Hi Yarrow, you don't have to have admin rights to install PHENIX - you can install it under your own account. So you can do it right now. Pavel. On 8/4/10 1:39 PM, [email protected] wrote:

Thanks Pavel, Unfortunately, I don't have admin privilidges so I will have to wait. Updating phenix appears to be low priority at the moment. Thank you for your help. -Yarrow

Hi Yarrow,

...

have you done what I suggested in my yesterday's email:

update to the latest PHENIX version:

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

?

If not, then please so it and then everything should work.

Pavel.

On 8/3/10 10:57 AM, [email protected] wrote:

...

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)

----------------------------------------------------------------------

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 }

------------------------------

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

------------------------------

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 --------------------------------------------------------------

------------------------------

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

Do you know the correct tar file for Fedora core 10? When I enter "uname -r" in the command line I get: 2.6.27.30-170.2.82.fc10.x86_64 I think this means I am running Fedora Core 10 but I don't see a .tar file for this to download. Will another work? Thanks -Yarrow

On Wed, Aug 4, 2010 at 1:59 PM, Pavel Afonine wrote

you don't have to have admin rights to install PHENIX - you can install

...

it under your own account.

which is done like this (for instance):

./install --prefix=/home/nat/software

You need at least 1.5GB of free space, but you can install it to any directory where you have write permission.

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

Thank you. I can't believe how easy that was. My phenix.maps problem is solved. It works as it should. I was also having a problem in not getting a pdb or mtz to export for wxc optimization (see below) so I will rerun this tonight and hopefully everything will go smoothly. Thanks again. -Yarrow - ============================== Exporting results ============================== Traceback (most recent call last): File "/usr/local/phenix-1.6-289/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.6-289/phenix/phenix/refinement/command_line.py", line 97, in run refine_object.write_refined_pdb(f_pdb) File "/usr/local/phenix-1.6-289/phenix/phenix/refinement/driver.py", line 903, in write_refined_pdb print >> self.log, "Writing refined structure to PDB file:\n %s" % f.name File "/usr/local/phenix-1.6-289/cctbx_project/libtbx/utils.py", line 666, in write file_object.write(str) IOError: [Errno 5] Input/output error

On Wed, Aug 4, 2010 at 3:37 PM, wrote:

...

Do you know the correct tar file for Fedora core 10? When I enter "uname -r" in the command line I get: 2.6.27.30-170.2.82.fc10.x86_64 I think this means I am running Fedora Core 10 but I don't see a .tar file for this to download. Will another work?

Usually, yes (we only very recently started building different 64-bit installers). I'd recommend starting with the fc8 installer.

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

...

Thanks, I run the jobs in the comand line in the background using & after the command. For some reason reason phenix is the only program that still displays even with & which I don't understand. I will try entering "screen_output &"

-Yarrow Thank you. I can't believe how easy that was. My phenix.maps problem

...

is solved. It works as it should. I was also having a problem in not getting a pdb or mtz to export for wxc optimization (see below) so I will rerun this tonight and hopefully everything will go smoothly. Thanks again. ... File "/usr/local/phenix-1.6-289/cctbx_project/libtbx/utils.py", line 666, in write file_object.write(str) IOError: [Errno 5] Input/output error

This probably means you lost your "stdout" or "stderr", e.g. by starting phenix.refine and then closing the terminal window or GUI. In case you run from the command line and anticipate your terminal window may not survive the entire run, it is best done like this:

phenix.refine some.pdb some.mtz some.params >& screen_output &

If it happens when running from the GUI Nat may have more to say.

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

You can prepend your command with nohup: nohup my_command & All outputs will go to the nohup.out file. Even if you log out of the machine or your xterm is closed, your command will continue to run until it finishes or is killed by someone. This is a good practice for long running calculations. Regards. F. [email protected] wrote:

...

...

Thanks, I run the jobs in the comand line in the background using & after the command. For some reason reason phenix is the only program that still displays even with & which I don't understand. I will try entering "screen_output &"

-Yarrow

Thank you. I can't believe how easy that was. My phenix.maps problem

...

...

is solved. It works as it should. I was also having a problem in not getting a pdb or mtz to export for wxc optimization (see below) so I will rerun this tonight and hopefully everything will go smoothly. Thanks again. ... File "/usr/local/phenix-1.6-289/cctbx_project/libtbx/utils.py", line 666, in write file_object.write(str) IOError: [Errno 5] Input/output error This probably means you lost your "stdout" or "stderr", e.g. by starting phenix.refine and then closing the terminal window or GUI. In case you run from the command line and anticipate your terminal window may not survive the entire run, it is best done like this:

phenix.refine some.pdb some.mtz some.params >& screen_output &

If it happens when running from the GUI Nat may have more to say.

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

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

In case the "problem" is related to 64 vs 32 bit installation, the only 32 bit installer is for Fedora core 3 and it works... If I remember correctly (that it was indeed fc3) Fred. [email protected] wrote:

Do you know the correct tar file for Fedora core 10? When I enter "uname -r" in the command line I get: 2.6.27.30-170.2.82.fc10.x86_64 I think this means I am running Fedora Core 10 but I don't see a .tar file for this to download. Will another work?

Thanks

-Yarrow

...

On Wed, Aug 4, 2010 at 1:59 PM, Pavel Afonine wrote

you don't have to have admin rights to install PHENIX - you can install

...

...

it under your own account.

which is done like this (for instance):

./install --prefix=/home/nat/software

You need at least 1.5GB of free space, but you can install it to any directory where you have write permission.

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

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