[phenixbb] phenixbb Digest, Vol 80, Issue 6

Yuri yuri.pompeu at ufl.edu
Fri Jul 13 12:37:38 PDT 2012


On Fri, 13 Jul 2012 12:13:15 -0700, phenixbb-request at phenix-online.org 
wrote:
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> Today's Topics:
>
>    1. Re: segmented rigid body refinement (Nathaniel Echols)
>    2. Re: segmented rigid body refinement (Pavel Afonine)
>    3. Re: average temperature factor (David Cobessi)
>    4. Re: segmented rigid body refinement (Gino Cingolani)
>    5. Re: average temperature factor (Pavel Afonine)
>    6. Re: output of labelit.check_pdb_symmetry (Nicholas Sauter)
>    7. Re: average temperature factor (Nathaniel Echols)
>
>
> 
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 12 Jul 2012 09:40:41 -0700
> From: Nathaniel Echols <nechols at lbl.gov>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] segmented rigid body refinement
> Message-ID:
> 	<CALeAa1NE=F6Quwvsm=ijGf_j-QMxwN1KqStpwiE6NJ7bmyKnsw at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On Thu, Jul 12, 2012 at 9:33 AM, Gino Cingolani <
> Gino.Cingolani at jefferson.edu> wrote:
>
>>  The latter....something more analytical to split individual chains 
>> into
>> smaller groups
>> (e.g. like to define tls groups).
>>
>
> Airlie McCoy just added some functionality to do this in Phaser using
> normal mode analysis.  It is still somewhat experimental and in flux 
> (i.e.
> the program name isn't even finalized), but I will email you off-list 
> with
> details.
>
> -Nat
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> ------------------------------
>
> Message: 2
> Date: Thu, 12 Jul 2012 09:42:27 -0700
> From: Pavel Afonine <pafonine at lbl.gov>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] segmented rigid body refinement
> Message-ID: <4FFEFE73.3080701 at lbl.gov>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> Hi Gino,
>
> you could use phenix.find_tls_groups but the tool requires 
> meaningfully
> refined B-factors and more or less good geometry so the secondary
> structure can be identified automatically. If this is your case then
> phenix.find_tls_groups might work for you.
>
> Pavel
>
> On 7/12/12 9:33 AM, Gino Cingolani wrote:
>> The latter....something more analytical to split individual chains
>> into smaller groups
>> (e.g. like to define tls groups).
>>
>> Thanks,
>>
>> Gino
>>
>>
>> 
>> ******************************************************************************
>> Gino Cingolani, Ph.D.
>> Associate Professor
>> Thomas Jefferson University
>> Dept. of Biochemistry & Molecular Biology
>> 233 South 10th Street - Room 826
>> Philadelphia PA 19107
>> Office (215) 503 4573
>> Lab    (215) 503 4595
>> Fax    (215) 923 2117
>> E-mail:   gino.cingolani at jefferson.edu
>> Website:  http://www.cingolanilab.org
>> 
>> ******************************************************************************
>> "Nati non foste per viver come bruti, ma per seguir virtute e 
>> canoscenza"
>> ("You were not born to live like brutes, but to follow virtue and
>> knowledge") Dante,
>> The Divine Comedy (Inferno,  XXVI, vv. 119-120)
>>
>> 
>> ------------------------------------------------------------------------
>> *From:* phenixbb-bounces at phenix-online.org
>> [phenixbb-bounces at phenix-online.org] on behalf of Nathaniel Echols
>> [nechols at lbl.gov]
>> *Sent:* Thursday, July 12, 2012 12:19 PM
>> *To:* PHENIX user mailing list
>> *Subject:* Re: [phenixbb] segmented rigid body refinement
>>
>> On Thu, Jul 12, 2012 at 9:16 AM, Gino Cingolani
>> <Gino.Cingolani at jefferson.edu <mailto:Gino.Cingolani at jefferson.edu>>
>> wrote:
>>
>>     I'm refining a large oligomeric structure at low res (~6A).
>>     I'd like to define groups to use for 'segmented rigid body
>>     refinement'.
>>     Is there any rational way to define 'segments'?
>>     My macromolecule is already an oligomer on its own, so, 
>> intuitively,
>>     each protomer is a segment.
