[phenixbb] ADP restraints - distance power, average power, etc

Joseph Noel noel at salk.edu
Mon Dec 20 12:19:29 PST 2010


Dear Ed,

Thanks so much for the suggestion about REFMAC but I seemed to have found out the issue. The positive density on Met sulfurs and backbone carbonyls and amide NHs does not appear when I calculate a "normal" sigmaa weighted mFo-dFc map. The positive density was appearing only when I checked the kicked map option. So the "extra" density seems to be due to generating kicked maps. Sorry about the confusion related to the sigma level. Just meant that the positive density was not insignificant in the kicked mFo-dFc maps. Density was visible on these specific areas starting around 3.5-4.0 sigma and visible in several places contoured up to 8 sigma.

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 Dec 20, 2010, at 12:00 PM, phenixbb-request at phenix-online.org wrote:

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> Today's Topics:
> 
>   1. ADP restraints - distance power, average power, etc (Joseph Noel)
>   2. Re: ADP restraints - distance power, average power, etc
>      (Ralf W. Grosse-Kunstleve)
>   3. Re: ADP restraints - distance power, average power, etc
>      (Pavel Afonine)
>   4. Secondary structure restraints - where to specify file	using
>      GUI? (Luke Rice)
>   5. Re: Secondary structure restraints - where to specify file
>      using GUI? (Nathaniel Echols)
>   6. Re: ADP restraints - distance power, average power, etc
>      (Joseph Noel)
>   7. Re: ADP restraints - distance power, average power, etc
>      (Joseph Noel)
>   8. Re: ADP restraints - distance power, average power, etc
>      (Ed Pozharski)
>   9. Re: Secondary structure restraints - where to specify file
>      using GUI? (Luke Rice)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Sun, 19 Dec 2010 12:58:43 -0800
> From: Joseph Noel <noel at salk.edu>
> To: phenixbb at phenix-online.org
> Subject: [phenixbb] ADP restraints - distance power, average power,
> 	etc
> Message-ID: <2E132727-1B34-4ED5-98DA-2210B7D1FF48 at salk.edu>
> Content-Type: text/plain; charset="us-ascii"
> 
> Hi All,
> 
> I am refining a very well ordered structure at 1.45 A and find that after doing just about everything including optimization of weights, etc that there are still areas of positive density residing over S atoms of Met, backbone atoms, etc. I have added hydrogens and used them during refinement as well. The maps are of a high quality and Free R factors are quite good, ~ 17%. Is there anything that can be played with more such as values used in the ADP restraints window to try and achieve a difference map with far fewer areas of significant positive density (all greater then or equal to 4 sigma)?
> 
> I am not sure exactly what effect the values of distance power, average power, etc will have on refinement. The other option I was thinking of was the scattering table options. I have other structures of this protein that extend to about 1.2.
> 
> Thanks!
> 
> 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
> ___________________________________________________________
> 
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> 
> ------------------------------
> 
> Message: 2
> Date: Sun, 19 Dec 2010 14:55:12 -0800 (PST)
> From: "Ralf W. Grosse-Kunstleve" <rwgk at yahoo.com>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] ADP restraints - distance power, average
> 	power, etc
> Message-ID: <40149.44857.qm at web111416.mail.gq1.yahoo.com>
> Content-Type: text/plain; charset="us-ascii"
> 
> Hi Joe,
> Below are some notes regarding our ADP restraints. At your resolution the 
> defaults may be too tight.
> The choice of scattering table shouldn't matter, except for small runtime 
> differences. (You can find some notes here:
> http://cci.lbl.gov/publications/download/iucrcompcomm_jan2004.pdf
> section 4.)
> Ralf
> 
> We use "local sphere restraints".
> 
>  adp_restraints {
>    iso {
>      sphere_radius = 5.0
>      distance_power = 1.69
>      average_power = 1.03
>    }
>  }
> 
> The basic idea is to restrain each adp to the average of all its
> neighbors within a sphere of a given radius (sphere_radius = 5). The
> contribution to the refinement target function is:
> 
>                                   (u_i - u_j)**2
>  1 / (r_ij ** distance_power) * ----------------------------------
>                                  ((u_i + u_j)/2) ** average_power
> 
> These terms are computed over a double sum: loop over each atom, loop
> over all neighbors of the atom. I'm not sure anymore how exactly we
> arrived at distance_power = 1.69 and average_power = 1.03.
> You can try different values for distance_power to change the
> tightness of the restraints as a function of the distance of
> a pair of atoms. The average_power links the tightness to the
> absolute value of the adp; average_power=0 turns this feature off.
