[Chimera-users] Chimera-users Digest, Vol 109, Issue 28
Boaz Shaanan
bshaanan at exchange.bgu.ac.il
Thu May 24 14:35:30 PDT 2012
Hi,
In answer to Nikolay's question about ESP values in various positions:
1) Elaine is absolutely right in pointing you to the APBS bb. If you look in their FAQ you'll notice that the question has been addressed several times.
2) There is an 'atompot' command that you can use when you run apbs. It'll print the values for each atom in the pdb, the only problem is that last time I tried it there were no atom names in output which was difficult for me (apbs team were supposed to add that feature) but x,y.z were there.
3) If atompot is not what you need somebody in the abps team will surely help you.
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
________________________________________
From: chimera-users-bounces at cgl.ucsf.edu [chimera-users-bounces at cgl.ucsf.edu] on behalf of chimera-users-request at cgl.ucsf.edu [chimera-users-request at cgl.ucsf.edu]
Sent: Thursday, May 24, 2012 10:00 PM
To: chimera-users at cgl.ucsf.edu
Subject: Chimera-users Digest, Vol 109, Issue 28
Send Chimera-users mailing list submissions to
chimera-users at cgl.ucsf.edu
To subscribe or unsubscribe via the World Wide Web, visit
http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
or, via email, send a message with subject or body 'help' to
chimera-users-request at cgl.ucsf.edu
You can reach the person managing the list at
chimera-users-owner at cgl.ucsf.edu
When replying, please edit your Subject line so it is more specific
than "Re: Contents of Chimera-users digest..."
Today's Topics:
1. Fwd: ESP calculations (Eric Pettersen)
2. APBS output format (Elaine Meng)
3. Hydrogen bond energy calculation (Aditya Padhi)
4. Re: Hydrogen bond energy calculation (Elaine Meng)
----------------------------------------------------------------------
Message: 1
Date: Wed, 23 May 2012 13:18:14 -0700
From: Eric Pettersen <pett at cgl.ucsf.edu>
To: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
Subject: [Chimera-users] Fwd: ESP calculations
Message-ID: <4C557064-D2EC-45A5-9523-B35E683C76D5 at cgl.ucsf.edu>
Content-Type: text/plain; charset="us-ascii"; Format="flowed";
DelSp="yes"
Begin forwarded message:
> From: Nikolay Igorovich Rodionov <nirodion at syr.edu>
> Date: May 21, 2012 12:43:34 PM PDT
> To: Eric Pettersen <pett at cgl.ucsf.edu>
> Subject: RE: [Chimera-users] ESP calculations
>
> Thank you both,
>
> Can either of you tell me how the information in a volume data set
> is organized? I am looking at a .dx file that I created using APBS
> which I would assume to be very similar to the volumetric data sets
> created by Chimera. What does each column of data represent? Is
> there any way for me to sort the ESP data based on position using
> Excel or Matlab? I am only concerned with ESP data for one region of
> molecule. If you could point me in the direction of some good
> documentation on this file type it would be great.
I don't know, so I'm forwarding this out to chimera-users land, where
someone might have an answer...
--Eric
>
> Thanks again,
> Nikolay Rodionov
>
> -----Original Message-----
> From: Eric Pettersen [mailto:pett at cgl.ucsf.edu]
> Sent: Monday, May 21, 2012 2:57 PM
> To: chimera-users at cgl.ucsf.edu BB
> Cc: Nikolay Igorovich Rodionov
> Subject: Re: [Chimera-users] ESP calculations
>
> Also, if you compute a volume, you can use the "Values at Atom
> Positions" tool to, um, get the values at atom positions (say, a
> ligand), if that's relevant to what you're doing.
>
> --Eric
>
> On May 21, 2012, at 9:09 AM, Elaine Meng wrote:
>
>> Hi Nikolay,
>> You can generate a grid of values with the "Compute grid" option of
>> Coulombic Surface Coloring (or corresponding option of the
>> "coulombic"
>> command). The grid is a volume data set, and when it is generated
>> the
>> Volume Viewer and Surface Color dialogs will automatically appear.
>>
>> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/
>> co
>> ulombic.html
>>>
>> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/
>> co
>> ulombic.html#volume
>>>
>>
>> You can save the grid to a file with the FIle menu of Volume Viewer.
>> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/
>> volumeviewer
>> /framevolumeviewer.html
>>>
>>
>> As for the values at each point of the surface, I don't know of a way
>> to write these all to a file, but in Surface Color if you click the
>> Options button and then turn on the option to "Report value at mouse
>> position" it will report the values in the status line at the bottom
>> of the Chimera window when you click into the graphics window and
>> then
>> mouse over the surface. I just noticed that to make this work it is
>> necessary to recolor the surface first by clicking the Color button
>> on
>> this dialog, which may be a bug, but that's the workaround!
>> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/
>> su
>> rfcolor.html
>>>
>>
>> If you have the grid file saved you can reopen it in Chimera later
>> and
>> use it in Surface Color without rerunning the ESP calculation.
>>
>> However, keep in mind that Coulombic ESP is more for qualitative
>> purposes of visualization or making comparisons between related
>> structures than for absolute quantitative accuracy. For example, you
>> could easily make all the ESP values half as large simply by doubling
>> the dielectric constant used in their calculation, as shown in the
>> equation in the Coulombic Surface Coloring manual page.
