[Chimera-users] APBS -> Chimera plugin - why not?
Boaz Shaanan
bshaanan at exchange.bgu.ac.il
Fri Jan 6 07:25:37 PST 2012
Hi Elaine,
Following on the recent exchange of messages: I've actually been wondering for quite some time why there isn't an APBS plugin for Chimera. Is it because of no interest on the APBS side? Should we ask them to develop one? I'm sure we can collect enough votes to promote that. For example, I find the Consurf and Castp plugins (maybe interfaces, whatever they should be called) very nice and useful, so why not APBS too?
Happy New Year to you all (still not too late).
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 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
________________________________________
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Today's Topics:
1. Re: APBS (Elaine Meng)
2. Re: APBS (Elaine Meng)
3. Re: APBS (Anjana Ramnath)
4. Re: How to place a metal ion in protein model (Suneel N.A.)
5. Re: How to place a metal ion in protein model (Elaine Meng)
----------------------------------------------------------------------
Message: 1
Date: Thu, 5 Jan 2012 12:04:22 -0800
From: Elaine Meng <meng at cgl.ucsf.edu>
To: Anjana Ramnath <anjanaram1 at gmail.com>
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] APBS
Message-ID: <4CE9538A-80A1-4A3B-B99D-D4F401A73A6E at cgl.ucsf.edu>
Content-Type: text/plain; charset=us-ascii
Hello Anjana,
Are you sure you're using Chimera? As far as I know there is no APBS plugin for Chimera, only for Pymol.
In Chimera,
(A) there are several ways to show distances, including selecting two atoms (Ctrl-click on one atom, Shift-Ctrl-click on the second atom) and using command: distance sel
(B) there is no tool especially for aromatic interactions, but you can use the tool Find Clashes/Contacts or command findclash to identify contacts between two sets of aromatic residues. For example, to identify contacts between aromatic amino acids in chain A and aromatic amino acids in chain B, command:
findclash :.a&aromatic test :.b&aromatic overlap -1 hb 0
(You would probably also want to display all atoms so you can see where the contacts are.)
The same thing could be done using the Find Clashes/Contacts graphical interface, in the menu under Tools... Structure Analysis. GUI documentation:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>
Command documentation:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
On Jan 4, 2012, at 9:02 PM, Anjana Ramnath wrote:
> Hello all,
> My question is simple: im trying to install the APBS plugin but have so far been unsuccessful. I am also trying to show the interactions between aromatic residues on a PDB molecule. how do i do this? im also having trouble with showing the distance between 2 residues. im using Fedora 12 and also WindowsXP. please do let me know. thank you very much!
> sincerely,
> Anjana.
------------------------------
Message: 2
Date: Thu, 5 Jan 2012 12:23:49 -0800
From: Elaine Meng <meng at cgl.ucsf.edu>
To: Anjana Ramnath <anjanaram1 at gmail.com>
Cc: Chimera BB <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] APBS
Message-ID: <5BAFC2C8-8868-4D58-A577-C2EE7DD1C6CE at cgl.ucsf.edu>
Content-Type: text/plain; charset=us-ascii
Hi Anjana,
After showing a surface, you can either
(A) open an electrostatic potential (ESP) map previously calculated with some other program (DelPhi, Grasp, UHBD, APBS) in Chimera and then use it to color the surface with "Electrostatic Surface Coloring" (in menu under Tools... Surface/Binding Analysis) or command "scolor"
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp>
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html>
or
(B) use the "Coulombic Surface Coloring" tool (in same menu as above) or command "coulombic" to calculate Coulombic ESP and color the surface based on those values
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/coulombic.html>
... for example, as in this tutorial:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>
Best,
Elaine
----------
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
On Jan 5, 2012, at 12:14 PM, Anjana Ramnath wrote:
> thanks so much for your prompt response! well actually, i was wondering if there was a way to show the electrostatic surface in chimera?
