[Chimera-users] Constructing biological assmebly
Boaz Shaanan
bshaanan at bgu.ac.il
Wed Apr 10 11:50:32 PDT 2019
Hi,
I suppose it's a new biological assembly that has to be put together.
The recommended program for doing this is Pisa which can be accessed either from one of the ccp4 gui's or directly through the PDBe/EMBL server http://www.ebi.ac.uk/pdbe/pisa/
Obviously, if it's a protein whose coordinates are in the PDB database there is an option to download the biological assembly (directly to Chimera, actually).
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: bshaanan at bgu.ac.il
Phone: 972-8-647-2220
Fax: 972-8-647-2992 or 972-8-646-1710
________________________________________
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Today's Topics:
1. Re: Constructing a biological assembly in Chimera (Elaine Meng)
2. Origin of transformation matrices (Daniel Asarnow)
3. Re: Origin of transformation matrices (Elaine Meng)
4. New tutorial: CALCULATE AND VISUALIZE THE ELECTROSTATIC
POTENTIAL OF A GLOBULAR PROTEIN (Thomas Evangelidis)
5. Re: New tutorial: CALCULATE AND VISUALIZE THE ELECTROSTATIC
POTENTIAL OF A GLOBULAR PROTEIN (Elaine Meng)
----------------------------------------------------------------------
Message: 1
Date: Tue, 9 Apr 2019 08:19:32 -0700
From: Elaine Meng <meng at cgl.ucsf.edu>
To: Ahmad Khalifa <underoath006 at gmail.com>
Cc: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Constructing a biological assembly in
Chimera
Message-ID: <6A14D1BB-0771-4D5C-A894-0296321D9882 at cgl.ucsf.edu>
Content-Type: text/plain; charset=utf-8
Sorry, I don?t know of a program to do it, but maybe other users on this list will have suggestions.
Elaine
> On Apr 8, 2019, at 6:22 PM, Ahmad Khalifa <underoath006 at gmail.com> wrote:
>
> Thank you, is there any other program that can make BIOMT? I know I can get the rotation and translation matrix of the BIOMT record if I do: measure rotation #spec1 #spec2. I wonder how I can iterate over a lot of #spec2 models and how to get the output matrices in a row text format?
>
> I intend to write a script that can write that information to my pdb BIOMT record.
>
> On Mon, Apr 8, 2019 at 5:19 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hello Ahmad,
> The sym command does not create BIOMT matrices. It adds symmetry copies of the atomic structure based on:
>
> (1) BIOMT matrices that are already included in the structure file (for example, use a text-editor to view the PDB file for 1FAV)
> - OR -
> (2) other symmetry specified manually on the command line
>
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html>
>
> There is no tool in Chimera for creating the BIOMT matrices or identifying symmetry from your fitted atomic copies that could be used in the ?sym? command, sorry. There is a ?measure symmetry? command for maps, but it has limitations and can only guess helical symmetries if you give it approximate rise and angle values.
>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#symmetry>
>
> Elaine
>
> > On Apr 8, 2019, at 10:14 AM, Ahmad Khalifa <underoath006 at gmail.com> wrote:
> >
> > Thanks Elaine. I've been looking into this and found some info about BIOMT records and the sym command. However, I couldn't get it to work.
> >
> > I think what can solve my problem is if I can copy/combine and fit monomers from the "main" monomer then use the sym command to generate a BIOMT record of all these fitted structure into the main monomer. That way any modifications I make to that "main monomer" will be present in the new structures that I generate using the biological unit function in Chimera.
> >
> > How can I do that using the sym command?
> >
> >
> >
> > On Mon, Apr 8, 2019 at 12:12 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Hello Ahmad,
> > There is no feature to automatically apply any changes in one monomer to all the other monomers. As far as I know, you would need to first modify the monomer and then create the biological assembly of the modified monomer.
