[Chimera-users] Maximum surface areas for each amino acid
Boaz Shaanan
bshaanan at bgu.ac.il
Wed Dec 15 01:02:17 PST 2010
Hi Elaine,
The values in the table you mentioned seem to correspond to side-chain accessibility only, if I compare them to those for Gly-X-Gly peptide as in the classical paper by Miller et al. (1987), 196, 641-656. Their table can also be found in the book by Creighton: Proteins, 2nd edition, p. 142.
Best regards,
Boaz
----- Original Message -----
From: chimera-users-request at cgl.ucsf.edu
Date: Tuesday, December 14, 2010 21:11
Subject: Chimera-users Digest, Vol 92, Issue 11
To: chimera-users at cgl.ucsf.edu
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> Today's Topics:
>
> 1. Maximum surface areas for each amino acid (Tom
> Goddard) 2. Center of segmentation regions (Tom Goddard)
> 3. Chimera Error (Kshatresh Dutta Dubey)
> 4. Re: Chimera Error (Elaine Meng)
> 5. Re: Maximum surface areas for each amino acid
> (Elaine Meng)
> 6. 3D-Stereo. (ayassin at wadsworth.org)
> 7. merging 3D volumes (Marlovits,Thomas)
> 8. Re: merging 3D volumes (Elaine Meng)
>
>
> -----------------------------------------------------------------
> -----
>
> Message: 1
> Date: Mon, 13 Dec 2010 18:08:11 -0800
> From: Tom Goddard <goddard at sonic.net>
> Subject: [Chimera-users] Maximum surface areas for each amino acid
> To: iropson at psu.edu
> Cc: 'Chimera BB' <chimera-users at cgl.ucsf.edu>
> Message-ID: <4D06D18B.7040806 at sonic.net>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Ira,
>
> I don't know of any table of maximal solvent
> accessible surface areas
> for each residue type when bounded by glycines. Maybe
> someone on the
> Chimera mailing list will know.
>
> A Chimera Python script could run through the PDB
> and accumulate
> per-residue surface area statistics. One trouble with that
> would be
> that surface calculation fails in Chimera in some percentage of
> cases
> (~5%) due to numerical problems.
>
> Tom
>
> > Hi Tom,
> >
> > Love the software. Do you have a table for calculating the
> maximum
> > available surface area for amino acids eg.(Gly-Xxx-Gly) so
> that I can
> > get a relative percentage exposed surface area from the
> calculations?
> > Do you know how to find one in the literature? Has anyone
> written a
> > program that describes the possible surface exposure for a
> residue in
> > a particular secondary structure and/or a particular sequence?
> This
> > maximal value would certainly be different depending on the
> local
> > sequence and structure. For example, a residue in the middle
> of a
> > helix would have to be shielded from the solvent by the i+4
> and i-4
> > residues, and the size of those residues would matter.
> >
> > Thanks,
> > Ira
> >
> >
> > On 12/10/10 2:41 PM, Tom Goddard wrote:
> >> Hi Sumitro,
> >>
> >> I made a Chimera video tutorial showing how to
> determine which
> >> residues are on the surface.
> >>
> >> http://www.cgl.ucsf.edu/chimera/videodoc/surfaceresidues/index.html
> >>
> >> Tom
>
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> ------------------------------
>
> Message: 2
> Date: Mon, 13 Dec 2010 18:55:05 -0800
> From: Tom Goddard <goddard at sonic.net>
> Subject: [Chimera-users] Center of segmentation regions
> To: twsteele2 at vcu.edu, "'Chimera BB'" <chimera-users at cgl.ucsf.edu>
> Message-ID: <4D06DC89.40101 at sonic.net>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Tyler,
>
> The Chimera Segger segmentation tool currently
> doesn't report the
> geometric center of segmentation regions or the principal
> axes. I've
> attached a Python script that will do that. Select the
> regions in
> Chimera then open the script (File / Open). The results
> will appear in
> the reply log (menu Favorites / Reply Log). The results
> are in physical
> coordinates (taking account of volume grid spacing), not grid
> index units.
