Is this map a total OMIT map like SFCHECK does or a SA-OMIT map like CNS does? Jianghai On Dec 29, 2006, at 12:53 PM, Thomas C. Terwilliger wrote:

Hi Miguel,

I'm sorry to have given incorrect instructions! Here is a corrected version of how to make a composite omit map with no rebuilding or refinement in phenix (I just did this to be sure).

If you use a script, add the following lines to your rebuild script:

rebuild_in_place True # rebuild existing model... rebuild_res_start_list 0 # rebuild only residues 0 to -1 (i.e., nothing) rebuild_res_end_list -1 refine False # don't refine input model n_cycle_rebuild_min 1 # just do one cycle n_cycle_rebuild_max 1

If you run from a GUI (I didn't test this, but it should work), set the same parameters above to these values and it should give you the omit map.

If you just get the overall_best.pdb_OMIT_REGION_1 files then it isn't working...if you also get overall_best.mtz_OMIT_REGION_1 then it is. The final map should be resolve_composite_map.mtz. It is produced after all the omit region maps are made

Let me know if this doesn't solve the problem! All the best,

-Tom T

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Hello everyone,

I'm trying to obtain a full omit map as it was described by Tom Terwilliger in a previous post:

http://www.phenix-online.org/pipermail/phenixbb/2006-October/ 000108.html

However, when I run the AutoBuild strategy asking for no rebuilding / no refinement all I get in the FULL_OMIT directory is a collection of pdb files named 'overall_best.pdb_OMIT_REGION_x' where 'x' correspond to each of the 'omit regions'. But I get no 'resolve_composite_map.mtz' whatsoever.

Surely I'm missing something. I would appreciate your guidance.

Have all of you an excellent year 2007! All the best,

Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900

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-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Tom, Thank you very much for checking this and for the explanation. If I understand correctly a full omit map like the one I wanted (with no rebuilding) might be useful to check, possibly at the end of refinement, whether there is significant bias. This should give similar information than the sfcheck omit map. However, we wanted to check a particular region of the model where the density is poor and not really improving with refinement. Hence, we wanted to ponder if there was bias but with the aim of building a new model for that region if required. Am I correct at deducing from your explanation that for this case it would be preferable calculating the full omit *with* iterative model-building? Cheers, Miguel En/na Thomas C. Terwilliger ha escrit:

Hi Jianghai,

The phenix full_omit map, if calculated with no model-building, is similar to both the SFCHECK map and the CNS composite SA-OMIT map.

The phenix full_omit map removes atoms in each omit box and in a 2 A radius around the omit box, then calculates phases, then puts all the omitted regions together. This is like the CNS SA-omit map with no simulated annealing. It is also like the SFCHECK OMIT map, except that SFCHECK does not remove atoms 2 A around the box.

The real power of the full_omit map is to calculate it WITH iterative model-building. In this case the atoms that get built inside the omit region get an occupancy of 0.0 each cycle. The model outside the omit region gets better and better, so that the omit density gets improved every cycle. Then when all the omit regions are recombined, the map is totally unbiased, but it can be much better than the starting omit map.

-Tom T

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Is this map a total OMIT map like SFCHECK does or a SA-OMIT map like CNS does?

Jianghai

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- -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 e-mail: [email protected] - ---------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.5 (Darwin) iD8DBQFFlX9NF6oOrDvhbQIRAkgxAJ9OhLXA7No/bk7r36M84l2D3FbgxACeJHHd Ew0XBx0j52BZjkKs7tUtpVE= =X+mM -----END PGP SIGNATURE-----