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

4 Aug 2010

      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