>
> Tom
>
> > Dr. Meng,
> >
> > I am using Segger in Chimera and displaying the principal axes
> for
> > some of my segmentations. I am wondering if there is a
> way to find
> > the XYZ coordinates of the origin of the principal axes for
> each of my
> > segments. Is there a way to put the coordinates for
> these axes in a
> > text file?
> >
> > Thank you,
> >
> > Tyler Steele
> >
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> ------------------------------
>
> Message: 3
> Date: Tue, 14 Dec 2010 11:17:44 +0530
> From: Kshatresh Dutta Dubey <kshatresh at gmail.com>
> Subject: [Chimera-users] Chimera Error
> To: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> Message-ID:
> <AANLkTin0BpYmzRNFCfax2t4AmJSE7k3oXg+0DufdEtpW at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear All,
> When i am trying to assign partial charge on a molecule, it is
> giving error
> something like this-
>
> AttributeError: '_chimera.Atom' object has no attribute 'gaffType'
> File "/opt/UCSF/Chimera64-1.5rc/share/WriteMol2/__init__.py",
> line 289, in
> writeMol2
> atomType = atom.gaffType
>
> I am using chimera 1.5 on linux 64-bit
>
> Kindly help to resolve this problem
> Thanks in advance
> kshatresh
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> ------------------------------
>
> Message: 4
> Date: Tue, 14 Dec 2010 09:36:54 -0800
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Chimera Error
> To: Kshatresh Dutta Dubey <kshatresh at gmail.com>
> Cc: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> Message-ID: <11989EB7-CB47-4ADE-81D6-5196DCFB4D43 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=us-ascii
>
> Hi Kshatresh,
> Please use "Help... Report a Bug" in the Chimera menu instead of
> sending mail to chimera-users. This will automatically
> include information about what version of Chimera and type of
> computer you are using. If you attach the molecule
> structure file, and enter a description of how to generate the
> error, we may be able to identify the problem. Otherwise
> it is not enough information. Also, if you want to hear
> back, please include your email address in the bugreport.
> Thanks,
> 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 Dec 13, 2010, at 9:47 PM, Kshatresh Dutta Dubey wrote:
>
> > Dear All,
> > When i am trying to assign partial charge on a molecule, it is
> giving error something like this-
> >
> > AttributeError: '_chimera.Atom' object has no attribute 'gaffType'
> > File "/opt/UCSF/Chimera64-1.5rc/share/WriteMol2/__init__.py",
> line 289, in writeMol2
> > atomType = atom.gaffType
> >
> > I am using chimera 1.5 on linux 64-bit
> >
> > Kindly help to resolve this problem
> > Thanks in advance
> > kshatresh
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 14 Dec 2010 09:55:14 -0800
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Maximum surface areas for each
> amino acid
> To: iropson at psu.edu
> Cc: Chimera BB <chimera-users at cgl.ucsf.edu>
> Message-ID: <B5A48344-3706-403C-8FA1-8DB7A5FC5830 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=us-ascii
>
> Hi Ira,
> There is such a table in the Getarea online manual (about
> halfway down this page):
>
> <http://curie.utmb.edu/area_man.html>
>
> >From that page, 'The "random coil" value of a residue X is the
> average solvent-accessible surface area of X in the tripeptide
> Gly-X-Gly in an ensemble of 30 random conformations.'
>
> Be aware, however, that various programs use different atomic
> radii and that those values will affect the surface areas.
> Chimera likely uses different radii than Getarea, but I believe
> both programs use reasonable values and that it may still be
> useful to normalize by the Getarea random coil values as long as
> you are aware of these issues. At least the default probe
> radius in Chimera and Getarea is the same, 1.4 Angstroms.
> It is unclear if Getarea uses the same random coil values even
> if you specify a different probe radius.
>
> Also be careful about solvent-excluded surface (which is what
> Chimera displays) versus solvent-accessible surface.
> Chimera gives both kinds of areas, whereas the Getarea random
> coil values are SAS. The SAS is farther out from the
> atomic centers and the values range much larger.
