Re: [phenixbb] follow up on message 2: phenix.maps --Message: not implemented

Hello Pavel, The averaged kicked map looks great! I am able to see loop density that I could not see before. However, I still have one question: The kicked map were created when I put the map parameters in my custom_par file however, I was unable to run Phenix.maps in the command line. When I do this I get a message "Not implemented". I would like to create a ccp4 map for viewing in pymol without running refinement again. Do you know what could be causing this message? If I create "maps.params" by inserting the commands from the .def file Phenix does not recognize this file format. Any help would be appreciated. Thank you. -Yarrow

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Today's Topics:

1. syntax for Averaged Kicked maps and maps.param ([email protected]) 2. Re: syntax for Averaged Kicked maps and maps.param (Pavel Afonine) 3. Re: Phenix Autobuild (Thomas C. Terwilliger) 4. New version complaint (Simon Kolstoe) 5. Re: New version complaint (Nathaniel Echols) 6. Re: New version complaint (Douglas Jacobsen) 7. Re: New version complaint (Nathaniel Echols) 8. Adequate size for Free R test set? (Joseph Noel)

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Message: 1 Date: Mon, 2 Aug 2010 17:38:05 -0700 From: [email protected] To: [email protected] Subject: [phenixbb] syntax for Averaged Kicked maps and maps.param Message-ID: Content-Type: text/plain;charset=iso-8859-1

Hello,

Disclaimer: I am a newbie to both crystallagraphy and Phenix.

I am running phenix.refine (v1.6-289) in the command line

1. I want to make averaged "kicked-maps" but I keep getting a syntax error. I tried renaming "maps.param" but this file was not recognized.

2. When I enter Phenix.maps into the command line I get a message that syas "not implemented" I am trying to get the latest versiou of phenix installed.

The following is the syntax I put in my custom_params file Thanks

-Yarrow

refinement.main.number_of_macro_cycles = 2 #refinement.main.fix_rotamers = True refinement.refine.strategy = individual_sites+individual_adp refinement.output.prefix = CIN4_refine_omit refinement.output.serial = 12 refinement.output.write_def_file = True refinement.target_weights_wxc.scale = 0.2 refinement.main.max_number_of_interations=15

refinement.electron_density_maps { map { mtz_label_amplitudes = "2FOFCWT_kick" mtz_label_phases = "PH2FOFCWT_kick" likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = True } map { mtz_label_amplitudes = "FOFCWT_kicked" mtz_label_phases = "PHFOFCWT_kicked" likelihood_weighted = True obs_factor = 1 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = false }

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Message: 2 Date: Mon, 02 Aug 2010 17:48:45 -0700 From: Pavel Afonine To: PHENIX user mailing list Subject: Re: [phenixbb] syntax for Averaged Kicked maps and maps.param Message-ID: <[email protected]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi Yarrow,

you can use GUI or the command line for doing this.

0) It would be best if you update to the latest version, although I believe it might work with the one you have too:

http://www.phenix-online.org/download/

1) GUI: launch PHENIX GUI and go to Maps -> Create Maps. then just add as many maps you want (or use pre-defined ones) and check a box for kick map.

2) From the command line type:

phenix.maps

and hit Enter (Return). That will create a file called something maps.params. Edit that file to add/remove the maps you need/ don't need and set

kicked = True

for the one you want to be "kicked", and then run

phenix.maps maps.params

Let me know if you have any questions or problems.

Good luck! Pavel.

On 8/2/10 5:38 PM, [email protected] wrote:

...

Hello,

Disclaimer: I am a newbie to both crystallagraphy and Phenix.

I am running phenix.refine (v1.6-289) in the command line

1. I want to make averaged "kicked-maps" but I keep getting a syntax error. I tried renaming "maps.param" but this file was not recognized.

2. When I enter Phenix.maps into the command line I get a message that syas "not implemented" I am trying to get the latest versiou of phenix installed.