>>
>> 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 May 21, 2012, at 8:05 AM, Nikolay Igorovich Rodionov wrote:
>>
>>> Hi all,
>>> I was wondering if there was a way to get an output data file
>>> regarding ESP coloring and calculations based on Coulomb's law. The
>>> visualization is great but I would also like to quantify the data.
>>> Thank you,
>>> Nikolay Rodionov
>>
>>
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>
>
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20120523/b2fde818/attachment-0001.html>
------------------------------
Message: 2
Date: Wed, 23 May 2012 13:53:19 -0700
From: Elaine Meng <meng at cgl.ucsf.edu>
To: Nikolay Igorovich Rodionov <nirodion at syr.edu>
Cc: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
Subject: [Chimera-users] APBS output format
Message-ID: <6E9CD745-D62E-4DFA-BE42-6AF8B05A61DB at cgl.ucsf.edu>
Content-Type: text/plain; charset=us-ascii
Since it is the APBS format, I could only suggest asking the APBS developers or looking at their documentation.
<http://www.poissonboltzmann.org/apbs/>
Many formats are not well documented anywhere, but I don't know if that is true of this format in particular.
In Chimera, the options would be to
(a) examine the code to read this format. This is beyond my knowledge, and no use unless you can understand code, but here is some info on where to look
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#newformats>
(b) write out the data in a different format for which you can find a description. Output format choices: MRC, NetCDF, Chimera map, or BRIX format.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output>
Some additional info on volume formats:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume>
Elaine
On May 23, 2012, at 1:18 PM, Eric Pettersen wrote:
> Begin forwarded message:
>
>> From: Nikolay Igorovich Rodionov <nirodion at syr.edu>
>> Date: May 21, 2012 12:43:34 PM PDT
>> To: Eric Pettersen <pett at cgl.ucsf.edu>
>> Subject: RE: [Chimera-users] ESP calculations
>>
>> Thank you both,
>>
>> Can either of you tell me how the information in a volume data set is organized? I am looking at a .dx file that I created using APBS which I would assume to be very similar to the volumetric data sets created by Chimera. What does each column of data represent? Is there any way for me to sort the ESP data based on position using Excel or Matlab? I am only concerned with ESP data for one region of molecule. If you could point me in the direction of some good documentation on this file type it would be great.
>
> I don't know, so I'm forwarding this out to chimera-users land, where someone might have an answer...
>
> --Eric
>
>>
>> Thanks again,
>> Nikolay Rodionov
>>
------------------------------
Message: 3
Date: Thu, 24 May 2012 09:27:07 +0530
From: Aditya Padhi <adi.uoh at gmail.com>
To: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
Subject: [Chimera-users] Hydrogen bond energy calculation
Message-ID:
<CABfSPKAuwjcP9BivbH5aLoTahQD=MXzL-O=fV+DkacR7bEG3Qg at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Dear Chimera users,
I want to calculate the "energy or force" exerted between amino
acid residues interacted by Hydrogen bonds throughout a total trajectory
from MD simulation of a protein performed using Amber 10.
(Example: H-bond between Isoleucine17-Asp15, Asp15-Ile46, Ile46-His13 etc,
I want to calculate the H-bond interaction energy between these pair of
residues and hence the net energy).
I searched in the tutorials and literature but could not able to find any
appropriate solutions. If anyone has the idea, please assist me finding the
solution of this problem.
Thanking you,
Regards
Aditya.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20120524/f90d1ffe/attachment-0001.html>
------------------------------
Message: 4
Date: Thu, 24 May 2012 08:20:06 -0700
From: Elaine Meng <meng at cgl.ucsf.edu>
To: Aditya Padhi <adi.uoh at gmail.com>
Cc: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Hydrogen bond energy calculation
Message-ID: <1C6E028E-0EDC-4CAD-A361-9BDF874D45C3 at cgl.ucsf.edu>
Content-Type: text/plain; charset=us-ascii
Hi Aditya,
Chimera calculates possible H-bonds, but it does not calculate their energies, sorry.
Chimera H-bond detection is a yes-or-no decision using geometric (distance and angle) cutoffs. You would have to use some other program to estimate H-bond interaction energies.
Regards,
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 May 23, 2012, at 8:57 PM, Aditya Padhi wrote:
> Dear Chimera users,
> I want to calculate the "energy or force" exerted between amino acid residues interacted by Hydrogen bonds throughout a total trajectory from MD simulation of a protein performed using Amber 10.
>
> (Example: H-bond between Isoleucine17-Asp15, Asp15-Ile46, Ile46-His13 etc, I want to calculate the H-bond interaction energy between these pair of residues and hence the net energy).
>
> I searched in the tutorials and literature but could not able to find any appropriate solutions. If anyone has the idea, please assist me finding the solution of this problem.
>
> Thanking you,
> Regards
> Aditya.
------------------------------
_______________________________________________
Chimera-users mailing list
Chimera-users at cgl.ucsf.edu
http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
End of Chimera-users Digest, Vol 109, Issue 28
**********************************************
More information about the Chimera-users
mailing list