> >
> > If you already have the biological assembly of the unmodified monomer, another possibility is to open several copies of modified one and match them onto the unmodified ones (possibly by writing your own script to do it since I imagine it would be a lot of repetitious commands), and then close the unmodified ones. However, that might be more work than just using the modified monomer to make the assembly in the first place, and might give a slightly different result.
> >
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> > > On Apr 7, 2019, at 6:07 AM, Ahmad Khalifa <underoath006 at gmail.com> wrote:
> > >
> > > Hello,
> > > I'm working with a lattice made of a tubulin monomer that I modeled and refined in Coot.
> > >
> > > I have fitted other units of the monomer along the length and to the side of my monomer in a cryo-EM map to study tubulin interactions with non tubulin proteins.
> > >
> > > Instead, I wonder if I can construct a biological assembly of just one unit, to have any modifications or changes in that unit reflected in the entire biological assembly.
> > >
> > > Any other help or suggestions would be appreciated.
> > > Regards.
> >
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------------------------------
Message: 2
Date: Tue, 9 Apr 2019 16:17:00 -0700
From: Daniel Asarnow <asarnow at msg.ucsf.edu>
To: chimera-users at cgl.ucsf.edu
Subject: [Chimera-users] Origin of transformation matrices
Message-ID:
<CALiNCbZaNphCqfBU9Hc7G7oeGCn32ZW5VY1kx6dt9VjXbgVkQQ at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi,
What's the origin for the rotation/translation output by measure rotation
or fit-in-map results? If the origin index is 0, is the transformation
calculated around (0, 0, 0)?
I'm extending my software for transforming single-particle EM alignment
parameters to accept a transformation matrix copy-pasted from Chimera and
am having a slight difficulty. For most EM maps, the origin MRC header is
not set, and the origin appears to be (0,0,0). Thus, if R and V are the
rotation and translation from Chimera, the formula R * O + V - O where O is
the real origin (boxsize / 2, boxsize / 2, boxsize / 2) should give the
correct translation. However, it's exactly one pixel short.
Best,
-da
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Message: 3
Date: Tue, 9 Apr 2019 16:40:08 -0700
From: Elaine Meng <meng at cgl.ucsf.edu>
To: Daniel Asarnow <asarnow at msg.ucsf.edu>
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Origin of transformation matrices
Message-ID: <3EEE6F5B-5D82-4454-9135-32AFE40E39B7 at cgl.ucsf.edu>
Content-Type: text/plain; charset=utf-8
Hi Daniel,
The sum total of my understanding here is in the ?measure rotation? description:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation>
The matrix describes a rotation and a translation in the coordinate system of the first model in the command. I believe this is in xyz coordinates, not grid units. You can see grid indices corresponding to XYZ (0,0,0) in the Volume Viewer by using menu: Features? Coordinates to show that section:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates>
Alternatively (going back to the?measure rotation? description) the transformation is described as an axis, rotation around that axis (not center of rotation, but I believe the axis is all you need, pinned in space by a point on that axis which is also given) and shift parallel to that axis.
Our expert in this area is away currently, so although he may be able to shed more light on this and whether there is a problem with your calculations, it may be a while, sorry.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco
> On Apr 9, 2019, at 4:17 PM, Daniel Asarnow <asarnow at msg.ucsf.edu> wrote:
>
> Hi,
> What's the origin for the rotation/translation output by measure rotation or fit-in-map results? If the origin index is 0, is the transformation calculated around (0, 0, 0)?
>
> I'm extending my software for transforming single-particle EM alignment parameters to accept a transformation matrix copy-pasted from Chimera and am having a slight difficulty. For most EM maps, the origin MRC header is not set, and the origin appears to be (0,0,0). Thus, if R and V are the rotation and translation from Chimera, the formula R * O + V - O where O is the real origin (boxsize / 2, boxsize / 2, boxsize / 2) should give the correct translation. However, it's exactly one pixel short.