> 
> There are some remarks about this in the "ADP refinement" section in
> this old newsletter article:
> 
>  http://www.phenix-online.org/papers/ccp4_july_2005_afonine.pdf
> 
> The formulas are a bit different (above is current), but the ideas
> still apply.
> 
> 
> 
>> 
>> From: Joseph Noel <noel at salk.edu>
>> To: phenixbb at phenix-online.org
>> Sent: Sun, December 19, 2010 12:58:43 PM
>> Subject: [phenixbb] ADP restraints - distance power, average power, etc
>> 
>> Hi All,
>> 
>> 
>> I am refining a very well ordered structure at 1.45 A and find that after doing 
>> just about everything including optimization of weights, etc that there are 
>> still areas of positive density residing over S atoms of Met, backbone atoms, 
>> etc. I have added hydrogens and used them during refinement as well. The maps 
>> are of a high quality and Free R factors are quite good, ~ 17%. Is there 
>> anything that can be played with more such as values used in the ADP restraints 
>> window to try and achieve a difference map with far fewer areas of significant 
>> positive density (all greater then or equal to 4 sigma)?
>> 
>> 
>> I am not sure exactly what effect the values of distance power, average power, 
>> etc will have on refinement. The other option I was thinking of was the 
>> scattering table options. I have other structures of this protein that extend to 
>> about 1.2.
>> 
>> 
>> Thanks!
>> 
>> 
>> 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
>> ___________________________________________________________
>> 
>> 
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> ------------------------------
> 
> Message: 3
> Date: Sun, 19 Dec 2010 17:12:43 -0800
> From: Pavel Afonine <pafonine at lbl.gov>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Cc: Joseph Noel <noel at salk.edu>
> Subject: Re: [phenixbb] ADP restraints - distance power, average
> 	power, etc
> Message-ID: <4D0EAD8B.5090604 at lbl.gov>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
>  Hi Joe,
> 
> at 1.45A resolution it is most likely the best to refine individual 
> anisotropic ADPs using phenix.refine (anisotropic for macro-molecule and 
> isotropic for the solvent). In that case the "local sphere restraints" 
> are not used ("local sphere restraints" are used in individual isotropic 
> ADP refinement only). All the relevant details are here:
> 
> see "On atomic displacement parameters (ADP) and their parametrization 
> in PHENIX" article:
> 
> http://www.phenix-online.org/newsletter/
> 
> I'm almost sure that refining isotropic ADPs instead of anisotropic 
> causes these residual densities around atoms. It's known effect and I 
> recall seeing it in at least two papers.
> 
> Another things to check:
> 
> - is it Met, or Se-Met?
> - radiation damage? Try refining occupancies of S. Although you said 
> it's not only S, so may be not.
> 
> Good luck!
> Pavel.
> 
>> I am refining a very well ordered structure at 1.45 A and find that 
>> after doing just about everything including optimization of weights, 
>> etc that there are still areas of positive density residing over S 
>> atoms of Met, backbone atoms, etc. I have added hydrogens and used 
>> them during refinement as well. The maps are of a high quality and 
>> Free R factors are quite good, ~ 17%. Is there anything that can be 
>> played with more such as values used in the ADP restraints window to 
>> try and achieve a difference map with far fewer areas of significant 
>> positive density (all greater then or equal to 4 sigma)?
>> 
>> I am not sure exactly what effect the values of distance power, 
>> average power, etc will have on refinement. The other option I was 
>> thinking of was the scattering table options. I have other structures 
>> of this protein that extend to about 1.2.
> 
> 
> ------------------------------
> 
> Message: 4
> Date: Mon, 20 Dec 2010 09:43:00 -0600
> From: Luke Rice <luke.rice at utsouthwestern.edu>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: [phenixbb] Secondary structure restraints - where to specify
> 	file	using GUI?
> Message-ID: <4D0F7984.5050505 at utsouthwestern.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> 
> Hi All,
> 
> I am trying to evaluate whether or not secondary structure restraints 
> are going to help me with the refinement I am working on. When I ran in 
> 'auto' mode, I noticed that by default phenix specifies several 
> a-helices as 3_10. So, I would like to use an edited list of secondary 
> structure restraints.
> 
> Can I specify this file in the GUI? (Like Joe Noel, I, too, have become 
> soft). I looked in what I thought to be the obvious places and did not 
> turn anything up.
> 
> Thanks for any help,
> 
> Luke
> 
> 
> 
> -- 
> Luke M. Rice
> Assistant Professor and
> Thomas O. Hicks Scholar in Medical Research
> Department of Biochemistry, ND10.300
> UT Southwestern Medical Center
> 5323 Harry Hines Blvd.
