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

Pavel Afonine pafonine at lbl.gov
Tue Aug 3 11:01:47 PDT 2010


  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, amadrona at uci.edu 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
>
>
>
>> Send phenixbb mailing list submissions to
>> 	phenixbb at phenix-online.org
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> 	http://phenix-online.org/mailman/listinfo/phenixbb
>> or, via email, send a message with subject or body 'help' to
>> 	phenixbb-request at phenix-online.org
>>
>> You can reach the person managing the list at
>> 	phenixbb-owner at phenix-online.org
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of phenixbb digest..."
>>
>>
>> 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
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL:
>> <http://phenix-online.org/pipermail/phenixbb/attachments/20100803/218ee6c8/attachment-0001.htm>
>>
>> ------------------------------
>>
>> 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
>>>
>>>
>> -------------- next part --------------
>> A non-text attachment was scrubbed...
>> Name: signature.asc
>> Type: application/pgp-signature
>> Size: 299 bytes
>> Desc: OpenPGP digital signature
>> URL:
>> <http://phenix-online.org/pipermail/phenixbb/attachments/20100803/f4201d5a/attachment-0001.sig>
>>
>> ------------------------------
>>
>> 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
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL:
>> <http://phenix-online.org/pipermail/phenixbb/attachments/20100803/3b7d7206/attachment-0001.htm>
>>
>> ------------------------------
>>
>> 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
>> ___________________________________________________________
>>
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL:
>> <http://phenix-online.org/pipermail/phenixbb/attachments/20100803/daf35b34/attachment.htm>
>>
>> ------------------------------
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
>>
>> End of phenixbb Digest, Vol 57, Issue 2
>> ***************************************
>>
>>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb




More information about the phenixbb mailing list