>
> Best,
> -da
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
------------------------------
Message: 4
Date: Wed, 10 Apr 2019 18:31:45 +0200
From: Thomas Evangelidis <tevang3 at gmail.com>
To: UCSF Chimera Mailing List <chimera-users at cgl.ucsf.edu>
Subject: [Chimera-users] New tutorial: CALCULATE AND VISUALIZE THE
ELECTROSTATIC POTENTIAL OF A GLOBULAR PROTEIN
Message-ID:
<CAACvdx2OAPk+-UTE2Wh-5UdrhYsxR-mVKBA0cE2itfV48ZNd3g at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi Chimera users,
I have written a tutorial about how to utilize Chimera's superior
capabilities in order to visualize the electrostatic potential of a buried
active site. In this case, the protein is BACE protease from D3R Challenge
2018. The binding pocket of this protein is negatively charged and the
average net charge of the ligands was +2, which both made accurate scoring
with free energy methods difficult. The same procedure can be applied to
any other globular protein.
https://github.com/tevang/tutorials/tree/master/Electrostatic_Potential_Globular_Protein
@Chimera's developers: can you put a link of this tutorial to your
dedicated Tutorials page https://www.cgl.ucsf.edu/chimera/tutorials.html
<https://www.cgl.ucsf.edu/chimera/tutorials.html>? I have much more scripts
and tutorials in my personal archive which I will gradually publish
whenever I find free time.
With best regards,
Thomas
--
======================================================================
Dr Thomas Evangelidis
Research Scientist
IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>
Prague, Czech Republic
&
CEITEC - Central European Institute of Technology <https://www.ceitec.eu/>
Brno, Czech Republic
email: tevang3 at gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Message: 5
Date: Wed, 10 Apr 2019 10:56:27 -0700
From: Elaine Meng <meng at cgl.ucsf.edu>
To: Thomas Evangelidis <tevang3 at gmail.com>
Cc: UCSF Chimera Mailing List <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] New tutorial: CALCULATE AND VISUALIZE THE
ELECTROSTATIC POTENTIAL OF A GLOBULAR PROTEIN
Message-ID: <F01F2D28-A0E8-4412-AFE8-3F09B723BAA4 at cgl.ucsf.edu>
Content-Type: text/plain; charset=us-ascii
Hi Thomas,
Thanks for creating the tutorial! Yes, we can add it to the Chimera tutorials page (I will send you a link privately to preview).
If you are planning to make several such tutorials available, it would be best if you could create an index page that lists all of your tutorials with short descriptions. Then our Chimera tutorials page can link to your index, and users will be able to see the list with all of your latest additions and updates without our having to update our own page this time. There is some overhead since I try to put descriptions and images with each.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco
> On Apr 10, 2019, at 9:31 AM, Thomas Evangelidis <tevang3 at gmail.com> wrote:
>
> Hi Chimera users,
>
> I have written a tutorial about how to utilize Chimera's superior capabilities in order to visualize the electrostatic potential of a buried active site. In this case, the protein is BACE protease from D3R Challenge 2018. The binding pocket of this protein is negatively charged and the average net charge of the ligands was +2, which both made accurate scoring with free energy methods difficult. The same procedure can be applied to any other globular protein.
>
> https://github.com/tevang/tutorials/tree/master/Electrostatic_Potential_Globular_Protein
>
> @Chimera's developers: can you put a link of this tutorial to your dedicated Tutorials page https://www.cgl.ucsf.edu/chimera/tutorials.html ? I have much more scripts and tutorials in my personal archive which I will gradually publish whenever I find free time.
>
> With best regards,
> Thomas
>
>
> --
> ======================================================================
> Dr Thomas Evangelidis
> Research Scientist
> IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
> Prague, Czech Republic
> &
> CEITEC - Central European Institute of Technology
> Brno, Czech Republic
>
> email: tevang3 at gmail.com
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
>
>
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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