[phenixbb] Adequate size for Free R test set?

Joseph Noel noel at salk.edu
Tue Aug 3 11:21:33 PDT 2010


Pavel,

Thanks so much for the suggestions. They are really helpful! A few questions relative to Phenix. Is there a way to check with Phenix the thin resolution shells? I created Free Rs in Phenix using the thin resolution shells options but removed the 2000 limit and instead used 5%. Maybe I over-did it relative to your reply. Just wondering how to check each of these thin shells. Alternatively, does Phenix ensure one has an adequate number of test reflections in each "thin shell" if this option is set? If so, what should I used for the maximum number of reflections and/or %?

Thanks again!

Joe
___________________________________________________________
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
___________________________________________________________

On Aug 3, 2010, at 11:02 AM, phenixbb-request at phenix-online.org wrote:

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> 
> Today's Topics:
> 
>   1. Re: Adequate size for Free R test set? (Pavel Afonine)
>   2. Re: follow up on message 2: phenix.maps --Message: not
>      implemented (amadrona at uci.edu)
>   3. Re: follow up on message 2: phenix.maps --Message: not
>      implemented (Pavel Afonine)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Tue, 03 Aug 2010 10:38:57 -0700
> From: Pavel Afonine <pafonine at lbl.gov>
> To: phenixbb at phenix-online.org
> Cc: Joseph Noel <noel at salk.edu>
> Subject: Re: [phenixbb] Adequate size for Free R test set?
> Message-ID: <4C585431.7000107 at lbl.gov>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
> 
>  Hi Joe,
> 
> I think almost every one has his/her own opinion on this... Here is what 
> I think:
> 
> 1) The test set should be such that each "relatively thin resolution 
> shell" receives at least 50 reflections, and we empirically found that 
> 150 is "good enough" withing phenix.refine framework.
> For "relatively thin resolution shell" definition see:
> Lunin & Skovoroda. Acta Cryst. (1995). A51, 880-887. "R-free 
> likelihood-based estimates of errors for phases calculated from atomic 
> models".
> 
> This basically defines how many test reflections you need.
> 
> 2) It is customary to set aside either 5 or 10% for test set, with the 
> total maximum 2000. These are all "magic numbers", that I presume more 
> or less satisfy "1)" so they became widely used.
> 
> 3) Presence of high-order NCS and selecting free-flags using "thin 
> shells" algorithm is a different story (Acta Cryst. (2006). D62, 
> 227--238). It is good to do that because it removes the cross-talk 
> between test and work reflections due to NCS, but at the same time it 
> invalidates the requirement "1)". So, this is a gray area (for me at least).
> 
> 4) Some people believe that the final refinement run should be done 
> using all reflections, arguing that taking away 5-10% of test 
> reflections worsens the maps. There is some truth in this, yes, removing 
> the data worsens the maps, but:
> a) it is noticeable (in a sense that it can reduce the interpretability 
> of some parts of the map) only in extreme cases of somewhat low 
> resolution or low completeness data, b) in most of all other cases it is 
> simply negligible, c) removing reflections randomly has much smaller 
> effect than removing them systematically (see page #40 here: 
> http://www.phenix-online.org/presentations/latest/pavel_maps.pdf and 
> some relevant references in 2010 PHENIX paper in Acta D). However, if 
> you do that "final run", you will invalidate the final refinement 
> statistics, Rfree and Rwork, and thus obtained final structure cannot 
> have the Rfree associated with it anymore.
> 
> Pavel.
> 
> 
> On 8/3/10 10:04 AM, Joseph Noel wrote:
>> 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 <mailto: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
>> ___________________________________________________________
>> 
>> 
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
> 
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> 
> ------------------------------
> 
> Message: 2
> Date: Tue, 3 Aug 2010 10:57:42 -0700
> From: amadrona at uci.edu
> To: phenixbb at phenix-online.org
> Subject: Re: [phenixbb] follow up on message 2: phenix.maps --Message:
> 	not	implemented
> Message-ID:
> 	<7954f99137ed98eb19a6d4a5c08f8e20.squirrel at webmail.uci.edu>
> Content-Type: text/plain;charset=iso-8859-1
> 
> 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 --------------
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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
>> ___________________________________________________________
>> 
>> -------------- next part --------------
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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
>> ***************************************
>> 
>> 
> 
> 
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Tue, 03 Aug 2010 11:01:47 -0700
> From: Pavel Afonine <pafonine at lbl.gov>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] follow up on message 2: phenix.maps --Message:
> 	not implemented
> Message-ID: <4C58598B.6060804 at lbl.gov>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
>  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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>>> When replying, please edit your Subject line so it is more specific
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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
>>> -------------- next part --------------
>>> An HTML attachment was scrubbed...
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>>> <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 --------------
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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
>>> ___________________________________________________________
>>> 
>>> -------------- next part --------------
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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
>>> ***************************************
>>> 
>>> 
>> 
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
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