From owner-chemistry@ccl.net Fri Oct 15 11:43:00 2010
From: "Andrew Voronkov drugdesign%x%yandex.ru" <owner-chemistry_-_server.ccl.net>
To: CCL
Subject: CCL: free software to measure RMSD and align proteins
Message-Id: <-42953-101015111440-15591-/SMjwJ4CcEoJPte3bWUX3Q_-_server.ccl.net>
X-Original-From: Andrew Voronkov <drugdesign * yandex.ru>
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Date: Fri, 15 Oct 2010 19:14:32 +0400
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Sent to CCL by: Andrew Voronkov [drugdesign/./yandex.ru]
Dear CCL users,
can you please recommend free software for homologic proteins comparison, alignment and RMSD measurements.
I know DS visualizer and VMD, but is there anything else?

Best regards,
Andrew


From owner-chemistry@ccl.net Fri Oct 15 12:17:00 2010
From: "Jon Mikel Azpiroz jmkimteo{=}hotmail.com" <owner-chemistry . server.ccl.net>
To: CCL
Subject: CCL: Energy partitioning scheme ADF - Electrostatic interaction
Message-Id: <-42954-101015114344-27105-q7WCQBJchYjE5tu8ipngBA . server.ccl.net>
X-Original-From: "Jon Mikel  Azpiroz" <jmkimteo : hotmail.com>
Date: Fri, 15 Oct 2010 11:43:43 -0400


Sent to CCL by: "Jon Mikel  Azpiroz" [jmkimteo:-:hotmail.com]
Dear members of CCL,

I am trying to reproduce the results given by the energy partitioning scheme of ADF for a system in which 2 fragments have been defined. In particular, I am trying to reproduce the electrostatic interaction, which is calculated "between the unperturbed charge distributions of the prepared fragments as they are brought together at their final positions". Consequently, I have taken the multipole derived charges (MCD-q) and computed the electrostatic interaction as the sum of the classical coulombic interactions between the atoms of fragment1 and fragment2. The electrostatic energies I get are 10 times smaller that the ones given by the program.

Even if I have approximate the atoms as puntual charges, I suspect that the agreement should be better.

Does anyone know the way in which ADF calculates the electrostatic interaction? Could anyone give an advice?

Thank you in advance for your attention.

Regards.

Jon Mikel Azpiroz
University of the Basque Country


From owner-chemistry@ccl.net Fri Oct 15 12:52:00 2010
From: "Tim Cheeseright tim=-=cresset-bmd.com" <owner-chemistry~~server.ccl.net>
To: CCL
Subject: CCL: New release of free molecule viewer/editor
Message-Id: <-42955-101015104228-1652-u9tGJiZjnb+6cnPNmzyCHA~~server.ccl.net>
X-Original-From: "Tim  Cheeseright" <tim::cresset-bmd.com>
Date: Fri, 15 Oct 2010 10:42:22 -0400


Sent to CCL by: "Tim  Cheeseright" [tim^_^cresset-bmd.com]
Hi CCLers
Cresset is proud to announce a new release of FieldView, our molecular editor and viewer that is free to all users. Following popular request we have introduced support for Mac OS X making FieldView our first native Mac application. We would love to hear what the Mac users think.

All platforms benefit from better import and export of data and improved integration with FieldScreen, our virtual screening platform. Existing FieldView users can get a new download by emailing support|-|cresset-group.com, new users can get FieldView by following the links on the FieldView product page: http://www.cresset-group.com/product/fieldview 

Tim Cheeseright
tim|-|cresset-group.com
Cresset
UK


From owner-chemistry@ccl.net Fri Oct 15 13:27:00 2010
From: "Marcel Swart marcel.swart|icrea.cat" <owner-chemistry#,#server.ccl.net>
To: CCL
Subject: CCL: Energy partitioning scheme ADF - Electrostatic interaction
Message-Id: <-42956-101015130729-1973-+o5OBk77QXrEBhaqmbbjVg#,#server.ccl.net>
X-Original-From: Marcel Swart <marcel.swart:_:icrea.cat>
Content-Type: multipart/alternative; boundary=Apple-Mail-5--382401197
Date: Fri, 15 Oct 2010 19:07:23 +0200
Mime-Version: 1.0 (Apple Message framework v1081)


Sent to CCL by: Marcel Swart [marcel.swart+/-icrea.cat]

--Apple-Mail-5--382401197
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain;
	charset=iso-8859-1

First of all, it would be better to ask this question on the ADF forums: =
http://www.scm.com/forums/

Second, a detailed description is given in:

F. M. Bickelhaupt, E. J. Baerends
Kohn-Sham Density Functional Theory: Predicting and Understanding =
Chemistry
In: Rev. Comput. Chem.; K. B. Lipkowitz and D. B. Boyd, Eds.; Wiley-VCH: =
New York, 2000, Vol. 15, pp. 1-86.

