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

amadrona at uci.edu amadrona at uci.edu
Tue Aug 3 10:57:42 PDT 2010


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 (amadrona at uci.edu)
>    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: amadrona at uci.edu
> To: phenixbb at phenix-online.org
> Subject: [phenixbb] syntax for Averaged Kicked maps and maps.param
> Message-ID:
> 	<c56fb1561f816b0462d50ccdeb996317.squirrel at webmail.uci.edu>
> 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 <pafonine at lbl.gov>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] syntax for Averaged Kicked maps and maps.param
> Message-ID: <4C57676D.9000901 at lbl.gov>
> 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, amadrona at uci.edu 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
>> }
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 3 Aug 2010 07:26:46 -0600 (MDT)
> From: "Thomas C. Terwilliger" <terwilliger at lanl.gov>
> To: "Md. Munan Shaik" <munanbt2004 at YAHOO.COM>
> Cc: phenixbb at phenix-online.org
> Subject: Re: [phenixbb] Phenix Autobuild
> Message-ID: <24375.128.165.0.81.1280842006.squirrel at webmail.lanl.gov>
> 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 <s.kolstoe at ucl.ac.uk>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: [phenixbb] New version complaint
> Message-ID: <8976EDFE-4E7E-42FD-96FE-319B56DE5413 at ucl.ac.uk>
> 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 <nechols at lbl.gov>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] New version complaint
> Message-ID:
> 	<AANLkTikU_SS2Z2VU0aZuqRNgrYUiiXLCTfztYy7NZjOF at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On Tue, Aug 3, 2010 at 7:31 AM, Simon Kolstoe <s.kolstoe at ucl.ac.uk> 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
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> ------------------------------
>
> Message: 6
> Date: Tue, 03 Aug 2010 10:41:10 -0400
> From: Douglas Jacobsen <djacobse at umich.edu>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] New version complaint
> Message-ID: <4C582A86.20303 at umich.edu>
> Content-Type: text/plain; charset="iso-8859-1"
>
>  On the linux version, the polygon works for me - but phenix.reel (both
> command line and GUI) crash.  I have tried this on two linux systems
> (RHEL 4 - has to be compiled - glibc too old; and an up-to-date gentoo
> box - has to be compiled - glibc too new).
> -Doug
>
> Douglas Jacobsen
> djacobse at umich.edu
>
> ------------- __o
> ---------- _ '\<,_
> ----------(_)/  (_)__________________________
>
>
>
> On 8/3/10 10:31 AM, Simon Kolstoe wrote:
>> 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
>> --------------------------------------------------------------
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
>>
>
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> ------------------------------
>
> Message: 7
> Date: Tue, 3 Aug 2010 09:58:04 -0700
> From: Nathaniel Echols <nechols at lbl.gov>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] New version complaint
> Message-ID:
> 	<AANLkTinhj+MAZbvYMDtV3d=AR=BSn7japF288yW4xaON at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On Tue, Aug 3, 2010 at 7:41 AM, Douglas Jacobsen <djacobse at umich.edu>
> wrote:
>
>>  On the linux version, the polygon works for me - but phenix.reel (both
>> command line and GUI) crash.  I have tried this on two linux systems
>> (RHEL 4 - has to be compiled - glibc too old; and an up-to-date gentoo
>> box - has to be compiled - glibc too new).
>>
>
> By "crash", do you mean "suddenly dies without explanation", or "prints
> out/pops up an error and quits"?  I suspect it is an OpenGL problem - this
> is not uncommon on Linux, unfortunately.  Could you please send me the
> output of the command 'glxinfo'?
>
> thanks,
> Nat
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> ------------------------------
>
> Message: 8
> Date: Tue, 3 Aug 2010 10:04:41 -0700
> From: Joseph Noel <noel at salk.edu>
> To: phenixbb at phenix-online.org
> Subject: [phenixbb] Adequate size for Free R test set?
> Message-ID: <257DBAE2-D059-43E4-96F3-B7768711839E at salk.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Folks,
>
> Its been a while since I personally refined many structures. In the past,
> I used as a default, 5% of my unique reflections for the Free R test set.
> I have a high resolution structure with 150,000 unique reflections and
> noticed that Phenix defaults are 5% or 2000 reflections which ever is
> smaller. What is the current consensus on an adequate number of unique
> reflections to use for cross-validation?
>
> Thanks!
> Joe
>
> P.S. I really, really love Phenix.
> ___________________________________________________________
> Joseph P. Noel, Ph.D.
> Investigator, Howard Hughes Medical Institute
> Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics
> The Salk Institute for Biological Studies
> 10010 North Torrey Pines Road
> La Jolla, CA  92037 USA
>
> Phone: (858) 453-4100 extension 1442
> Cell: (858) 349-4700
> Fax: (858) 597-0855
> E-mail: noel at salk.edu
>
> Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37
> Web Site (HHMI): http://hhmi.org/research/investigators/noel.html
> ___________________________________________________________
>
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>
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