Incrementing high resolution cutoff in phenix.mtz2map or phenix.cut_out_density

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Andrew Morin

30 Nov 2016 30 Nov '16

6:21 a.m.

Hello, I am trying to find a convenient way to generate maps using phenix.mtz2map at increasingly greater values of d_min. For example: I have a .mtz file of a structure solved at 2.4A. I run phenix.mtz2map with d_min=none and obtain a map using all of the resolution data. I would like to also create 10 more maps with d_min = 3.4, 4.4, 5.4, 6.4,...12.4A. An mtz of 1.7A would increment at 2.7, 3.7...11.7A, etc. Might anyone know of a handy way to automate this over a large number of mtz files? ALTERNATIVELY - I am performing a phenix.cut_out_density step prior to this. So if it might be easier to automate a incrementing high resolution cutoff in phenix.cut_out_density, that would also work. Thanks for your help. -Andrew

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Pavel Afonine

30 Nov 30 Nov

6:35 a.m.

New subject: Incrementing high resolution cutoff in phenix.mtz2map or phenix.cut_out_density

Hi Andrew, best way is to write a Python script that will use CCTBX to do this. If you know Python and CCTBX then luck is with you! I envisage a page long script that would do everything. If I do it myself that would cost me about 30 minutes or so.. Pavel On 11/29/16 14:21, Andrew Morin wrote:

...

Hello,

I am trying to find a convenient way to generate maps using phenix.mtz2map at increasingly greater values of d_min.

For example:

I have a .mtz file of a structure solved at 2.4A. I run phenix.mtz2map with d_min=none and obtain a map using all of the resolution data. I would like to also create 10 more maps with d_min = 3.4, 4.4, 5.4, 6.4,...12.4A. An mtz of 1.7A would increment at 2.7, 3.7...11.7A, etc.

Might anyone know of a handy way to automate this over a large number of mtz files?

ALTERNATIVELY - I am performing a phenix.cut_out_density step prior to this. So if it might be easier to automate a incrementing high resolution cutoff in phenix.cut_out_density, that would also work.

Thanks for your help.

-Andrew

Tim Gruene

4:16 p.m.

New subject: Incrementing high resolution cutoff in phenix.mtz2map or phenix.cut_out_density

Hi Andrew,

in case you are familiar with scripting, you can use code like

my_d_min=$(mtzdmp  lys2_final.mtz  | grep -A2 "Resolution Range" | tail -n1 | 
awk '{print $6 }')

(all in one line) and use the command line calculator 'bc' to increase 
my_d_min in a loop.

As a remark, I would use equal volumes rather than equal distances, as the 
number of reflections is linear to the volume of the Ewald sphere, not linear 
to the resolution.

Best,
Tim

On Tuesday, November 29, 2016 05:21:56 PM Andrew Morin wrote:
> Hello,
> 
> I am trying to find a convenient way to generate maps using phenix.mtz2map
> at increasingly greater values of d_min.
> 
> For example:
> 
> I have a .mtz file of a structure solved at 2.4A. I run phenix.mtz2map with
> d_min=none and obtain a map using all of the resolution data. I would like
> to also create 10 more maps with d_min = 3.4, 4.4, 5.4, 6.4,...12.4A.
> An mtz of 1.7A would increment at 2.7, 3.7...11.7A, etc.
> 
> Might anyone know of a handy way to automate this over a large number of
> mtz files?
> 
> ALTERNATIVELY - I am performing a phenix.cut_out_density step prior to
> this. So if it might be easier to automate a incrementing high resolution
> cutoff in phenix.cut_out_density, that would also work.
> 
> Thanks for your help.
> 
> -Andrew
-- 
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Dr. Tim Gruene
- persoenlich -
Principal Investigator
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Phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A

Edward A. Berry

1 Dec 1 Dec

1:34 a.m.

New subject: Incrementing high resolution cutoff in phenix.mtz2map or phenix.cut_out_density

I had a related question- is it possible to have env. variables evaluated in an eff file? (Like in cns, {===>} parameter_infile_1="CNS_TOPPAR:protein_rep.param";, CNS_TOPPAR is env var) If not, do command line parameters override what is in the eff file? Like: foreach HIRES ( 2.5 2.4 2.3 2.2 ) phenix.refine refine.eff refinement.xray_data.high_resolution=$HIRES refinement.output.prefix=ref${HIRES} end where the shell (tcsh) would substitute the variables before submitting to phenix? On 11/29/2016 05:21 PM, Andrew Morin wrote:

...