I'm sure that if you ask Matthias Bickelhaupt (fm.bickelhaupt-,-few.vu.nl) =
he could provide
you with a reprint of it.

Finally, this term is simply what it says, the electrostatic interaction =
of the charge densities,
not point charges. These two terms can not be simply related, unless the =
fragments are far away
> from each other, and hence there would be no overlapping charge =
densities. In this latter case,
you should probably see similar energies.

Marcel

On 15 Oct 2010, at 17:43, Jon Mikel Azpiroz jmkimteo{=3D}hotmail.com =
wrote:

> Dear members of CCL,
>=20
> I am trying to reproduce the results given by the energy partitioning =
scheme of ADF for a system in which 2 fragments have been defined. In =
particular, I am trying to reproduce the electrostatic interaction, =
which is calculated "between the unperturbed charge distributions of the =
prepared fragments as they are brought together at their final =
positions". Consequently, I have taken the multipole derived charges =
(MCD-q) and computed the electrostatic interaction as the sum of the =
classical coulombic interactions between the atoms of fragment1 and =
fragment2. The electrostatic energies I get are 10 times smaller that =
the ones given by the program.
>=20
> Even if I have approximate the atoms as puntual charges, I suspect =
that the agreement should be better.
>=20
> Does anyone know the way in which ADF calculates the electrostatic =
interaction? Could anyone give an advice?
>=20
> Thank you in advance for your attention.
>=20
> Regards.
>=20
> Jon Mikel Azpiroz
> University of the Basque Country


=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
dr. Marcel Swart

ICREA Research Professor at
Institut de Qu=EDmica Computacional
Universitat de Girona

Parc Cient=EDfic i Tecnol=F2gic
Edifici Jaume Casademont (despatx A-27)
Pic de Peguera 15
17003 Girona
Catalunya (Spain)

tel
+34-972-183240
fax
+34-972-183241
e-mail
marcel.swart-,-icrea.cat
marcel.swart-,-udg.edu
web
http://www.marcelswart.eu
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D






--Apple-Mail-5--382401197
Content-Transfer-Encoding: quoted-printable
Content-Type: text/html;
	charset=iso-8859-1