The following is the syntax I put in my custom_params file Thanks

-Yarrow

refinement.main.number_of_macro_cycles = 2 #refinement.main.fix_rotamers = True refinement.refine.strategy = individual_sites+individual_adp refinement.output.prefix = CIN4_refine_omit refinement.output.serial = 12 refinement.output.write_def_file = True refinement.target_weights_wxc.scale = 0.2 refinement.main.max_number_of_interations=15

refinement.electron_density_maps { map { mtz_label_amplitudes = "2FOFCWT_kick" mtz_label_phases = "PH2FOFCWT_kick" likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = True } map { mtz_label_amplitudes = "FOFCWT_kicked" mtz_label_phases = "PHFOFCWT_kicked" likelihood_weighted = True obs_factor = 1 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = false }

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Message: 3 Date: Tue, 3 Aug 2010 07:26:46 -0600 (MDT) From: "Thomas C. Terwilliger" To: "Md. Munan Shaik" Cc: [email protected] Subject: Re: [phenixbb] Phenix Autobuild Message-ID: <[email protected]> Content-Type: text/plain;charset=iso-8859-1

Hi Munan Shaik,

Phenix autobuild can read several types of sequence files, but the basic format is very simple: enter one copy of the sequence of each chain, separated by a blank line or a line starting with ">" between chains. You can optionally add any lines starting with ">" which will be ignored. So here is an example:

...

...

...

alpha subunit (type 1) MTMPYYASAEQIMRDRSELARKGIARGRSVVVLTFRDGVLFVAENPSTALHKVSELYDRL GFAAVGKYNEFENLRRAGIVHADMRGYSYDRRDVTGRSLANAYAQTLGTIFTEQPKPYEV EICVAEVGRVGSPKAPQLYRITYDGSIVDEQHFVVMGGTTEPIATAMRESYRADLDLEAA VGIAVNALRQGGAGEGEKRNVDVASLEVAVLDQSRPRRAFRRIAGTALEQLVPAEPAAAS ESAPEPKPDTETKPADTQD beta subunit (type 1) MTADRPALRTGDRDTRLSFGSNLSSFTDYLRGHAPELLPENRIGHRSHSTRGGDGMESGD LAPHGTTIVALTYKGGVLLAGDRRATQGNLIASRDVEKVYVTDEYSAAGIAGTAGIAIEL VRLFAVELEHYEKIEGVPLTFDGKANRLASMVRGNLGAAMQGLAVVPLLVGYDLDADDES RAGRIVSYDVVGGRYEERAGYHAVGSGSLFAKSALKKIYSPDSDEETALRAAIESLYDAA DDDSATGGPDLTRGIYPTAVTITQAGAVHVSEETTSELARRIVAERTEQGGSAR

Please let me know if that doesn't do it!

All the best, Tom T

...

...

Hi everybody, I have a problem with Phenix autobuild. I want to input sequence file together with the pdb and mtz that I got from molecular replacement. But I have no idea which types of sequence files its required. if anybody please help me out.

thanks =================================================== Md. Munan Shaik Department of Chemical Biology University of Padova via G. Colombo 03 Padova 35131, Italy

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Message: 4 Date: Tue, 3 Aug 2010 15:31:46 +0100 From: Simon Kolstoe To: PHENIX user mailing list Subject: [phenixbb] New version complaint Message-ID: <[email protected]> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

Hi there,

I've been using version 1.6.2-432 on a Macbook and was particularly enjoying the "Show Histograms" button on the POLYGON results page. However today I updated to version 1.6.4-486 using the dmg installer, and that useful option has disappeared! Is there a good reason for the absence of this function, and if not can we get it back?

Thanks,

Simon

--------------------------------------------------------------- Dr Simon Kolstoe Laboratory for Protein Crystallography Centre for Amyloidosis & Acute Phase Proteins UCL Medical School Rowland Hill Street, London NW3 2PF

Tel: 020 7433 2765 http://www.ucl.ac.uk/~rmhasek --------------------------------------------------------------

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Message: 5 Date: Tue, 3 Aug 2010 07:39:11 -0700 From: Nathaniel Echols To: PHENIX user mailing list Subject: Re: [phenixbb] New version complaint Message-ID: Content-Type: text/plain; charset="iso-8859-1"

On Tue, Aug 3, 2010 at 7:31 AM, Simon Kolstoe wrote:

...

I've been using version 1.6.2-432 on a Macbook and was particularly enjoying the "Show Histograms" button on the POLYGON results page. However today I updated to version 1.6.4-486 using the dmg installer, and that useful option has disappeared! Is there a good reason for the absence of this function, and if not can we get it back?

There is a reason, but not a good one. I'll fix it later today. FYI, the "PDB Statistics" tool offers another way to view histograms, although it requires that you manually specify the resolution range.

-Nat