> Dallas, TX 75390-8816
> phone: (214) 645-5931
> email: Luke.Rice at UTSouthwestern.edu
> 
> 
> ------------------------------
> 
> Message: 5
> Date: Mon, 20 Dec 2010 08:09:59 -0800
> From: Nathaniel Echols <nechols at lbl.gov>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] Secondary structure restraints - where to
> 	specify file using GUI?
> Message-ID:
> 	<AANLkTik8gYTDHm7bxG0AqouzGegv7Di72Ur7Abr5M1q=@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> On Mon, Dec 20, 2010 at 7:43 AM, Luke Rice <luke.rice at utsouthwestern.edu> wrote:
>> I am trying to evaluate whether or not secondary structure restraints are
>> going to help me with the refinement I am working on. When I ran in 'auto'
>> mode, I noticed that by default phenix specifies several a-helices as 3_10.
>> So, I would like to use an edited list of secondary structure restraints.
> 
> Interesting, usually it's the reverse problem (3_10 helices annotated
> as alpha) - but the annotation program can be a little twitchy.  I had
> intended for this to be graphically editable, but now that I've
> checked I see there's no way to actually change the helix type in the
> GUI.  Will fix that soon.
> 
>> Can I specify this file in the GUI? (Like Joe Noel, I, too, have become
>> soft). I looked in what I thought to be the obvious places and did not turn
>> anything up.
> 
> You can just drag it into the main input file list.  Any parameter
> file may be used this way, with the caveat that the GUI will not
> actually display the parameters it contains (but they will be
> incorporated into the final config file).  For this reason I recommend
> against using complete .eff or .def files from command line runs, but
> the output of phenix.secondary_structure_restraints (or the edited
> version thereof) is pretty safe.
> 
> Alternately, if you drag the parameter file onto the phenix.refine
> icon in the main GUI and release the mouse button, it should launch
> the phenix.refine GUI with all parameters in the file loaded in
> displayed in the GUI.  (Since this isn't very obvious, I'll add a menu
> item somewhere to do the same thing less opaquely.)
> 
> -Nat
> 
> 
> ------------------------------
> 
> Message: 6
> Date: Mon, 20 Dec 2010 09:06:56 -0800
> From: Joseph Noel <noel at salk.edu>
> To: Pavel Afonine <pafonine at lbl.gov>
> Cc: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] ADP restraints - distance power, average
> 	power, etc
> Message-ID: <A1DA442C-A869-4EE3-84C0-F56F93679736 at salk.edu>
> Content-Type: text/plain; charset=us-ascii
> 
> Hi Pavel,
> 
> I've refined individual ADPs (anisotropic for the protein and isotropic for solvent). Still quite a bit of positive density on methionine sulfurs and most carbonyls. They start around 7.5 sigma and extend to 4 sigma. There are no other Fo-Fc peaks appearing for solvent yet to be modeled, etc. so maybe I should play with ADP weights. All positive density is appearing on atoms with occupancies of 1 so not much more I can do to lower the positive density. 
> 
> 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 Dec 19, 2010, at 5:12 PM, Pavel Afonine wrote:
> 
>> Hi Joe,
>> 
>> at 1.45A resolution it is most likely the best to refine individual anisotropic ADPs using phenix.refine (anisotropic for macro-molecule and isotropic for the solvent). In that case the "local sphere restraints" are not used ("local sphere restraints" are used in individual isotropic ADP refinement only). All the relevant details are here:
>> 
>> see "On atomic displacement parameters (ADP) and their parametrization in PHENIX" article:
>> 
>> http://www.phenix-online.org/newsletter/
>> 
>> I'm almost sure that refining isotropic ADPs instead of anisotropic causes these residual densities around atoms. It's known effect and I recall seeing it in at least two papers.
>> 
>> Another things to check:
>> 
>> - is it Met, or Se-Met?
>> - radiation damage? Try refining occupancies of S. Although you said it's not only S, so may be not.
>> 
>> Good luck!
>> Pavel.
>> 
>>> I am refining a very well ordered structure at 1.45 A and find that after doing just about everything including optimization of weights, etc that there are still areas of positive density residing over S atoms of Met, backbone atoms, etc. I have added hydrogens and used them during refinement as well. The maps are of a high quality and Free R factors are quite good, ~ 17%. Is there anything that can be played with more such as values used in the ADP restraints window to try and achieve a difference map with far fewer areas of significant positive density (all greater then or equal to 4 sigma)?
