Hi, I am trying to find the answer to a question that was discussed long time ago at this forum, but there is no mechanism to find old discussions. You have to go through each month and figure out from the subjects where was a particular discussion. Could you, the phenix team, make it easier to find answers to those questions that had been answered previously. I remember, there was a question how to generate maps without refinement. I finished the refinement, but I need a map (in explor format) to show the 2fo-fc density in the publication. Maia Pavel Afonine wrote:

Hi Tirumala,

I agree, you are not the first who confused by this and an example right in the message would help.

First, your MTZ file contains the following data: (FP,SIGFP) and (Fav,SIGFav) and it is your choice to select the one that you want to use in refinement.

Second, once decided on the data - for example it is FP, then just add to your command line this:

refinement.input.xray_data.labels=FP

or, which is the same

xray_data.labels="FP,SIGFP"

Pavel.

On 9/9/09 11:10 AM, Tirumala Kumar Chowdary wrote:

...

Hi,

I am trying to run phenix.refine with a sharp output MTZ file (column labels H K L NUMORB FB PHIB FOM HX HY FH PHIH FP SIGFP HLA HLB HLC HLD HL0 Fcent PHIcent FOMcent Fmap PHImap FHref PHIHref Fav SIGFav).

Phenix.refine stopped at

'Multiple equally suitable arrays of observed xray data found.

Possible choices: sharp_sad_se_eden.mtz:FP,SIGFP sharp_sad_se_eden.mtz:Fav,SIGFav

Please use refinement.input.xray_data.labels'

Can someone tell me on how to use this 'refinement.input.xray_data.labels' and how to specify which column labels to use. There is nothing written in the documentation about it.

Thanks Tirumal

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I believe macro_cycles =0 in phenix.refine will give you only 2fo-fc. its in the section where one can ordered_solvent and simulated annealing. FR On Sep 9, 2009, at 1:22 PM, Maia Cherney wrote:

Hi,

I am trying to find the answer to a question that was discussed long time ago at this forum, but there is no mechanism to find old discussions.

You have to go through each month and figure out from the subjects where was a particular discussion.

Could you, the phenix team, make it easier to find answers to those questions that had been answered previously.

I remember, there was a question how to generate maps without refinement. I finished the refinement, but I need a map (in explor format) to show the 2fo-fc density in the publication.

Maia

Pavel Afonine wrote:

...

Hi Tirumala,

I agree, you are not the first who confused by this and an example right in the message would help.

First, your MTZ file contains the following data: (FP,SIGFP) and (Fav,SIGFav) and it is your choice to select the one that you want to use in refinement.

Second, once decided on the data - for example it is FP, then just add to your command line this:

refinement.input.xray_data.labels=FP

or, which is the same

xray_data.labels="FP,SIGFP"

Pavel.

On 9/9/09 11:10 AM, Tirumala Kumar Chowdary wrote:

...

Hi,

I am trying to run phenix.refine with a sharp output MTZ file (column labels H K L NUMORB FB PHIB FOM HX HY FH PHIH FP SIGFP HLA HLB HLC HLD HL0 Fcent PHIcent FOMcent Fmap PHImap FHref PHIHref Fav SIGFav).

Phenix.refine stopped at

'Multiple equally suitable arrays of observed xray data found.

Possible choices: sharp_sad_se_eden.mtz:FP,SIGFP sharp_sad_se_eden.mtz:Fav,SIGFav

Please use refinement.input.xray_data.labels'

Can someone tell me on how to use this 'refinement.input.xray_data.labels' and how to specify which column labels to use. There is nothing written in the documentation about it.

Thanks Tirumal

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--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

Hi Maia, 1) You can use phenix.refine for this: phenix.refine model.pdb data.mtz strategy=none main.number_of_macro_cycles=1 output.prefix=maps_only Remarks: - you need to use strategy=none to tell phenix.refine to not refine atomic parameters (such as B-factors, coordinates, etc.); - you need to use "main.number_of_macro_cycles=1" (or its shortcut "main.number_of_mac=1"), so phenix.refine does bulk-solvent correction and anisotropic scaling, which is critical to get good maps. - of course, in twin-refinement, you also need to append a twin law to the above command, for example: phenix.refine model.pdb data.mtz strategy=none main.number_of_macro_cycles=1 output.prefix=maps_only twin_law="k,-k,-l" 2) You can use new PHENIX GUI for this, just type: phenix.create_maps 3) Recent version of phenix.model_vs_data has "--map" keyword: phenix.model_vs_data model.pdb data.mtz --map="2mFo-DFc" Pavel.

I remember, there was a question how to generate maps without refinement. I finished the refinement, but I need a map (in explor format) to show the 2fo-fc density in the publication.

Hi Maia,

...

This is the example from the website:

Run AutoMR using coords.pdb as search model, native.sca as data, assume RMS between coords.pdb and true model is about 0.85 A, the sequence of true model is seq.dat and there is 1 copy in the unit cell:

phenix.automr coords.pdb native.sca RMS=0.85 seq.dat copies=1 \ n_cycle_rebuild_max=2 n_cycle_build_max=2

1. 1 copy of what: model.pdb or seq.dat? Model.pdb could be a dimer and seq.dat a monomer.