>>
>>
>> Not sure I understand the question - do you mean you want to split 
>> the
>> individual chains into smaller groups, and you're looking for an
>> analytical method for determining these groups?
>>
>> -Nat
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
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> ------------------------------
>
> Message: 3
> Date: Thu, 12 Jul 2012 18:43:35 +0200
> From: David Cobessi <David.Cobessi at ibs.fr>
> To: phenixbb at phenix-online.org
> Subject: Re: [phenixbb] average temperature factor
> Message-ID: <4FFEFEB7.50202 at ibs.fr>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Ursula,
> Have you tried Baverage from CCP4? I think that it is doing it.
> Kind regards,
> David
>
> On 07/12/2012 06:24 PM, Ursula Schulze-Gahmen wrote:
>> Hi Pavel,
>>
>> Yes, I see the baverage in the header of the pdb file. But I would
>> like to get the baverage for the different chains in  the structure. 
>> I
>> tried using "phenix.pdbtools model.pdb model_statistics=true" on
>> separate chains, but I don't get a value for Baverage from this.
>>
>> Ursula
>>
> --
> David Cobessi
> Institut de Biologie Structurale
> 41, Rue Jules Horowitz
> 38027 Grenoble Cedex-1, France
> Tel:33(0)438789613
>     33(0)608164340
> Fax:33(0)438785122
>
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 12 Jul 2012 16:44:13 +0000
> From: Gino Cingolani <Gino.Cingolani at jefferson.edu>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] segmented rigid body refinement
> Message-ID:
> 
> 	<8305BB02F59BB04BB0C3BF6E1F4FFE391B8DA672 at CH1PRD0510MB357.namprd05.prod.outlook.com>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> thanks for the prompt reply!
>
> Gino
>
> 
> ******************************************************************************
> Gino Cingolani, Ph.D.
> Associate Professor
> Thomas Jefferson University
> Dept. of Biochemistry & Molecular Biology
> 233 South 10th Street - Room 826
> Philadelphia PA 19107
> Office (215) 503 4573
> Lab    (215) 503 4595
> Fax    (215) 923 2117
> E-mail:   gino.cingolani at jefferson.edu
> Website:  http://www.cingolanilab.org
> 
> ******************************************************************************
> "Nati non foste per viver come bruti, ma per seguir virtute e 
> canoscenza"
> ("You were not born to live like brutes, but to follow virtue and
> knowledge") Dante,
> The Divine Comedy (Inferno,  XXVI, vv. 119-120)
>
> ________________________________
> From: phenixbb-bounces at phenix-online.org
> [phenixbb-bounces at phenix-online.org] on behalf of Pavel Afonine
> [pafonine at lbl.gov]
> Sent: Thursday, July 12, 2012 12:42 PM
> To: PHENIX user mailing list
> Subject: Re: [phenixbb] segmented rigid body refinement
>
> Hi Gino,
>
> you could use phenix.find_tls_groups but the tool requires
> meaningfully refined B-factors and more or less good geometry so the
> secondary structure can be identified automatically. If this is your
> case then phenix.find_tls_groups might work for you.
>
> Pavel
>
> On 7/12/12 9:33 AM, Gino Cingolani wrote:
> The latter....something more analytical to split individual chains
> into smaller groups
> (e.g. like to define tls groups).
>
> Thanks,
>
> Gino
>
>
> 
> ******************************************************************************
> Gino Cingolani, Ph.D.
> Associate Professor
> Thomas Jefferson University
> Dept. of Biochemistry & Molecular Biology
> 233 South 10th Street - Room 826
> Philadelphia PA 19107
> Office (215) 503 4573
> Lab    (215) 503 4595
> Fax    (215) 923 2117
> E-mail:   
> gino.cingolani at jefferson.edu<mailto:gino.cingolani at jefferson.edu>
> Website:  http://www.cingolanilab.org
> 
> ******************************************************************************
> "Nati non foste per viver come bruti, ma per seguir virtute e 
> canoscenza"
> ("You were not born to live like brutes, but to follow virtue and
> knowledge") Dante,
> The Divine Comedy (Inferno,  XXVI, vv. 119-120)
>
> ________________________________
> From:
> 
> phenixbb-bounces at phenix-online.org<mailto:phenixbb-bounces at phenix-online.org>
> 
> [phenixbb-bounces at phenix-online.org<mailto:phenixbb-bounces at phenix-online.org>]
> on behalf of Nathaniel Echols
> [nechols at lbl.gov<mailto:nechols at lbl.gov>]
> Sent: Thursday, July 12, 2012 12:19 PM
> To: PHENIX user mailing list
> Subject: Re: [phenixbb] segmented rigid body refinement
>
> On Thu, Jul 12, 2012 at 9:16 AM, Gino Cingolani
> <Gino.Cingolani at jefferson.edu<mailto:Gino.Cingolani at jefferson.edu>>
> wrote:
> I'm refining a large oligomeric structure at low res (~6A).
> I'd like to define groups to use for 'segmented rigid body 
> refinement'.
> Is there any rational way to define 'segments'?
> My macromolecule is already an oligomer on its own, so, intuitively,
> each protomer is a segment.
>
> Not sure I understand the question - do you mean you want to split
> the individual chains into smaller groups, and you're looking for an
> analytical method for determining these groups?
>
> -Nat
>
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>
> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
>
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> ------------------------------
>
> Message: 5
> Date: Thu, 12 Jul 2012 09:49:41 -0700
> From: Pavel Afonine <pafonine at lbl.gov>
> To: phenixbb at phenix-online.org
> Subject: Re: [phenixbb] average temperature factor
> Message-ID: <4FFF0025.8030504 at lbl.gov>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> Hi Ursula,
>
> here is a solution, not nice though:
>
> step 1: get a pdb file with chain in question:
>
> phenix.pdbtools model.pdb keep="chain A" 
> output.file_name="chain_A.pdb"
>
> step 2: then this will give you average B
>
> phenix.pdbtools chain_A.pdb model_statistics=true
>
> Other suggestions (by David & Christian) might work too, but I have 
> no
> idea how these programs handle TLS contribution to ADP and ANISOU
> records. Though since phenix.refine outputs total ADPs I guess this
> should be just fine.
>
> Pavel
>
> On 7/12/12 9:24 AM, Ursula Schulze-Gahmen wrote:
>> Hi Pavel,
>>
>> Yes, I see the baverage in the header of the pdb file. But I would
>> like to get the baverage for the different chains in  the structure. 
>> I
>> tried using "phenix.pdbtools model.pdb model_statistics=true" on
>> separate chains, but I don't get a value for Baverage from this.
>>
>> Ursula
>>
>> On Wed, Jul 11, 2012 at 11:58 AM, Pavel Afonine <pafonine at lbl.gov
>> <mailto:pafonine at lbl.gov>> wrote:
>>
>>     Hi Ursula,
>>
>>
>>         Is there an easy way to calculate average temperature 
>> factors
>>         in phenix or another program after ADP + TLS refinement in 
>> phenix?
>>
>>
>>     yes. If you PDB file is after phenix.refine run, then the 
>> average
>>     ADP is reported in PDB file header as well as in refinement log 
>> file.
>>     For a PDB file you can calculate average ADP using this command:
>>
>>     phenix.pdbtools model.pdb model_statistics=true
>>
>>     It does not matter where PDB file come from as long as ATOM 
>> or/and
>>     ANISOU records contain the correct ADPs.
>>
>>     Pavel
>>     _______________________________________________
>>     phenixbb mailing list
>>     phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
>>     http://phenix-online.org/mailman/listinfo/phenixbb
>>
>>
>>
>>
>> --
>> Ursula Schulze-Gahmen, Ph.D.
>> Assistant Researcher
>> UC Berkeley, QB3
>> 356 Stanley Hall #3220
>> Berkeley, CA 94720-3220
>>
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
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> ------------------------------
>
> Message: 6
> Date: Thu, 12 Jul 2012 10:44:35 -0700
> From: Nicholas Sauter <nksauter at lbl.gov>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] output of labelit.check_pdb_symmetry
> Message-ID:
> 	<CAMkkSynOA8WTP4DL4kws16hW5uqbQhLx4=a5zwWbiYumscWNnA at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Oliver,
>
> peak_cutoff only changes the tolerance on the fTF correlation 
> coefficient;
> however the program is probably still not finding a solution with a
> reasonable weighted phase-difference score Phi(g).  The tolerance for
> this (default=0.25) can be increased with the score_tol= command line
> argument.  You can send me your output file offlist for a closer 
> look.
>
> Nick
>
> On Thu, Jul 12, 2012 at 8:44 AM, "Weiergr?ber, Oliver H." <
> o.h.weiergraeber at fz-juelich.de> wrote:
>
>> Hello,
>>
>> I am using labelit.check_pdb_symmetry in order to evaluate a crystal
>> structure with sg P21 (2 copies/asu) and all angles 
>> indistinguishable from
>> 90 degs for potential higher (i.e. orthorhombic) symmetry. 
>> Comparison of
>> refinement statistics clearly indicates that the most likely 
>> scenario is
>> perfect pseudomerohedral twinning of a true P21 crystal 
>> (Rfree=0.21).
>> Accordingly, labelit.check_pdb_symmetry reports a striking 
>> discrepancy
>> between Rsymop(Iobs) and Rsymop(Icalc): 8 % vs 31 %, i.e. there is 
>> an
>> additional (apparent) 2-fold symmetry in the data which cannot be 
>> explained
>> by the model.
>> In an attempt to force a solution for comparison and visualization
>> purposes, I have increased the r_symop_tol parameter to 0.35; the 
>> program
>> starts to evaluate possible space groups with fTF, yielding scores 
>> (these
>> are correlation coefficients, right?) way above 90 %. Still, in the 
>> end it
>> reports there are no higher symmetry solutions.
>>
>> Why is this? Does the program check for the contrast between the 
>> best
>> solution and the others? Changing peak_cutoff to a "discriminative" 
>> value
>> did not help...
>>
>> Best regards,
>> Oliver
>>
>>
>>
>>
>>
>> 
>> ------------------------------------------------------------------------------------------------
>>
>> 
>> ------------------------------------------------------------------------------------------------
>> Forschungszentrum Juelich GmbH
>> 52425 Juelich
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>>
>> 
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>>
>> 
>> ------------------------------------------------------------------------------------------------
>>
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>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
>
>
>
> --
> Nicholas K. Sauter, Ph. D.
> Computer Staff Scientist, Physical Biosciences Division
> Lawrence Berkeley National Laboratory
> 1 Cyclotron Rd., Bldg. 64R0121
> Berkeley, CA 94720-8118
> (510) 486-5713
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> ------------------------------
>
> Message: 7
> Date: Fri, 13 Jul 2012 12:10:37 -0700
> From: Nathaniel Echols <nechols at lbl.gov>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] average temperature factor
> Message-ID:
> 	<CALeAa1Mh0nO-gB1=Jg2VRh9vBx9i3h-4PPrDcXzPSo9UzxSacA at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On Thu, Jul 12, 2012 at 9:49 AM, Pavel Afonine <pafonine at lbl.gov> 
> wrote:
>
>>  here is a solution, not nice though:
>>
>> step 1: get a pdb file with chain in question:
>>
>> phenix.pdbtools model.pdb keep="chain A" 
>> output.file_name="chain_A.pdb"
>>
>> step 2: then this will give you average B
>>
>> phenix.pdbtools chain_A.pdb model_statistics=true
>>
>> Other suggestions (by David & Christian) might work too, but I have 
>> no
>> idea how these programs handle TLS contribution to ADP and ANISOU 
>> records.
>> Though since phenix.refine outputs total ADPs I guess this should be 
>> just
>> fine.
>>
>
> Since this question has come up before, I've added a window for 
> displaying
> this in the GUI.  Clicking the magnifying glass icon next to any PDB 
> file
> will already open a panel showing an overview of the model contents, 
> and
> now there will also be a button labeled "B-factors by chain" for any 
> file
> with multiple chains.  Clicking this button will display the 
> isotropic
> B-factors statistics by chain.  Under the circumstances, I'm assuming 
> the
> B-factor field in the PDB file is already the total B-factor.
>
> This will be available in the next nightly build.
>
> -Nat
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> ------------------------------
>
> _______________________________________________
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>
>
> End of phenixbb Digest, Vol 80, Issue 6
> ***************************************

-- 
Yuri Pompeu


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