>>> 
>>> I am not sure exactly what effect the values of distance power, average power, etc will have on refinement. The other option I was thinking of was the scattering table options. I have other structures of this protein that extend to about 1.2.
>> 
> 
> 
> 
> ------------------------------
> 
> Message: 7
> Date: Mon, 20 Dec 2010 10:45:33 -0800
> From: Joseph Noel <noel at salk.edu>
> To: Pavel Afonine <pafonine at lbl.gov>
> Cc: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] ADP restraints - distance power, average
> 	power, etc
> Message-ID: <78C01B37-B62D-4FA8-B077-A2CEB2758BC9 at salk.edu>
> Content-Type: text/plain; charset=us-ascii
> 
> Pavel et al.,
> 
> So it turns out I was generating "kicked" sigmaa weighted maps and not the traditional sigmaa weighted maps. When I return to the default mtz maps of phenix, then the positive density appearing on heavy atoms disappears. Has anyone seen similar results with kicked maps? One other thing, I have also unchecked the reject outliers option but in the results window of the GUI it still seems to be rejecting a few reflections. Is there a way to double check things to ensure no reflections are being rejected during refinements and map calculations?
> 
> 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 Dec 19, 2010, at 5:12 PM, Pavel Afonine wrote:
> 
>> Hi Joe,
>> 
>> at 1.45A resolution it is most likely the best to refine individual anisotropic ADPs using phenix.refine (anisotropic for macro-molecule and isotropic for the solvent). In that case the "local sphere restraints" are not used ("local sphere restraints" are used in individual isotropic ADP refinement only). All the relevant details are here:
>> 
>> see "On atomic displacement parameters (ADP) and their parametrization in PHENIX" article:
>> 
>> http://www.phenix-online.org/newsletter/
>> 
>> I'm almost sure that refining isotropic ADPs instead of anisotropic causes these residual densities around atoms. It's known effect and I recall seeing it in at least two papers.
>> 
>> Another things to check:
>> 
>> - is it Met, or Se-Met?
>> - radiation damage? Try refining occupancies of S. Although you said it's not only S, so may be not.
>> 
>> Good luck!
>> Pavel.
>> 
>>> I am refining a very well ordered structure at 1.45 A and find that after doing just about everything including optimization of weights, etc that there are still areas of positive density residing over S atoms of Met, backbone atoms, etc. I have added hydrogens and used them during refinement as well. The maps are of a high quality and Free R factors are quite good, ~ 17%. Is there anything that can be played with more such as values used in the ADP restraints window to try and achieve a difference map with far fewer areas of significant positive density (all greater then or equal to 4 sigma)?
>>> 
>>> I am not sure exactly what effect the values of distance power, average power, etc will have on refinement. The other option I was thinking of was the scattering table options. I have other structures of this protein that extend to about 1.2.
>> 
> 
> 
> 
> ------------------------------
> 
> Message: 8
> Date: Mon, 20 Dec 2010 14:01:26 -0500
> From: Ed Pozharski <epozh001 at umaryland.edu>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] ADP restraints - distance power, average
> 	power, etc
> Message-ID: <1292871686.2190.4464.camel at shardik.rx.umaryland.edu>
> Content-Type: text/plain; charset="UTF-8"
> 
> Refine with refmac and see if the positive density shows up there too.
> If it does, then either there is something peculiar about your structure
> or both programs suffer from the same bug that somehow only shows up
> with your particular dataset.  If not, then it is indeed phenix bug
> (still rather specific to your dataset).
> 
> Are positive density peaks centered around the corresponding atoms?
> 
> Not sure what you mean by saying that peaks "extend to 4 sigma".
> 
> To verify your suspicion about ADP weights, consider manually resetting
> B-factor of, say, one of the offending sulfurs and calculating the
> corresponding map.
> 
> On Mon, 2010-12-20 at 09:06 -0800, Joseph Noel wrote:
>> Hi Pavel,
>> 
>> I've refined individual ADPs (anisotropic for the protein and isotropic for solvent). Still quite a bit of positive density on methionine sulfurs and most carbonyls. They start around 7.5 sigma and extend to 4 sigma. There are no other Fo-Fc peaks appearing for solvent yet to be modeled, etc. so maybe I should play with ADP weights. All positive density is appearing on atoms with occupancies of 1 so not much more I can do to lower the positive density. 
