Re: [phenixbb] Request for C shell script file for phenix.refine

Partha Modified residues can be handled by eLBOW. Run phenix.elbow file.pdb --do-all --opt to get a CIF file to pass to phenix.elbow. The option --opt is optional but recommended. Nigel On 10/1/2007 5:59 AM, Partha Chakrabarti wrote:

Hi Peter,

Thanks a lot for your suggestions. Its close but not completely happy yet. So, I generated the file as you suggested, several of the commands are understandable, and I can run it after modification as:

$ phenix.refine

but would be easier if there is a scrip for phenix.refine as available for SOLVE/RESOLVE. Could you point me to the not so easy way of doing that?

One particular problem seems to be modified residues, in my case, a phosphothr (TPO), had to delete the phosphate and rename TPO as THR.. is there any wayout?

Best, Partha

On 9/28/07, *Peter Zwart* mailto:[email protected]> wrote:

The easiest way is to have a parameter file that you edit. The easiest way to get a parameter file is by typing

phenix.refine <model> <data> --dry_run

and use the subsequently generated ???_refine_001.eff file.

rename that eff file to something like

parameters.def

which you can use for subsequent customisations and editing of parameters.

Not ethat every time you finish a refinement job, a new def file is generated of rthe next round, updating the model info for further rounds of refinement.

P

2007/9/28, Partha Chakrabarti < [email protected] mailto:[email protected]>: > Hi, > > I am wondering if one can have master scripts (C shell) for the macro cycle > of phenix.refine that can be used from the command line. It is easier to > comment out an option than having to type the whole thing.. has anybody > tried it? Similar scripts exist for solve/resolve and phaser.. > > I should not say it, I am myself not adverse to using the GUI, it is just > easier when the poor postdoc sits with the boss.. typically I face the > question: where is the script file & where is the log file :)) > > Cheers, Partha > > > -- > MRC National Institute for Medical Research > Division of Molecular Structure > The Ridgeway, NW7 1AA, UK > Email: [email protected] mailto:[email protected] > Phone: + 44 208 816 2515 > _______________________________________________ > phenixbb mailing list > [email protected] mailto:[email protected] > http://www.phenix-online.org/mailman/listinfo/phenixbb > > _______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

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