[Chimera-users] 2. Unit of electrostatic surface coloring within Chimera

Boaz Shaanan bshaanan at exchange.bgu.ac.il
Tue Feb 19 10:08:47 PST 2013


Hi Florian,

The units for the electrostatic surface generated by APSB (andDelphi) are kT/e, which is what Chimera uses for determining the threshold when  colouring the electrostatic surface. I'm quite sure that's the case.

  Cheers,

            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. Algorithm for areaSAS calculations (Korbus, Michael)
   2. Unit of electrostatic surface coloring within     Chimera
      (Florian.Capito at external.merckgroup.com)
   3. Drug-Protein Interaction (kanika sharma)
   4. Re: New user-visualizing coulombic (Elaine Meng)
   5. Re: session file/HID (Tom Goddard)
   6. Re: questions about modeller and task panel (Elaine Meng)
   7. Re: Drug-Protein Interaction (Elaine Meng)
   8. Re: Algorithm for areaSAS calculations (Elaine Meng)


----------------------------------------------------------------------

Message: 1
Date: Mon, 18 Feb 2013 10:27:44 +0100
From: "Korbus, Michael" <michael.korbus at h-da.de>
To: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
Subject: [Chimera-users] Algorithm for areaSAS calculations
Message-ID:
        <0781A55E8298FD4CBCAAA70C4AF2EDB6350489B0BA at Virgon.h-da.local>
Content-Type: text/plain; charset="us-ascii"

Dear Ladies and Gentlemen,

I have a question concerning calculation of areaSAS with chimera. Which algorithm is used? A Shrake-Rupley based algorithm?

Thank you for your help.

Sincerely,

Michael Korbus


Michael Korbus
Dipl.-Ing. Biotechnologie (FH)

Hochschule Darmstadt
University of Applied Sciences
Fachbereich Chemie u. Biotechnologie
Schnittspahnstr. 12
D-64287 Darmstadt

Tel +49/6151/16-8630
Fax +49/6151/16-8404




------------------------------

Message: 2
Date: Mon, 18 Feb 2013 14:09:24 +0100
From: Florian.Capito at external.merckgroup.com
To: chimera-users at cgl.ucsf.edu
Subject: [Chimera-users] Unit of electrostatic surface coloring within
        Chimera
Message-ID:
        <OF57DE4D54.6BC4EDF1-ONC1257B16.004734C6-C1257B16.004845D9 at merck.de>
Content-Type: text/plain; charset=ISO-8859-1


To whom it may concern,

I am using Chimera to color surfaces of proteins according to electrostatic
potential files calculated by APBS.
Now, in Chimera, there is the option to select a threshold, e.g. at which
value the surface should be colored in red and at which value it is colored
in blue.

Now i would like to know in which unit this threshold works? Is it kcal
(mol?e)-1?

While this has been described for the Coloumbic surface coloring within
Chimera Help, I could not find any explanation for this in the help menu,
when loading external APBS potential files into Chimera.

Thank You very much for Your time and help!!!


Mit freundlichen Gr?ssen/ With best regards

Florian Capito
MM-PTD-New Downstream Darmstadt
Location A17/217
Postcode: A046/509
Phone: +49 6151 72-7168
Email: florian.capito at external.merckgroup.com
Merck KGaA
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------------------------------

Message: 3
Date: Mon, 18 Feb 2013 12:24:37 +0100
From: kanika sharma <ksharma997 at gmail.com>
To: chimera-users at cgl.ucsf.edu
Subject: [Chimera-users] Drug-Protein Interaction
Message-ID:
        <CAAo-yeL3vs_KH76GdFQT0iP39-K2zcYRuBvmUG8pgfTxt8ivAQ at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi All,

I docked a drug to a protein structure using Autodock Vina. To view the
result, I am using View Dock. I now have 5 positions in which the drug is
docked into the protein. Is there a way to figure out which residues in the
protein are interacting with the drug molecule at each position?

--
*Regards,*
*
*
*Kanika Sharma*
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Message: 4
Date: Tue, 19 Feb 2013 09:22:16 -0800
From: Elaine Meng <meng at cgl.ucsf.edu>
To: "Minor, Armond" <minoav69 at suny.oneonta.edu>
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] New user-visualizing coulombic
Message-ID: <7EC6C1E2-78EB-4332-AFF5-E25BCEB30673 at cgl.ucsf.edu>
Content-Type: text/plain; charset=us-ascii

Hi Armond,
There are different methods of calculating electrostatic potential.