Hello,

I am trying to find a convenient way to generate maps using phenix.mtz2map at increasingly greater values of d_min.

For example:

I have a .mtz file of a structure solved at 2.4A. I run phenix.mtz2map with d_min=none and obtain a map using all of the resolution data. I would like to also create 10 more maps with d_min = 3.4, 4.4, 5.4, 6.4,...12.4A. An mtz of 1.7A would increment at 2.7, 3.7...11.7A, etc.

Might anyone know of a handy way to automate this over a large number of mtz files?

ALTERNATIVELY - I am performing a phenix.cut_out_density step prior to this. So if it might be easier to automate a incrementing high resolution cutoff in phenix.cut_out_density, that would also work.

Thanks for your help.

-Andrew

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Oleg Sobolev

1:47 a.m.

New subject: Incrementing high resolution cutoff in phenix.mtz2map or phenix.cut_out_density

Hi Edward, I had a related question- is it possible to have env. variables evaluated

...

in an eff file? (Like in cns, {===>} parameter_infile_1="CNS_TOPPAR:protein_rep.param";, CNS_TOPPAR is env var)

I'm afraid no.

...

If not, do command line parameters override what is in the eff file? Like:

Yes, whatever is in command-line arguments overrides values in .eff file. I think simple bash/tsch script would be the easiest way to solve the original Andrew's problem. Best regards, Oleg Sobolev.

...

On 11/29/2016 05:21 PM, Andrew Morin wrote:

...
Hello,

I am trying to find a convenient way to generate maps using phenix.mtz2map at increasingly greater values of d_min.

For example:

I have a .mtz file of a structure solved at 2.4A. I run phenix.mtz2map with d_min=none and obtain a map using all of the resolution data. I would like to also create 10 more maps with d_min = 3.4, 4.4, 5.4, 6.4,...12.4A. An mtz of 1.7A would increment at 2.7, 3.7...11.7A, etc.

Might anyone know of a handy way to automate this over a large number of mtz files?

ALTERNATIVELY - I am performing a phenix.cut_out_density step prior to this. So if it might be easier to automate a incrementing high resolution cutoff in phenix.cut_out_density, that would also work.

Thanks for your help.

-Andrew

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Pavel Afonine

1:52 a.m.

New subject: Incrementing high resolution cutoff in phenix.mtz2map or phenix.cut_out_density

As an update: I wrote a Python script that hopefully does what Andrew wanted. The script does not use command line tools (like phenix.something) but instead it is using CCTBX functions directly (90 lines of Python code). Pavel On 11/30/16 09:47, Oleg Sobolev wrote:

...

Hi Edward,

I had a related question- is it possible to have env. variables evaluated in an eff file? (Like in cns, {===>} parameter_infile_1="CNS_TOPPAR:protein_rep.param";, CNS_TOPPAR is env var)

I'm afraid no.

If not, do command line parameters override what is in the eff file? Like:

Yes, whatever is in command-line arguments overrides values in .eff file. I think simple bash/tsch script would be the easiest way to solve the original Andrew's problem.

Best regards, Oleg Sobolev.

On 11/29/2016 05:21 PM, Andrew Morin wrote:

Hello,

I am trying to find a convenient way to generate maps using phenix.mtz2map at increasingly greater values of d_min.

For example:

I have a .mtz file of a structure solved at 2.4A. I run phenix.mtz2map with d_min=none and obtain a map using all of the resolution data. I would like to also create 10 more maps with d_min = 3.4, 4.4, 5.4, 6.4,...12.4A. An mtz of 1.7A would increment at 2.7, 3.7...11.7A, etc.

Might anyone know of a handy way to automate this over a large number of mtz files?

ALTERNATIVELY - I am performing a phenix.cut_out_density step prior to this. So if it might be easier to automate a incrementing high resolution cutoff in phenix.cut_out_density, that would also work.

Thanks for your help.

-Andrew

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participants (5)

Andrew Morin
Edward A. Berry
Oleg Sobolev
Pavel Afonine
Tim Gruene