>> 
>> 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 Dec 19, 2010, at 5:12 PM, Pavel Afonine wrote:
>> 
>>> Hi Joe,
>>> 
>>> at 1.45A resolution it is most likely the best to refine individual anisotropic ADPs using phenix.refine (anisotropic for macro-molecule and isotropic for the solvent). In that case the "local sphere restraints" are not used ("local sphere restraints" are used in individual isotropic ADP refinement only). All the relevant details are here:
>>> 
>>> see "On atomic displacement parameters (ADP) and their parametrization in PHENIX" article:
>>> 
>>> http://www.phenix-online.org/newsletter/
>>> 
>>> I'm almost sure that refining isotropic ADPs instead of anisotropic causes these residual densities around atoms. It's known effect and I recall seeing it in at least two papers.
>>> 
>>> Another things to check:
>>> 
>>> - is it Met, or Se-Met?
>>> - radiation damage? Try refining occupancies of S. Although you said it's not only S, so may be not.
>>> 
>>> Good luck!
>>> Pavel.
>>> 
>>>> I am refining a very well ordered structure at 1.45 A and find that after doing just about everything including optimization of weights, etc that there are still areas of positive density residing over S atoms of Met, backbone atoms, etc. I have added hydrogens and used them during refinement as well. The maps are of a high quality and Free R factors are quite good, ~ 17%. Is there anything that can be played with more such as values used in the ADP restraints window to try and achieve a difference map with far fewer areas of significant positive density (all greater then or equal to 4 sigma)?
>>>> 
>>>> I am not sure exactly what effect the values of distance power, average power, etc will have on refinement. The other option I was thinking of was the scattering table options. I have other structures of this protein that extend to about 1.2.
>>> 
>> 
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
> 
> -- 
> "I'd jump in myself, if I weren't so good at whistling."
>                               Julian, King of Lemurs
> 
> 
> 
> ------------------------------
> 
> Message: 9
> Date: Mon, 20 Dec 2010 13:23:30 -0600
> From: Luke Rice <luke.rice at utsouthwestern.edu>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] Secondary structure restraints - where to
> 	specify file using GUI?
> Message-ID: <4D0FAD32.8080201 at utsouthwestern.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Hi Nat,
> 
> I tried what you suggested (dragging my ss restraints file into the 
> input area), and it does not seem to be working (i.e. my edited 
> restraints do not show up; also the filename never appears in the box). 
> I tried changing the fsuix to .eff or .def or .txt, none worked. If 
> instead I drag my restraints file onto the phenix.refine icon, I get a 
> warning about 'this application does not support the filetype ...'.
> 
> I assume that as usual I am doing something wrong. Any ideas?
> 
> Thanks,
> 
> Luke
> 
> 
> Nathaniel Echols wrote:
>> On Mon, Dec 20, 2010 at 7:43 AM, Luke Rice <luke.rice at utsouthwestern.edu> wrote:
>>> I am trying to evaluate whether or not secondary structure restraints are
>>> going to help me with the refinement I am working on. When I ran in 'auto'
>>> mode, I noticed that by default phenix specifies several a-helices as 3_10.
>>> So, I would like to use an edited list of secondary structure restraints.
>> 
>> Interesting, usually it's the reverse problem (3_10 helices annotated
>> as alpha) - but the annotation program can be a little twitchy.  I had
>> intended for this to be graphically editable, but now that I've
>> checked I see there's no way to actually change the helix type in the
>> GUI.  Will fix that soon.
>> 
>>> Can I specify this file in the GUI? (Like Joe Noel, I, too, have become
>>> soft). I looked in what I thought to be the obvious places and did not turn
>>> anything up.
>> 
>> You can just drag it into the main input file list.  Any parameter
>> file may be used this way, with the caveat that the GUI will not
>> actually display the parameters it contains (but they will be
>> incorporated into the final config file).  For this reason I recommend
>> against using complete .eff or .def files from command line runs, but
>> the output of phenix.secondary_structure_restraints (or the edited
>> version thereof) is pretty safe.
>> 
>> Alternately, if you drag the parameter file onto the phenix.refine
>> icon in the main GUI and release the mouse button, it should launch
>> the phenix.refine GUI with all parameters in the file loaded in
>> displayed in the GUI.  (Since this isn't very obvious, I'll add a menu
>> item somewhere to do the same thing less opaquely.)
>> 
>> -Nat
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>> 
> 
> -- 
> Luke M. Rice
> Assistant Professor and
> Thomas O. Hicks Scholar in Medical Research
> Department of Biochemistry, ND10.300
> UT Southwestern Medical Center
> 5323 Harry Hines Blvd.
> Dallas, TX 75390-8816
> phone: (214) 645-5931
> email: Luke.Rice at UTSouthwestern.edu
> 
> 
> ------------------------------
> 
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> 
> End of phenixbb Digest, Vol 61, Issue 21
> ****************************************
> 




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