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

[email protected]



On Aug 27, 2015, at 6:42 AM, [email protected] 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 <[email protected]>
To: Billy Poon <[email protected]>
Cc: PHENIX user mailing list <[email protected]>
Subject: Re: [phenixbb] phenix.refine automatic linking options
Message-ID: <[email protected]>
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 <[email protected]
<mailto:[email protected]>> 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

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Message: 2
Date: Fri, 21 Aug 2015 00:45:16 -0700
From: Xiao Lei <[email protected]>
To: PHENIX user mailing list <[email protected]>
Subject: [phenixbb] external passive 3D monitor with macbook pro or
imac for coot and pymol stereo view
Message-ID:
<CABaNifwLZK7sGot44G5GtZNLv+8bzQ3Jwdv089HDLPds6y8-wA@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" <[email protected]>
To: "PHENIX user mailing list" <[email protected]>
Subject: [phenixbb] Rank-scaled map
Message-ID: <1440178906104.6b60500b@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 <[email protected]>
To: Jianghai Zhu <[email protected]>, PHENIX user mailing list
<[email protected]>
Subject: Re: [phenixbb] Rank-scaled map
Message-ID: <[email protected]>
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 <[email protected]>
To: [email protected]
Subject: Re: [phenixbb] on the starting mtz file for phenix refine
Message-ID: <[email protected]>
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
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------------------------------

Message: 6
Date: Sun, 23 Aug 2015 23:14:24 -0400
From: Manoj saxena <[email protected]>
To: [email protected]
Subject: [phenixbb] Ligand addition in COOT for later refinement in
Phenix.refine
Message-ID:
<CAEwpOy7GDq=N_ySw5cdnQvkW7vuQddp=TDQGrpW28PNNiPOBiw@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 <[email protected]>
To: Manoj saxena <[email protected]>
Cc: "[email protected]" <[email protected]>
Subject: Re: [phenixbb] Ligand addition in COOT for later refinement
in Phenix.refine
Message-ID:
<CADd3otFzEtGR0jaCRYOHBpuwaLZ4Tgdkuq3p54Efa_D_La5ypA@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 <[email protected]> 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



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Message: 8
Date: Tue, 25 Aug 2015 15:00:08 +0000
From: Nigel Moriarty <[email protected]>
To: PHENIX user mailing list <[email protected]>, cctbx
mailing list <[email protected]>, [email protected],
[email protected]
Subject: [phenixbb] Computational Crystallography Newsletter - Volume
6, Number 2
Message-ID: <[email protected]>
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
[email protected] 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 : [email protected]
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 <[email protected]>
To: "[email protected]" <[email protected]>
Subject: [phenixbb] Starting structure as reference model - crashing
in 1.10-2142
Message-ID:
<BY1PR0101MB1174A17E69C643EC5DC88E27DD6F0@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 <[email protected]>
To: Tristan Croll <[email protected]>,
"[email protected]" <[email protected]>
Subject: Re: [phenixbb] Starting structure as reference model -
crashing in 1.10-2142
Message-ID: <[email protected]>
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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End of phenixbb Digest, Vol 117, Issue 9
****************************************