<html><head></head><body style=3D"word-wrap: break-word; =
-webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">First =
of all, it would be better to ask this question on the ADF =
forums:&nbsp;<a =
href=3D"http://www.scm.com/forums/">http://www.scm.com/forums/</a><div><br=
></div><div>Second, a detailed description is given =
in:</div><div><br></div><div>F. M. Bickelhaupt, E. J. =
Baerends<br>Kohn-Sham Density Functional Theory: Predicting and =
Understanding Chemistry<br>In:&nbsp;Rev. Comput. Chem.; K. B. Lipkowitz =
and D. B. Boyd, Eds.; Wiley-VCH: New York,&nbsp;2000,&nbsp;Vol. 15, pp. =
1-86.</div><div><br></div><div>I'm sure that if you ask Matthias =
Bickelhaupt (<a =
href=3D"mailto:fm.bickelhaupt-,-few.vu.nl">fm.bickelhaupt-,-few.vu.nl</a>) =
he could provide</div><div>you with a reprint of =
it.</div><div><br></div><div>Finally, this term is simply what it says, =
the electrostatic interaction of the charge =
<b>densities</b>,</div><div>not point charges. These two terms can not =
be simply related, unless the fragments are far away</div><div>from each =
other, and hence there would be no overlapping charge densities. In this =
latter case,</div><div>you should probably see similar =
energies.</div><div><br></div><div>Marcel</div><div><br></div><div><div><d=
iv>On 15 Oct 2010, at 17:43, Jon Mikel Azpiroz jmkimteo{=3D}hotmail.com =
wrote:</div><br class=3D"Apple-interchange-newline"><blockquote =
type=3D"cite">Dear members of CCL,<br><br>I am trying to reproduce the =
results given by the energy partitioning scheme of ADF for a system in =
which 2 fragments have been defined. In particular, I am trying to =
reproduce the electrostatic interaction, which is calculated "between =
the unperturbed charge distributions of the prepared fragments as they =
are brought together at their final positions". Consequently, I have =
taken the multipole derived charges (MCD-q) and computed the =
electrostatic interaction as the sum of the classical coulombic =
interactions between the atoms of fragment1 and fragment2. The =
electrostatic energies I get are 10 times smaller that the ones given by =
the program.<br><br>Even if I have approximate the atoms as puntual =
charges, I suspect that the agreement should be better.<br><br>Does =
anyone know the way in which ADF calculates the electrostatic =
interaction? Could anyone give an advice?<br><br>Thank you in advance =
for your attention.<br><br>Regards.<br><br>Jon Mikel =
Azpiroz<br>University of the Basque =
Country<br></blockquote></div><br><div>
<span class=3D"Apple-style-span" style=3D"border-collapse: separate; =
color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; =
font-variant: normal; font-weight: normal; letter-spacing: normal; =
line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; =
text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; =
-webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: =
0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: =
auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span =
class=3D"Apple-style-span" style=3D"border-collapse: separate; color: =
rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: =
normal; font-variant: normal; font-weight: normal; letter-spacing: =
normal; line-height: normal; orphans: 2; text-indent: 0px; =
text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; =
-webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: =
0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: =
auto; -webkit-text-stroke-width: 0px; "><div style=3D"word-wrap: =
break-word; -webkit-nbsp-mode: space; -webkit-line-break: =
after-white-space; "><span class=3D"Apple-style-span" =
style=3D"border-collapse: separate; color: rgb(0, 0, 0); font-family: =
Helvetica; font-size: medium; font-style: normal; font-variant: normal; =
font-weight: normal; letter-spacing: normal; line-height: normal; =
orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; =
widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; =
-webkit-border-vertical-spacing: 0px; =
-webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: =
auto; -webkit-text-stroke-width: 0px; "><div style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal =
normal normal 12px/normal Helvetica; "><br =
class=3D"Apple-interchange-newline">=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D</div><d=
iv style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; font: normal normal normal 12px/normal Helvetica; =
">dr. Marcel Swart</div><div style=3D"margin-top: 0px; margin-right: =
0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal =
12px/normal Helvetica; min-height: 14px; "><br></div><div =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; font: normal normal normal 12px/normal Helvetica; =
">ICREA Research Professor at</div><div style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal =
normal normal 12px/normal Helvetica; ">Institut de Qu=EDmica =
Computacional</div><div style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; font: normal normal normal =
12px/normal Helvetica; ">Universitat de Girona</div><div =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; font: normal normal normal 12px/normal Helvetica; =
min-height: 14px; "><br></div><div style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal =
normal normal 12px/normal Helvetica; ">Parc Cient=EDfic i =
Tecnol=F2gic</div><div style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; font: normal normal normal =
12px/normal Helvetica; ">Edifici Jaume Casademont (despatx =
A-27)</div><div style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; font: normal normal normal =
12px/normal Helvetica; ">Pic de Peguera 15</div><div style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: =
normal normal normal 12px/normal Helvetica; ">17003 Girona</div><div =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; font: normal normal normal 12px/normal Helvetica; =
">Catalunya (Spain)</div><div style=3D"margin-top: 0px; margin-right: =
0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal =
12px/normal Helvetica; min-height: 14px; "><br></div><div =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; font: normal normal normal 12px/normal Helvetica; =
">tel</div><div style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; font: normal normal normal =
12px/normal Helvetica; ">+34-972-183240</div><div style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: =
normal normal normal 12px/normal Helvetica; ">fax</div><div =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; font: normal normal normal 12px/normal Helvetica; =
">+34-972-183241</div><div style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; font: normal normal normal =
12px/normal Helvetica; ">e-mail</div><div style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal =
normal normal 12px/normal Helvetica; "><a =
href=3D"mailto:marcel.swart-,-icrea.cat">marcel.swart-,-icrea.cat</a></div><di=
v style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; font: normal normal normal 12px/normal Helvetica; "><a =
href=3D"mailto:marcel.swart-,-udg.edu">marcel.swart-,-udg.edu</a></div><div =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; font: normal normal normal 12px/normal Helvetica; =
">web</div><div style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; font: normal normal normal =
12px/normal Helvetica; "><a =
href=3D"http://www.marcelswart.eu">http://www.marcelswart.eu</a></div><div=
 style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; font: normal normal normal 12px/normal Helvetica; =
">=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D</div><div style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal =
normal normal 12px/normal Helvetica; min-height: 14px; =
"><br></div></span><br =
class=3D"Apple-interchange-newline"></div></span><br =
class=3D"Apple-interchange-newline"></span><br =
class=3D"Apple-interchange-newline">
</div>
<br></div></body></html>=

