will be tried and lowest R/Rfree will be used)

(3) In the former case (A), if ATOM B records contain both TLS (isotropic conversion) and residual B, TLS-isotropic B will be substracted from ATOM B records. The later case (B) is straightforward. (Both will be tried and lowest R/Rfree will be used)

*************

Pls let me know if I am wrong somewhere. Thanks a lot!

Best Regards, Hailiang

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb