[phenixbb] phenixbb Digest, Vol 117, Issue 9
Cesar Santiago
csantiag at cnb.csic.es
Thu Aug 27 00:21:36 PDT 2015
Hi Mark!
Anybody for the 24th trip to Alba?
I'll be away from the 1st - 16th of September but I can still arrange the trip before leaving.
César.
------------------------------------------------------------------
Cesar Santiago, Ph. D.
Dept. of Macromolecules Structure at CNB, CSIC.
X-ray Crystallography Facility.
Campus Universidad Autónoma.
Madrid, 28049
csantiag at cnb.csic.es
On Aug 27, 2015, at 6:42 AM, phenixbb-request at phenix-online.org wrote:
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> Today's Topics:
>
> 1. Re: phenix.refine automatic linking options (Engin ?zkan)
> 2. external passive 3D monitor with macbook pro or imac for coot
> and pymol stereo view (Xiao Lei)
> 3. Rank-scaled map (Jianghai Zhu)
> 4. Re: Rank-scaled map (Pavel Afonine)
> 5. Re: on the starting mtz file for phenix refine (Pavel Afonine)
> 6. Ligand addition in COOT for later refinement in Phenix.refine
> (Manoj saxena)
> 7. Re: Ligand addition in COOT for later refinement in
> Phenix.refine (Oleg Sobolev)
> 8. Computational Crystallography Newsletter - Volume 6, Number 2
> (Nigel Moriarty)
> 9. Starting structure as reference model - crashing in 1.10-2142
> (Tristan Croll)
> 10. Re: Starting structure as reference model - crashing in
> 1.10-2142 (Pavel Afonine)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 20 Aug 2015 15:41:31 -0500
> From: Engin ?zkan <eozkan at uchicago.edu>
> To: Billy Poon <bkpoon at lbl.gov>
> Cc: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] phenix.refine automatic linking options
> Message-ID: <55D63B7B.6000707 at uchicago.edu>
> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>
> Dear Billy and Nigel,
>
> Thank you. Phenix.refine GUI in the latest nightly/release candidate no
> longer has the master enable/disable button, and so the problem is resolved.
>
> Engin
>
> On 8/13/15 11:28 AM, Billy Poon wrote:
>> Hi Engin,
>>
>> Thanks! We updated that part of the GUI so that it should be more
>> intuitive. There is now a button that lets you apply automatic linking
>> to all the components and a button that disables all automatic
>> linking. You can, of course, still pick which components to enable by
>> checking the specific boxes.
>>
>> On Tue, Aug 11, 2015 at 7:40 AM, Engin ?zkan <eozkan at uchicago.edu
>> <mailto:eozkan at uchicago.edu>> wrote:
>>
>> Dear Developers,
>>
>> Using the latest phenix nightly, I observed something odd in the
>> phenix.refine UI, and I thought I should report it. If one
>> unchecks Automatic ligand linking, this seems to not override its
>> options, as the instructions in the Options window suggest.
>> Specifically, if "Automatic Ligand Linking" is unchecked, but the
>> "Link metals" is checked within its Options window, metal link
>> restraints are still created.
>>
>> I checked the .geo file to confirm this.
>>
>> Thanks,
>> Engin
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
>> http://phenix-online.org/mailman/listinfo/phenixbb
>> Unsubscribe: phenixbb-leave at phenix-online.org
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>>
>>
>
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> ------------------------------
>
> Message: 2
> Date: Fri, 21 Aug 2015 00:45:16 -0700
> From: Xiao Lei <xiaoleiusc at gmail.com>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: [phenixbb] external passive 3D monitor with macbook pro or
> imac for coot and pymol stereo view
> Message-ID:
> <CABaNifwLZK7sGot44G5GtZNLv+8bzQ3Jwdv089HDLPds6y8-wA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear phenixbb members,
>
> I'm thinking to view stereo 3D structure on coot and pymol with passive 3D
> monitor, does anyone have experience of doing this with a macbook pro or
> imac and a external passive 3D monitor connected using HDMI port?
>
> If mac does not support this, should I buy a PC and a passive 3D monitor to
> do it?
>
> Thanks ahead.
>
> Xiao
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> ------------------------------
>
> Message: 3
> Date: Fri, 21 Aug 2015 10:41:46 -0700 (PDT)
> From: "Jianghai Zhu" <zhu at crystal.harvard.edu>
> To: "PHENIX user mailing list" <phenixbb at phenix-online.org>
> Subject: [phenixbb] Rank-scaled map
> Message-ID: <1440178906104.6b60500b at Nodemailer>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
>
> I know PHENIX can calculate a rank-scaled density map. ?Could anyone inform me which program in PHENIX actually does this? ?
>
>
> Thanks.
>
>
> Best,
>
> ?
> ?--Jianghai
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> ------------------------------
>
> Message: 4
> Date: Fri, 21 Aug 2015 10:58:41 -0700
> From: Pavel Afonine <pafonine at lbl.gov>
> To: Jianghai Zhu <zhu at crystal.harvard.edu>, PHENIX user mailing list
> <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] Rank-scaled map
> Message-ID: <55D766D1.30406 at lbl.gov>
> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>
> Hi Jianghai,
>
> it is available in cctbx and it is used as part of FEM, phenix.fem [*],
> and phenix.map_comparison [**] but there is no standalone
> user-accessible program that would take your map and turn it into
> rank-scaled one.
>
> It is trivial to add so I'm adding it right now and chances are you will
> have it in tomorrow's nightly build.
>
> All the best,
> Pavel
>
> [*]
> Acta Cryst. (2015). D71, 646-666.
> FEM: feature-enhanced map
> P. V. Afonine, N. W. Moriarty, M. Mustyakimov, O. V. Sobolev, T. C.
> Terwilliger, D. Turk, A. Urzhumtsev and P. D. Adams
>
> [**]
> Acta Cryst. (2014). D70, 2593-2606.
> Metrics for comparison of crystallographic maps
> A. Urzhumtsev, P. V. Afonine, V. Y. Lunin, T. C. Terwilliger and P. D. Adams
>
>
>
> On 8/21/15 10:41, Jianghai Zhu wrote:
>> Hi,
>>
>> I know PHENIX can calculate a rank-scaled density map. Could anyone
>> inform me which program in PHENIX actually does this?
>>
>> Thanks.
>>
>> Best,
>> ? ?--Jianghai
>
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> ------------------------------
>
> Message: 5
> Date: Fri, 21 Aug 2015 17:08:27 -0700
> From: Pavel Afonine <pafonine at lbl.gov>
> To: phenixbb at phenix-online.org
> Subject: Re: [phenixbb] on the starting mtz file for phenix refine
> Message-ID: <55D7BD7B.8060805 at lbl.gov>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Experimental data in both *data.mtz and any other *.mtz from
> phenix.refine are identical. What's in *.mtz file is described in
> details in phenix.refine documentation:
>
> http://phenix-online.org/documentation/reference/refinement.html
>
> You can use any of the two files as input to phenix.refine and that will
> not make any difference.
>
> Pavel
>
> On 8/17/15 06:28, Smith Lee wrote:
>> Dear All,
>>
>> In the on-line phenix document, there is,
>>
>> "Should I use the MTZ file output by phenix.refine as input for the next round of refinement?
>>
>> The only time this is necessary is when you refined against a dataset that did not include R-free flags, and let phenix.refine generate a new test set. In this case, you should use the file ending in "_data.mtz" for all future rounds of refinement. You do not need to update the input file in each round, as the actual raw data (and R-free flags) are not modified".
>>
>> When we have phenic adding R-free flgas in the first time we process the mtz data by phenix.refine, besides the *data.mtz, phenix also create a *.mtz. In the future phenix.refine, can I refine by always using the *.mtz created in the R-free flag adding step, rather than refine by always using the *data.mtz created in the R-free flag adding step? What is the difference between that *data.mtz and that *.mtz? And what is the side-effect if in the future steps I refine by always using the *.mtz created in the R-free flag adding step?
>>
>> Best regards.
>>
>> Smith
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>> Unsubscribe: phenixbb-leave at phenix-online.org
>
>
>
> ------------------------------
>
> Message: 6
> Date: Sun, 23 Aug 2015 23:14:24 -0400
> From: Manoj saxena <mks131 at gmail.com>
> To: phenixbb at phenix-online.org
> Subject: [phenixbb] Ligand addition in COOT for later refinement in
> Phenix.refine
> Message-ID:
> <CAEwpOy7GDq=N_ySw5cdnQvkW7vuQddp=TDQGrpW28PNNiPOBiw at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Greetings
> I am trying to place a ligand (CIT) in
> a protein model that already have some citrate ligands placed. I am doing
> this using Coot's option "get monomer", and after the fitting of ligand in
> the density I tried to refine the model using the ligand and the protein
> pdb as input models. Refinement did not start and I got an error message in
> Phenix- "Number of groups of duplicate atom labels:....."
> Could someone please explain how could I get past this error message and
> what is the correct way to add a ligand to a model that already has some of
> the ligands
> of the same type.
>
> Many thanks in advance
>
> Regards
>
> Manoj Saxena
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> ------------------------------
>
> Message: 7
> Date: Mon, 24 Aug 2015 10:14:27 -0700
> From: Oleg Sobolev <osobolev at lbl.gov>
> To: Manoj saxena <mks131 at gmail.com>
> Cc: "phenixbb at phenix-online.org" <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] Ligand addition in COOT for later refinement
> in Phenix.refine
> Message-ID:
> <CADd3otFzEtGR0jaCRYOHBpuwaLZ4Tgdkuq3p54Efa_D_La5ypA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Manoj,
>
> The error says that chain id, residue id and atom name are the same for
> several atoms. And there should be listing of such atoms after the error.
> You may try to change chain id or residue number of your new ligand, if
> this is the case.
>
> Best regards,
> Oleg Sobolev.
>
> On Sun, Aug 23, 2015 at 8:14 PM, Manoj saxena <mks131 at gmail.com> wrote:
>
>> Greetings
>> I am trying to place a ligand (CIT) in
>> a protein model that already have some citrate ligands placed. I am doing
>> this using Coot's option "get monomer", and after the fitting of ligand in
>> the density I tried to refine the model using the ligand and the protein
>> pdb as input models. Refinement did not start and I got an error message in
>> Phenix- "Number of groups of duplicate atom labels:....."
>> Could someone please explain how could I get past this error message and
>> what is the correct way to add a ligand to a model that already has some of
>> the ligands
>> of the same type.
>>
>> Many thanks in advance
>>
>> Regards
>>
>> Manoj Saxena
>>
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>> Unsubscribe: phenixbb-leave at phenix-online.org
>>
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> ------------------------------
>
> Message: 8
> Date: Tue, 25 Aug 2015 15:00:08 +0000
> From: Nigel Moriarty <nwmoriarty at lbl.gov>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>, cctbx
> mailing list <cctbxbb at phenix-online.org>, industry at phenix-online.org,
> developers at phenix-online.org
> Subject: [phenixbb] Computational Crystallography Newsletter - Volume
> 6, Number 2
> Message-ID: <1440514809861-9080b291-d7469201-2e4a7309 at lbl.gov>
> Content-Type: text/plain; charset="utf-8"
>
> I am pleased to announce the publication of the latest issue of the
> Computational Crystallography Newsletter:
>
> http://www.phenix-online.org/newsletter/
>
> A listing of the articles and short communications is given below. Please
> note that the newsletter accepts articles of a general nature of interest
> to all crystallographers. Please send any articles to me at
> NWMoriarty at lbl.gov noting that there is a Word Template on the website to
> streamline production.
>
> July 2015 <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf>
>
> Articles
> - A context-sensitive guide to RNA & DNA base-pair & base-stack geometry
> <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=22>
>
> Short Communications
> - New Phaser-MR search panel in Phenix
> <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=7>
> - Quantum chemical techniques for minimising ligand geometries in the
> active site
> <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=10>
> - 13 typical occupancy refinement scenarios and available options in
> *phenix.refine*
> <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12>
>
> Fitting tips #10 ? How do your base pairs touch and twist?
> <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=3>
>
> Cheers
>
> Nigel
>
> ---
> Nigel W. Moriarty
> Building 33R0349, Physical Biosciences Division
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Phone : 510-486-5709 Email : NWMoriarty at LBL.gov
> Fax : 510-486-5909 Web : CCI.LBL.gov
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> ------------------------------
>
> Message: 9
> Date: Thu, 27 Aug 2015 03:30:02 +0000
> From: Tristan Croll <tristan.croll at qut.edu.au>
> To: "phenixbb at phenix-online.org" <phenixbb at phenix-online.org>
> Subject: [phenixbb] Starting structure as reference model - crashing
> in 1.10-2142
> Message-ID:
> <BY1PR0101MB1174A17E69C643EC5DC88E27DD6F0 at BY1PR0101MB1174.prod.exchangelabs.com>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
>
> When I attempt to run a refinement in Phenix 1.10-2142 using the starting structure as a reference model, it crashes with the complaint that the reference (actually, the error states NCS - despite no NCS being present or enabled. I guess internally it's using the same code?) is too dissimilar to the model, and a calculated RMSD of >90 (degrees? I'm using torsion-angle restraints in any case). The same settings work without complaint on the same structure in dev-2006. I'm running from the GUI, checking "Reference model restraints" in the main phenix.refine window, and then "use starting model as reference" under "All parameters... Reference model restraints...".
>
>
> Thanks,
>
>
> Tristan
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> ------------------------------
>
> Message: 10
> Date: Wed, 26 Aug 2015 21:42:24 -0700
> From: Pavel Afonine <pafonine at lbl.gov>
> To: Tristan Croll <tristan.croll at qut.edu.au>,
> "phenixbb at phenix-online.org" <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] Starting structure as reference model -
> crashing in 1.10-2142
> Message-ID: <55DE9530.7090800 at lbl.gov>
> Content-Type: text/plain; charset="windows-1252"; Format="flowed"
>
> Hi Tristan,
>
> could you please send me files (off list) and tell how to reproduce the
> problem?
>
> Thanks,
> Pavel
>
>
> On 8/26/15 20:30, Tristan Croll wrote:
>>
>> Hi,
>>
>>
>> When I attempt to run a refinement in Phenix 1.10-2142 using the
>> starting structure as a reference model, it crashes with the complaint
>> that the reference (actually, the error states NCS - despite no NCS
>> being present or enabled. I guess internally it's using the same
>> code?) is too dissimilar to the model, and a calculated RMSD of >90
>> (degrees? I'm using torsion-angle restraints in any case). The same
>> settings work without complaint on the same structure in dev-2006. I'm
>> running from the GUI, checking "Reference model restraints" in the
>> main phenix.refine window, and then "use starting model as reference"
>> under "All parameters... Reference model restraints...".
>>
>>
>> Thanks,
>>
>>
>> Tristan
>>
>
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>
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>
>
> End of phenixbb Digest, Vol 117, Issue 9
> ****************************************
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