>
> 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 Dec 13, 2010, at 6:08 PM, Tom Goddard wrote:
>
> > Hi Ira,
> > I don't know of any table of maximal solvent
> accessible surface areas for each residue type when bounded by
> glycines. Maybe someone on the Chimera mailing list will know.
> > A Chimera Python script could run through the PDB
> and accumulate per-residue surface area statistics. One
> trouble with that would be that surface calculation fails in
> Chimera in some percentage of cases (~5%) due to numerical problems.
> > Tom
> >
> >> Hi Tom,
> >> Love the software. Do you have a table for calculating the
> maximum available surface area for amino acids eg.(Gly-Xxx-Gly)
> so that I can get a relative percentage exposed surface area
> from the calculations? Do you know how to find one in the
> literature? Has anyone written a program that describes the
> possible surface exposure for a residue in a particular
> secondary structure and/or a particular sequence? This maximal
> value would certainly be different depending on the local
> sequence and structure. For example, a residue in the middle of
> a helix would have to be shielded from the solvent by the i+4
> and i-4 residues, and the size of those residues would matter.
> >> Thanks,
> >> Ira
> >
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Sun, 12 Dec 2010 21:26:14 -0500 (EST)
> From: ayassin at wadsworth.org
> Subject: [Chimera-users] 3D-Stereo.
> To: chimera-users at cgl.ucsf.edu
> Message-ID:
> <5424fe290c060bb1af2e8af55521f253.squirrel at webmailz1.wadsworth.org>
> Content-Type: text/plain;charset=iso-8859-1
>
> Hello,
>
> Will the sequential stereo work with the Nvidia 3D vision kit
> availablewith the Toshiba 3DV series laptops? if not, What would
> be the best option
> for sequential stereo?
>
> Thank You.
>
> Aymen Yassin.
>
>
>
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> ------------------------------
>
> Message: 7
> Date: Tue, 14 Dec 2010 13:10:12 +0100
> From: "Marlovits,Thomas" <Thomas.Marlovits at imba.oeaw.ac.at>
> Subject: [Chimera-users] merging 3D volumes
> To: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
> Message-ID: <F5165B14-33C1-4055-A942-57B1B334F3E2 at imp.ac.at>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
>
> I was wondering, whether a 3D map can be placed into a box
> with a user defined number or x/y/z planes ? Ideally, I
> would like to place several 3D maps into boxes of the same
> dimensions and would like then to merge all maps into one 3D map
> file. Is this possible ?
>
> Tx for your fast answer,
> Best,
> -Thomas
>
>
>
>
> Thomas C Marlovits
> Research Group Leader
> marlovits at imp.ac.at
>
>
>
>
>
>
> ------------------------------
>
> Message: 8
> Date: Tue, 14 Dec 2010 11:10:06 -0800
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] merging 3D volumes
> To: "Marlovits,Thomas" <Thomas.Marlovits at imba.oeaw.ac.at>
> Cc: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
> Message-ID: <9E99068D-40F3-4C06-B8C8-2FB752AAB4AB at cgl.ucsf.edu>
> Content-Type: text/plain; charset=us-ascii
>
> Hi Thomas,
> The command "vop add" merges maps. (There is a similar "vop
> subtract" command too.) If the maps are not on the same
> grid, this resamples as needed. It lets you specify a subregion
> (which planes to use) from the reference map.
>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#add>
>
> I hope this is what you had in mind,
> 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 Dec 14, 2010, at 4:10 AM, Marlovits,Thomas wrote:
>
> > Hi,
> > I was wondering, whether a 3D map can be placed into a
> box with a user defined number or x/y/z planes ? Ideally,
> I would like to place several 3D maps into boxes of the same
> dimensions and would like then to merge all maps into one 3D map
> file. Is this possible ?
> > Tx for your fast answer,
> > Best,
> > -Thomas
> >
>
>
>
> ------------------------------
>
> _______________________________________________
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> Chimera-users at cgl.ucsf.edu
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>
>
> End of Chimera-users Digest, Vol 92, Issue 11
> *********************************************
>
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
Phone: 972-8-647-2220 ; Fax: 646-1710
Skype: boaz.shaanan
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