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G Y

13 Oct 2011 13 Oct '11

9:43 a.m.

Dear Experts, I run phaser in phenix with GUI and script using params.eff. For both case, I can not find .sol file in the outputs. What option or command I should used in GUI and params.eff to generate the .sol file in the outputs? Thanks for your kind help! GY

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Nathaniel Echols

13 Oct 13 Oct

11:01 p.m.

On Thu, Oct 13, 2011 at 2:43 AM, G Y wrote:

I run phaser in phenix with GUI and script using params.eff. For both case, I can not find .sol file in the outputs. What option or command I should used in GUI and params.eff to generate the .sol file in the outputs? Thanks for your kind help!

There isn't a way to do this right now - Phaser saves the result as a Python "pickle" file, which encapsulates (among other things) the information contained in the .sol file. When this saved result is loaded back into Phaser the solution information is read directly, without an intermediate file. Does I need to add an option to write out the .sol too? I had assumed there wasn't any information in it that was interpretable by humans. -Nat

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Ed Pozharski

14 Oct 14 Oct

2:01 p.m.

On Thu, 2011-10-13 at 16:01 -0700, Nathaniel Echols wrote:

Does I need to add an option to write out the .sol too? I had assumed there wasn't any information in it that was interpretable by humans.

It lists the angles/shifts that describe the solution. You probably mean that there are ways (in phenix) to deal with phaser without using this file, but it's sure is interpretable. -- "Hurry up before we all come back to our senses!" Julian, King of Lemurs

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G Y

24 Oct 24 Oct

1:15 p.m.

Thank you for your kind answer. In fact, what I need are the euler angles, translation vectors and Z-scores for each solution. I run phenix.phaser from a shell script by phenix.phaser params.eff, not from GUI, still I can not file a .sol file. How can I get those information if there is no .sol file? I found in output log file there are some information like that. But they are not summarized in a nice list and located at different part of the log file which makes it difficult to grep these informations. Is there any easy way to obtain a list for euler angles, translation vectors, Z-socre for all the solutions in a nice format? Thank you again. On Fri, Oct 14, 2011s at 1:01 AM, Nathaniel Echols wrote:

On Thu, Oct 13, 2011 at 2:43 AM, G Y wrote:

...
I run phaser in phenix with GUI and script using params.eff. For both case, I can not find .sol file in the outputs. What option or command I should used in GUI and params.eff to generate the .sol file in the outputs? Thanks for your kind help!

There isn't a way to do this right now - Phaser saves the result as a Python "pickle" file, which encapsulates (among other things) the information contained in the .sol file. When this saved result is loaded back into Phaser the solution information is read directly, without an intermediate file. Does I need to add an option to write out the .sol too? I had assumed there wasn't any information in it that was interpretable by humans.

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

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Nathaniel Echols

3:52 p.m.

On Mon, Oct 24, 2011 at 6:15 AM, G Y wrote:

Thank you for your kind answer. In fact, what I need are the euler angles, translation vectors and Z-scores for each solution. I run phenix.phaser from a shell script by phenix.phaser params.eff, not from GUI, still I can not file a .sol file. How can I get those information if there is no .sol file? I found in output log file there are some information like that. But they are not summarized in a nice list and located at different part of the log file which makes it difficult to grep these informations. Is there any easy way to obtain a list for euler angles, translation vectors, Z-socre for all the solutions in a nice format?

It looks like Airlie just checked in some code to enable this, which I've modified slightly to fit better into the GUI. So, starting tomorrow: phaser.keywords.general.keywords=True will cause it to output the .sol file, which for the very simple example I ran looks like this: # this is the job title SPACEGROUP P 21 21 21 SOLU SET RFZ=16.6 TFZ=27.4 PAK=0 LLG=1362 TFZ==26.9 LLG=1362 SOLU 6DIM ENSE 1l3r EULER 180.199 180.000 0.000 FRAC -0.50025 -0.00071 0.00010 BFAC 0.00000 Does this have everything that you need? -Nat

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G Y

25 Oct 25 Oct

12:45 p.m.

I check this morning again with the phenix version 1.7.2-869, which is download from http://www.phenix-online.org/download/. There is no keyword called keywords under phaser:keywords:general. So, I can not enable it. It seems that version 1.7.2-869 is already the newest one although the marked date is 09-26-2011. What would be the problem? On Fri, Oct 14, 2011 at 1:01 AM, Nathaniel Echols wrote:

On Thu, Oct 13, 2011 at 2:43 AM, G Y wrote:

...
I run phaser in phenix with GUI and script using params.eff. For both case, I can not find .sol file in the outputs. What option or command I should used in GUI and params.eff to generate the .sol file in the outputs? Thanks for your kind help!

There isn't a way to do this right now - Phaser saves the result as a Python "pickle" file, which encapsulates (among other things) the information contained in the .sol file. When this saved result is loaded back into Phaser the solution information is read directly, without an intermediate file. Does I need to add an option to write out the .sol too? I had assumed there wasn't any information in it that was interpretable by humans.

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

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Nathaniel Echols

2:20 p.m.

On Tue, Oct 25, 2011 at 5:45 AM, G Y wrote:

I check this morning again with the phenix version 1.7.2-869, which is download from http://www.phenix-online.org/download/. There is no keyword called keywords under phaser:keywords:general. So, I can not enable it. It seems that version 1.7.2-869 is already the newest one although the marked date is 09-26-2011. What would be the problem?

You need the latest nightly build, dev-892: https://www.phenix-online.org/download/nightly_builds.cgi -Nat

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Randy Read

14 Oct 14 Oct

2:52 p.m.

Hi, Phaser is set up so that if you run it from a script (which is also effectively how it is run from ccp4i), it writes out a .sol file that can be read in as part of the script for a subsequent run. Because it is run from Python in the Phenix GUI, and not from a script, it doesn't write out a .sol file in that circumstance. Instead, the Phaser-MR GUI writes out the equivalent information in a Python pickle file, which can be used in the same way as information for a subsequent run. Advanced users occasionally want to edit the .sol file to do things that hadn't been anticipated. Since I want to do that sometimes myself, I can see why you would want to get the .sol files. On the other hand, most people who understand Phaser well enough to manipulate .sol files also understand how to run it from scripts! That's why we haven't put the ability to read and write .sol files into the Phenix GUI environment. If there's enough of a need, we could either make it possible to read and write .sol files from the Phenix GUI, or perhaps come up with a way to manipulate the contents of the pickle files. Best wishes, Randy Read On 13 Oct 2011, at 10:43, G Y wrote:

Dear Experts,

I run phaser in phenix with GUI and script using params.eff. For both case, I can not find .sol file in the outputs. What option or command I should used in GUI and params.eff to generate the .sol file in the outputs?

Thanks for your kind help!

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

------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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Ed Pozharski
G Y
Nathaniel Echols
Randy Read