If you want to use Coulomb's law, just use the Coulombic Surface Coloring tool.  It is not necessary to run any other programs or tools.  The Coulombic method is simple and Chimera does all the calculations, as described here:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html>

Some other programs perform a more complicated "continuum electrostatics" calculation: they solve the Poisson-Boltzmann equation.  These programs include APBS, DelPhi, and UHBD.   You used PDB2PQR to prepare the structure for APBS (PDB2PQR associates atoms with charge and radius values and writes out the format needed by APBS), and then you ran APBS, which produced the *.dx file.  That file is the electrostatic potential map.   When someone uses one of the continuum electrostatics programs to calculate an electrostatic potential map, they can open the map in Chimera and then use the Electrostatic Surface Coloring tool to color the molecular surface by the values.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html>

Several years ago I wrote a short explanation of continuum electrostatics calculations.  This is not part of the Chimera manual, but might be useful if you want to know more about them...
<http://www.cgl.ucsf.edu/home/meng/grpmt/escalc.html>

However, it sounds like you just want to display the  molecular surface and then use Coulombic Surface Coloring, not those other programs or tools.

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 Feb 15, 2013, at 6:04 PM, Minor, Armond wrote:

> Hello,
>   I am just starting out using the program for a project with my Biochemistry professor.  We are trying to develop a simple procedure to visualize the Coulombic surface of short DNA sequences.  I have very little experience working with Chimera and do not know if I am going about it in correct way that will yield meaningful data.  I have tried following the instruction but must of them seem to be for people who are more familiar with the programs than I am.  Basically what I have tried is opening a pdb file, running PDB2PQR, opening the pqr file then running APBS on that. I am not sure what to do with the .dx file that comes out and how to use it to color the surface.  If I use it to color the Electrostatic potential map I get a range of values that seem to be not what my professor is expecting.  If I instead use the coulombic surface tool I get values like she expects but I am not sure if these are connected to the .dx file or just the pdb2pqr file.  Any help would be gre!
 atly appreciated thank you.
>
> Armond Minor
> Student, Biochemistry, SUNY Oneonta




------------------------------

Message: 5
Date: Tue, 19 Feb 2013 08:56:26 -0800
From: Tom Goddard <goddard at sonic.net>
To: "Dougherty, Matthew T" <matthewd at bcm.edu>
Cc: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] session file/HID
Message-ID: <86B64776-B8AD-4EC6-B6D7-0E4483CE3B24 at sonic.net>
Content-Type: text/plain; charset=us-ascii

Hi Matt,

  I can send you a bit of Python code for a keyboard shortcut that does savepos using a name pN where N is the next available integer.  If you want to save some state in session files better to make a separate Chimera extension instead of modifying standard_accelerators.py.  I can provide an example of that.  What state do you want to save?  With the above method of choosing the next available savepos name you don't need to save in sessions the last N used since it can be figured out from the existing savepos names which are already saved in sessions.  I'll try to post the example late today, taking cat to vet this morning.

        Tom


On Feb 17, 2013, at 10:16 PM, "Dougherty, Matthew T" wrote:

> I am developing some USB HID midware code utilizing keyboard shortcuts.
> This is being done using controllermate to generate an organized system of text strings across devices, and corresponding additions in standard_accelerators.py
>
> One thing I need to write is an automated method that will increment keyframe names to be used for savepos.
> On a more general level, how do I create variables in standard_accelerators.py that willbe saved in the session file, so I can retrieve them at a later session?
>
> thanks,
>
> Matthew Dougherty
> National Center for Macromolecular Imaging
> Baylor College of Medicine
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>




------------------------------

Message: 6
Date: Tue, 19 Feb 2013 09:43:56 -0800
From: Elaine Meng <meng at cgl.ucsf.edu>
To: "Smith, Susan Margaret Ellen" <smsmit7 at emory.edu>
Cc: UCSF Chimera Mailing List <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] questions about modeller and task panel
Message-ID: <4409AF75-A0A4-4071-85EA-657995D44D89 at cgl.ucsf.edu>
Content-Type: text/plain; charset=us-ascii

Hi Susan,
When I run Modeller calculations via Chimera and open the Task Manager, there is a "Cancel" button on the far right, and clicking it aborts the job.

However, in your case it might be confused and think the job is running when it has actually already failed due to the installation problem.  From the error message, it does really appear to be an installation problem, not where to put the output. The bottom of the traceback just says the output file doesn't exist.

You could try running using the web service instead of your local installation, and in that case the Cancel button on Task Manager should function because the job is actually running.

As for the installation problem, I don't know what to say, because I have that same version of Modeller installed on my Mac and have not had any problems running it locally.  I just ran the automatic installer and did what it told me to do.  However, I am specifying the Modeller binary as
/Library/modeller-9.11/bin/mod9.11
NOT
> /Library/modeller-9.11/bin/mod9.11_mac10v4
as shown in your traceback.  You might try using the former instead and seeing if that helps.  If not, I can only say to ask the Modeller help about the installation problem.

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 Feb 17, 2013, at 2:43 PM, Smith, Susan Margaret Ellen wrote:

> Hello,
> I am trying to use Chimera as an interface to a local installation of Modeller on my Mac.
>
> I have two questions:
> 1) When I open the task panel, I can see the current tasks and the completed tasks (nice visual cuing), but I do not see any way to kill a job.  How can I select a job and how can I stop it?
>
> 2) When I run the tutorial example for Modeller, I get the following message, which seems like it is telling me that something is wrong (although the job appears to still be running in the task panel).  I have re-installed the Modeller package, but I don't know what 'environment variable' was not set ... It seems like the program doesn't know where to put the output, although I specified a path for the temporary output.  Can you help with this?
>
> Thanks,
> Susan
>
> Target seq: oprd_human
> Template structures:
>        4DKL (#0)Run locally, the Modeller binary location: /Library/modeller-9.11/bin/mod9.11_mac10v4
> Now, modeller is running locally...
> MODELLER process output
> -----------------------
> FATAL ERROR: MODINSTALL9v11 environment variable not set: incomplete MODELLER installation
> -----------------------
> MODELLER process errors
> -----------------------
> -----------------------
> Traceback (most recent call last):
>  File "/Applications/Chimera.app/Contents/Resources/share/chimera/tasks.py", line 179, in runStatusCB
>    task.statusCBList[0]()
>  File "/Applications/Chimera.app/Contents/Resources/share/chimera/SubprocessMonitor.py", line 166, in statusCB
>    self.finished()
>  File "/Applications/Chimera.app/Contents/Resources/share/chimera/SubprocessMonitor.py", line 201, in finished
>    self._after(self._aborted)
>  File "/Applications/Chimera.app/Contents/Resources/share/MultAlignViewer/ModellerBase.py", line 635, in _collectResultsCB
>    OKModels = self._showingOKmodels(self.pathTemp)
>  File "/Applications/Chimera.app/Contents/Resources/share/MultAlignViewer/ModellerBase.py", line 646, in _showingOKmodels
>    modelsInfoFile = osOpen(os.path.join(outputPath, "ok_models.dat"))
>  File "/Applications/Chimera.app/Contents/Resources/share/OpenSave/__init__.py", line 324, in osOpen
>    raise UserError(val)
> UserError: [Errno 2] No such file or directory: '/Users/dlambe/Desktop/ok_models.dat'
>




------------------------------

Message: 7
Date: Tue, 19 Feb 2013 09:49:00 -0800
From: Elaine Meng <meng at cgl.ucsf.edu>
To: kanika sharma <ksharma997 at gmail.com>
Cc: UCSF Chimera Mailing List <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Drug-Protein Interaction
Message-ID: <3778D393-BFE4-4BFB-9A95-D93D70A495A6 at cgl.ucsf.edu>
Content-Type: text/plain; charset=us-ascii

Please see previous answer to same question:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-February/008461.html>

On Feb 18, 2013, at 3:24 AM, kanika sharma wrote:

> Hi All,
>
> I docked a drug to a protein structure using Autodock Vina. To view the result, I am using View Dock. I now have 5 positions in which the drug is docked into the protein. Is there a way to figure out which residues in the protein are interacting with the drug molecule at each position?
>
> --
> Regards,
>
> Kanika Sharma




------------------------------

Message: 8
Date: Tue, 19 Feb 2013 09:53:03 -0800
From: Elaine Meng <meng at cgl.ucsf.edu>
To: "Korbus, Michael" <michael.korbus at h-da.de>
Cc: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Algorithm for areaSAS calculations
Message-ID: <05BEF74A-0539-4810-A403-535DED23B61A at cgl.ucsf.edu>
Content-Type: text/plain; charset=us-ascii

Dear Michael,
The SAS and SES values come from the MSMS package.  I don't know what algorithm is used, but it may be described somewhere in the MSMS website or reference linked to that site:

<http://mgltools.scripps.edu/packages/MSMS/>

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 Feb 18, 2013, at 1:27 AM, Korbus, Michael wrote:

> Dear Ladies and Gentlemen,
>
> I have a question concerning calculation of areaSAS with chimera. Which algorithm is used? A Shrake-Rupley based algorithm?
>
> Thank you for your help.
>
> Sincerely,
>
> Michael Korbus




------------------------------

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