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

Pavel Afonine pafonine at lbl.gov
Wed Aug 4 13:59:30 PDT 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, amadrona at uci.edu 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, 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
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
>>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb




More information about the phenixbb mailing list