--Apple-Mail-5--382401197--


From owner-chemistry@ccl.net Fri Oct 15 14:02:00 2010
From: "Goedele Roos groos{=}vub.ac.be" <owner-chemistry(0)server.ccl.net>
To: CCL
Subject: CCL: free software to measure RMSD and align proteins
Message-Id: <-42957-101015132738-21671-1Qo/XhKoDVgHGW1RYaGhBg(0)server.ccl.net>
X-Original-From: Goedele Roos <groos~!~vub.ac.be>
Date: Fri, 15 Oct 2010 19:26:59 +0200


Sent to CCL by: Goedele Roos [groos .. vub.ac.be]
You can try PYMOl

http://www.pymol.org/

it's free for teaching purposes and for open source users





>Sent to CCL by: Andrew Voronkov [drugdesign/./yandex.ru]
>Dear CCL users,
>can you please recommend free software for homologic proteins comparison, alignment and RMSD measurements.
>I know DS visualizer and VMD, but is there anything else?
>
>Best regards,
>Andrew>
>
>
>

_____________________________

Goedele Roos, PhD

Department of General Chemistry 
VIB Department of Molecular and Cellular Interactions | http://www.vib.be/
Structural Biology Brussels, Vrije Universiteit Brussel | http://www.structuralbiology.be/
Brussels Center for Redox Biology | http://redox.vub.ac.be/

Vrije Universiteit Brussel, Building G, room 10G714
Pleinlaan 2, 1050 Brussels,Belgium
phone: +32 2 6293312
fax: +32 2 6293317
E-mail: groos:vub.ac.be


From owner-chemistry@ccl.net Fri Oct 15 14:37:01 2010
From: "Michel Petitjean petitjean.chiral() gmail.com" <owner-chemistry-,-server.ccl.net>
To: CCL
Subject: CCL: free software to measure RMSD and align proteins
Message-Id: <-42958-101015134250-3632-klLzgQ8t/R86nwJL4UpC3w-,-server.ccl.net>
X-Original-From: Michel Petitjean <petitjean.chiral]~[gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Date: Fri, 15 Oct 2010 19:42:10 +0200
MIME-Version: 1.0


Sent to CCL by: Michel Petitjean [petitjean.chiral:-:gmail.com]
Please have a look at CSR:
http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#CSR
Best regards,
Michel.

Michel Petitjean,
MTi, INSERM UMR-S 973, University Paris 7
35 rue Helene Brion, 75205 Paris Cedex 13, France.
Phone: +331 5727 8386; Fax: +331 5727 8372
E-mail: petitjean.chiral_._gmail.com
http://petitjeanmichel.free.fr/itoweb.petitjean.html

2010/10/15 Andrew Voronkov drugdesign%x%yandex.ru <owner-chemistry_._ccl.net>:
>
> Sent to CCL by: Andrew Voronkov [drugdesign/./yandex.ru]
> Dear CCL users,
> can you please recommend free software for homologic proteins comparison, alignment and RMSD measurements.
> I know DS visualizer and VMD, but is there anything else?
>
> Best regards,
> Andrew
>


From owner-chemistry@ccl.net Fri Oct 15 15:13:00 2010
From: "Andrew Orry andy-$-molsoft.com" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL: free software to measure RMSD and align proteins
Message-Id: <-42959-101015144541-7848-zfssAWCNtI9yOb/sIkYOCA+*+server.ccl.net>
X-Original-From: Andrew Orry <andy,molsoft.com>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Fri, 15 Oct 2010 11:44:56 -0700
MIME-Version: 1.0


Sent to CCL by: Andrew Orry [andy_._molsoft.com]

You can do this in the free ICM-Browser 
http://www.molsoft.com/icm_browser.html
1. Load proteins for comparison.
2. Select the proteins or region of the proteins you wish to superimpose.
3. Select the superimpose button in Display Tab.
4. RMSD will be displayed in terminal window.