>
------------------------------
Message: 3
Date: Fri, 6 Jan 2012 01:56:19 +0530
From: Anjana Ramnath <anjanaram1 at gmail.com>
To: Chimera BB <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] APBS
Message-ID:
<CAAwO1H_Lt3ZRSnjqTNx+qXDpYa7jhF3=-hf+F5TMM1QRjGnj8w at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
thanks so much Elaine! let me just say that Chimera user support is waayy
better than any other popular graphics program ive come across! youve got a
chimera fan here now. :)
On Fri, Jan 6, 2012 at 1:53 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Anjana,
> After showing a surface, you can either
>
> (A) open an electrostatic potential (ESP) map previously calculated with
> some other program (DelPhi, Grasp, UHBD, APBS) in Chimera and then use it
> to color the surface with "Electrostatic Surface Coloring" (in menu under
> Tools... Surface/Binding Analysis) or command "scolor"
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp>
> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html
> >
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html>
>
> or
> (B) use the "Coulombic Surface Coloring" tool (in same menu as above) or
> command "coulombic" to calculate Coulombic ESP and color the surface based
> on those values
> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html
> >
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/coulombic.html>
>
> ... for example, as in this tutorial:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>
>
> Best,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
> On Jan 5, 2012, at 12:14 PM, Anjana Ramnath wrote:
>
> > thanks so much for your prompt response! well actually, i was wondering
> if there was a way to show the electrostatic surface in chimera?
> >
>
>
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Message: 4
Date: Thu, 5 Jan 2012 14:00:40 -0800
From: "Suneel N.A." <leptolysin at gmail.com>
To: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] How to place a metal ion in protein model
Message-ID:
<CAKiyN3yOjhsUuSg9+VQ7Vp3yROCLZsGfLoLPRAiTmj8Gtrq=5w at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi Elaine
Thank you very much for the timely reply. I am glad to see it. The
information you sent was really helpful. Here are some of the details for
your suggestions/queries
(a) I used 1ZWX for homology modelling. The other closest models are 2DDR
and 3I5V. They are crystallised with bound metal ions.As you suggested I
will try to superimpose with the metal ion (though I am not that good in
using chimera).
I have another query: I am trying to model a protein based on homology
modelling strategy. I came to know that Chimera can model the protein based
on the same strategy. When I attempted modelling using the Modeller tool of
chimera it gives me an error "Running modeller for query via web service
failed; see reply log for more information. When I see the reply log :
Import modeller, Import error:No module named modeller".
Infact I even got the licence key from the modeller website and used it in
the dialogue box but still this error message is shown.
Another query is, for modelling a protein (whose structure is unknown) ,
how do we import the sequences into chimera? In one of the chimera videos
on modelling, they show that the protein sequence is imported/fetched from
Uniport. But in my chimera software under the Fetch tab I don't see an
Uniprot option. In this regard please tell me how to import sequences.
Please do the needful. Will be looking for the reply.
Thanking you in anticipation
Yours Sincerely
suneel
On Wed, Jan 4, 2012 at 10:21 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Suneel,
> Chimera doesn't have a tool to predict metal binding sites from a
> structure. There is a tool called "Add Ions" which will roughly place ions
> around a structure, but it is meant for adding counterions for simulation
> purposes and is ineffective for binding site prediction.
>
> First, I would consider the following:
>
> (a) what protein was used as the template for the homology model? Does it
> bind metal? If so, the site is probably in the same place. You could just
> superimpose the template (with metal ion included) and model structures to
> see the binding site.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
>
> (b) do you have any other data about which residues bind the metal? You
> may be able to create a metal ion with Build Structure (under Tools...
> Structure Editing) and place the metal near the protein yourself,
> interactively, with the mouse.
> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html
> >
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>
>
> (c) I believe there are several web servers that will try to identify
> metal-binding sites and other active sites from your uploaded protein
> structure. I would recommend doing some literature or web searching to
> find these. I have used some in the past, but it was a few years ago.