In this example we are assuming that model.pdb is a monomer and seq.dat is the sequence of that monomer.

...

2. 1 copy in the unit cell. Is it really in the unit cell? Usually we use number of copies in the asymmetric unit.

That one is a very bad typo. Yes, I meant one in the asymmetric unit. I have just fixed that in the documentation... All the best, Tom T

Hi Maia, The "copies" keyword is a shorthand for convenience in the common case that both your model and the sequence refer to a monomer, and what it does is set two separate keywords, copies_to_find and component_copies, to the same value. If you want to set these separately (e.g. you're searching for one copy of a dimer but your sequence is for the monomer), then you should be able to say "copies_to_find=1 component_copies=2". Regards, Randy On 12 Sep 2009, at 01:56, Maia Cherney wrote:

Hi Tom, thank you for your reply. Still, the first question remains, if a model has two identical copies, but the sequence is for a monomer, what number of copies should I use: of model or of monomers?

Maia

Thomas C. Terwilliger wrote:

...

Hi Maia,

...

...

This is the example from the website:

Run AutoMR using coords.pdb as search model, native.sca as data, assume RMS between coords.pdb and true model is about 0.85 A, the sequence of true model is seq.dat and there is 1 copy in the unit cell:

phenix.automr coords.pdb native.sca RMS=0.85 seq.dat copies=1 \ n_cycle_rebuild_max=2 n_cycle_build_max=2

1. 1 copy of what: model.pdb or seq.dat? Model.pdb could be a dimer and seq.dat a monomer.

In this example we are assuming that model.pdb is a monomer and seq.dat is the sequence of that monomer.

...

...

2. 1 copy in the unit cell. Is it really in the unit cell? Usually we use number of copies in the asymmetric unit.

That one is a very bad typo. Yes, I meant one in the asymmetric unit. I have just fixed that in the documentation...

All the best, Tom T

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------ 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

Hi, I noticed that if you run phenix in the background, you cannot close the terminal. Otherwise, the job stops. I want to run a job remotely in the background and then put my computer to sleep. Did not work. The remote job stopped when I put my computer to sleep. Maia

Hi, I want to suppress some maps. I type in the .def file: suppress = "2FOFCWT_no_fill" suppress = "FOFCWT_no_fill" but I get only first map suppressed. What is the correct syntax for two maps? Maia

Maia Cherney wrote:

Hi, I want to suppress some maps. I type in the .def file:

suppress = "2FOFCWT_no_fill" suppress = "FOFCWT_no_fill"

but I get only first map suppressed. What is the correct syntax for two maps?

Maia

Put both strings on the same line: suppress = "2FOFCWT_no_fill" "FOFCWT_no_fill" There is an inconsistency here, because different parameters with type=strings are handled differently. For Fobs labels, two strings are written as a comma-separated list, which does not work for the suppress parameter. Joe Krahn

You can also use 'screen' to launch unix jobs in the background and you'll be able to close the terminal. You will, however, not be able to put your computer to sleep as most sleep modes halt the computer hardware. cheers FR On Sep 17, 2009, at 12:27 PM, Maia Cherney wrote:

Hi,

I noticed that if you run phenix in the background, you cannot close the terminal. Otherwise, the job stops. I want to run a job remotely in the background and then put my computer to sleep. Did not work. The remote job stopped when I put my computer to sleep.

Maia

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--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

Hi Maia, I can even close my laptop and open it and phenix starts running where it was. I can run jobs remotely and log out just fine. Are you sure you are running your job like this: Something like phenix.refine bla bla bla > refine.log &

is for directing the output from the default [usually the terminal] to a someplace else, like a log file. & is for running a job in the background.

Engin On 9/17/09 11:39 AM, Francis E Reyes wrote:

You can also use 'screen' to launch unix jobs in the background and you'll be able to close the terminal.

You will, however, not be able to put your computer to sleep as most sleep modes halt the computer hardware.

cheers

FR

On Sep 17, 2009, at 12:27 PM, Maia Cherney wrote:

...

Hi,

I noticed that if you run phenix in the background, you cannot close the terminal. Otherwise, the job stops. I want to run a job remotely in the background and then put my computer to sleep. Did not work. The remote job stopped when I put my computer to sleep.

Maia

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8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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-- Engin Özkan Post-doctoral Scholar Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111

On Thu, 17 Sep 2009, Maia Cherney wrote:

I did not do the > refine.log thing, as I always get log files

program-that-makes-output > /dev/null -bryan

I run phenix from home on machines at work. Some jobs take a lot of time and I want to put my home computer to sleep. Will the nohup or screen help me? How to use them? I have an ubuntou linux at home and at work. Phenix.refine stopped when I put the job in the background and closed the terminal and put my home computer to sleep. Interestingly, the remote job did not stop at once, it ran a bit longer and stopped later. I will check again about the way I logged out of the remote session. Folmer Fredslund wrote:

Dear Maia

2009/9/17 Maia Cherney :

...

Hi,

I noticed that if you run phenix in the background, you cannot close the terminal. Otherwise, the job stops. I want to run a job remotely in the background and then put my computer to sleep. Did not work. The remote job stopped when I put my computer to sleep.

If you by "remote" mean on another machine try the nohup command.

Regards, Folmer Fredslund

...

Maia

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