On 10/15/2010 8:14 AM, Andrew Voronkov drugdesign%x%yandex.ru wrote:
> Sent to CCL by: Andrew Voronkov [drugdesign/./yandex.ru]
> Dear CCL users,
> can you please recommend free software for homologic proteins comparison, alignment and RMSD measurements.
> I know DS visualizer and VMD, but is there anything else?
>
> Best regards,
> Andrew>


-- 
Andrew Orry Ph.D.
Senior Research Scientist
MolSoft LLC
3366 North Torrey Pines Court
Suite 300
La Jolla
CA 92037
Tel: 858-625-2000 x108
Fax: 828-625-2888
www.molsoft.com


From owner-chemistry@ccl.net Fri Oct 15 15:47:01 2010
From: "Mikko Vainio mikko.vainio#abo.fi" <owner-chemistry,server.ccl.net>
To: CCL
Subject: CCL: free software to measure RMSD and align proteins
Message-Id: <-42960-101015142532-16466-TJhKZTvju9eVU0Z9o8volQ,server.ccl.net>
X-Original-From: Mikko Vainio <mikko.vainio~!~abo.fi>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Fri, 15 Oct 2010 21:25:23 +0300
MIME-Version: 1.0


Sent to CCL by: Mikko Vainio [mikko.vainio..abo.fi]
  On 10/15/2010 06:14 PM, Andrew Voronkov drugdesign%x%yandex.ru wrote:
> Sent to CCL by: Andrew Voronkov [drugdesign/./yandex.ru]
> Dear CCL users,
> can you please recommend free software for homologic proteins comparison, alignment and RMSD measurements.
> I know DS visualizer and VMD, but is there anything else?
>
> Best regards,
> Andrew
Dear Andrew,

Bodil is a free-of-charge program for protein structure visualization 
and alignment. It has plugins for sequence alignment and homology 
modeling as well. Bodil is available for Linux, Windows and IRIX at
http://users.abo.fi/bodil/
Please take a look at the tutorial included in the download package (or 
at http://users.abo.fi/bodil/bodil_tutorial.zip, the link on the page 
seems to be broken) in order to get started.
In particular, Tools/Superimpose/Vertaa superimposes protein structures 
based on alpha-carbon packing density. No sequence alignment is 
necessary. Tools/Superimpose/RMSD can then be used to compute the RMSD 
on the pairs of matching alpha-carbon atoms.

Cheers,
Mikko


From owner-chemistry@ccl.net Fri Oct 15 16:22:00 2010
From: "Vincent Leroux vincent.leroux=-=loria.fr" <owner-chemistry,server.ccl.net>
To: CCL
Subject: CCL: free software to measure RMSD and align proteins
Message-Id: <-42961-101015154143-5904-OEvQ4LBIfQEyMQCxyQ2k8A,server.ccl.net>
X-Original-From: Vincent Leroux <vincent.leroux=-=loria.fr>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=ISO-8859-1
Date: Fri, 15 Oct 2010 21:41:34 +0200
MIME-Version: 1.0


Sent to CCL by: Vincent Leroux [vincent.leroux_._loria.fr]

Hi Andrew,

VMD is open source and free of cost for academics but not free in the
GPL sense. You might need to pay if you use it for commercial purposes.