> Here are some web server names to search for and try: PAR-3D, PDBSiteScan,
> PINTS, ProFunc, Protemot, SuMo
>
> Chimera has a Metal Geometry tool (under Tools... Structure Analysis), but
> it is meant to analyze the binding geometry of structures that already
> contain the metal ion, or to analyze the possibilities after you have
> manually placed the metal ion.
> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/metalgeom/metalgeom.html
> >
>
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
> On Jan 2, 2012, at 1:36 AM, Suneel N.A. wrote:
>
> > Hi
> > Its my pleasure to introduce myself, I am Suneel, graduate student from
> India. I am not a bioinformatician by profession but a eager aspirant of
> learning bioinformatics. I am new to Chimera, but as I started using it,
> the desire for leraning Bioinformatics increased more and more. Chimera is
> such an awesome tool packed with so many options. I love it . I have small
> question for you.
> > I have a predicted the structure of protein using in silico tools (based
> on homology modeling). Literature sates that this protein binds to
> Magnesium. Now I would like to know if I can use chimera to place the metal
> in the modeled structure and prove/validate it based on metal geometry.
> > Please do the needful.
> > Thanking you in anticipation
> > yours sincerely
> > suneel
> >
>
>
--
*Suneel Narayanavari. A*
Graduate Student
Prof. Manjula Sritharan's Laboratory of Infection Biology
Department of Animal Sciences
School of Life Sciences
University of Hyderabad
Hyderabad-46
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Message: 5
Date: Thu, 5 Jan 2012 16:22:55 -0800
From: Elaine Meng <meng at cgl.ucsf.edu>
To: "Suneel N.A." <leptolysin at gmail.com>
Cc: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] How to place a metal ion in protein model
Message-ID: <0DBD80B6-8A44-4A4A-B3BA-D390AF3A651B at cgl.ucsf.edu>
Content-Type: text/plain; charset=us-ascii
Hi Suneel,
The UniProt fetch is fairly new, you would need to get a recent daily build:
<http://www.cgl.ucsf.edu/chimera/download.html#daily>
<http://www.cgl.ucsf.edu/chimera/docs/relnotes/snapshot.html>
In older (but not too old) versions another approach is to get a file of the sequence in fasta format, then open it with "File... Open" in the Chimera menu.
If you get a newer Chimera and still have the modelling error, please use "Help... Report a Bug" in the menu to report it -- it will include information on your computer and what version you are using. This chimera-users email address is mainly for questions, not bugreports. Thanks!
There are explanations of how to superimpose structures (such as your template and model to see where the metal site would be) here:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
Good luck,
Elaine
----------
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
On Jan 5, 2012, at 2:00 PM, Suneel N.A. wrote:
> Hi Elaine
> Thank you very much for the timely reply. I am glad to see it. The information you sent was really helpful. Here are some of the details for your suggestions/queries
> (a) I used 1ZWX for homology modelling. The other closest models are 2DDR and 3I5V. They are crystallised with bound metal ions.As you suggested I will try to superimpose with the metal ion (though I am not that good in using chimera).
>
> I have another query: I am trying to model a protein based on homology modelling strategy. I came to know that Chimera can model the protein based on the same strategy. When I attempted modelling using the Modeller tool of chimera it gives me an error "Running modeller for query via web service failed; see reply log for more information. When I see the reply log : Import modeller, Import error:No module named modeller".
> Infact I even got the licence key from the modeller website and used it in the dialogue box but still this error message is shown.
>
> Another query is, for modelling a protein (whose structure is unknown) , how do we import the sequences into chimera? In one of the chimera videos on modelling, they show that the protein sequence is imported/fetched from Uniport. But in my chimera software under the Fetch tab I don't see an Uniprot option. In this regard please tell me how to import sequences.
>
> Please do the needful. Will be looking for the reply.
> Thanking you in anticipation
> Yours Sincerely
> suneel
>
------------------------------
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