[phenixbb] follow up on message 2: phenix.maps --Message: not implemented
amadrona at uci.edu
amadrona at uci.edu
Wed Aug 4 13:39:31 PDT 2010
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
>>
>>
>>
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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
>>> -------------- next part --------------
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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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>>> ------------------------------
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>
>>>
>>> End of phenixbb Digest, Vol 57, Issue 2
>>> ***************************************
>>>
>>>
>>
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>
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