CHIMERA has a similar licence:
http://www.cgl.ucsf.edu/chimera/

These two are really free:
http://www.theseus3d.org/
http://theobald.brandeis.edu/qcp/

Regards,
VL



Le 15/10/10 18:07, Andrew Voronkov drugdesign%x%yandex.ru a écrit :
> 
> Sent to CCL by: Andrew Voronkov [drugdesign/./yandex.ru]
> Dear CCL users,
> can you please recommend free software for homologic proteins comparison, alignment and RMSD measurements.
> I know DS visualizer and VMD, but is there anything else?
> 
> Best regards,
> Andrew
> 
>


From owner-chemistry@ccl.net Fri Oct 15 16:57:01 2010
From: "Elaine Meng meng:cgl.ucsf.edu" <owner-chemistry]|[server.ccl.net>
To: CCL
Subject: CCL: free software to measure RMSD and align proteins
Message-Id: <-42962-101015152400-20019-mMhCc7zLGCfLZ0QczuOQMA]|[server.ccl.net>
X-Original-From: "Elaine  Meng" <meng!=!cgl.ucsf.edu>
Date: Fri, 15 Oct 2010 15:23:57 -0400


Sent to CCL by: "Elaine  Meng" [meng a cgl.ucsf.edu]
Hi Andrew,
Another possibility is Chimera, free for noncommercial use (if commercial, see
http://www.cgl.ucsf.edu/chimera/docs/licensing.html).

Chimera homepage:
http://www.cgl.ucsf.edu/chimera/index.html

Using Chimera to superimpose proteins:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html

.. creating sequence alignments from superpositions:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchalign.html

.. morphing between superimposed structures:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html

Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


From owner-chemistry@ccl.net Fri Oct 15 17:32:00 2010
From: "Vladimir Chupakhin chupvl * gmail.com" <owner-chemistry/a\server.ccl.net>
To: CCL
Subject: CCL: free software to measure RMSD and align proteins
Message-Id: <-42963-101015162750-25218-T7yviSR9l3Pr14/KIyM1xQ/a\server.ccl.net>
X-Original-From: Vladimir Chupakhin <chupvl[]gmail.com>
Content-Type: multipart/alternative; boundary=0016364266bb79f4990492ada8be
Date: Fri, 15 Oct 2010 22:27:20 +0200
MIME-Version: 1.0


Sent to CCL by: Vladimir Chupakhin [chupvl(0)gmail.com]
--0016364266bb79f4990492ada8be
Content-Type: text/plain; charset=UTF-8

Hi,
Chimera have very good protein superposition tool, as also Pymol have (some
plugins also exists).
Wiki article also mention several good tools -
http://en.wikipedia.org/wiki/Structural_alignment

<http://en.wikipedia.org/wiki/Structural_alignment>Regrads,
Vladimir Chupakhin

On Fri, Oct 15, 2010 at 5:14 PM, Andrew Voronkov drugdesign%x%yandex.ru <
owner-chemistry::ccl.net> wrote:

>
> Sent to CCL by: Andrew Voronkov [drugdesign/./yandex.ru]
> Dear CCL users,
> can you please recommend free software for homologic proteins comparison,
> alignment and RMSD measurements.
> I know DS visualizer and VMD, but is there anything else?
>
> Best regards,
> Andrew>
>
>

--0016364266bb79f4990492ada8be
Content-Type: text/html; charset=UTF-8
Content-Transfer-Encoding: quoted-printable

<div>Hi,</div>Chimera have very good protein superposition tool, as also Py=
mol have (some plugins also exists).<div>Wiki article also mention several =
good tools -=C2=A0<a href=3D"http://en.wikipedia.org/wiki/Structural_alignm=
ent">http://en.wikipedia.org/wiki/Structural_alignment</a></div>

<div><br></div><div><a href=3D"http://en.wikipedia.org/wiki/Structural_alig=
nment"></a>Regrads,</div><div>Vladimir Chupakhin<br><br><div class=3D"gmail=
_quote">On Fri, Oct 15, 2010 at 5:14 PM, Andrew Voronkov drugdesign%x%<a hr=
ef=3D"http://yandex.ru">yandex.ru</a> <span dir=3D"ltr">&lt;<a href=3D"mail=
to:owner-chemistry::ccl.net">owner-chemistry::ccl.net</a>&gt;</span> wrote:<b=
r>

<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex;"><br>
Sent to CCL by: Andrew Voronkov [drugdesign/./<a href=3D"http://yandex.ru" =
target=3D"_blank">yandex.ru</a>]<br>
Dear CCL users,<br>
can you please recommend free software for homologic proteins comparison, a=
lignment and RMSD measurements.<br>
I know DS visualizer and VMD, but is there anything else?<br>
<br>
Best regards,<br>
Andrew<br>
<br>
<br>
<br>
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