From chemistry-request@ccl.net Thu Aug 7 09:03:00 2003 Received: from uni-freiburg.de (ms.ruf.uni-freiburg.de [132.230.2.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h77D2xNG003564 for ; Thu, 7 Aug 2003 09:03:00 -0400 Received: from [132.230.171.124] (account ) by uni-freiburg.de (CommuniGate Pro WebUser 4.0.6) with HTTP id 10269117 for ; Thu, 07 Aug 2003 15:03:05 +0200 From: "Thomas Steinbrecher" Subject: CCL: Tool for secondary structure prediction To: X-Mailer: CommuniGate Pro Web Mailer v.4.0.6 Date: Thu, 07 Aug 2003 15:03:05 +0200 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: 8bit Dear CCLers, I am looking for a tool to predict secondary structure elements for a protein of known sequence but without 3D-structure. There are no homologues with known structure. Please point me to references for a program (ideally open source/freeware) that can do such a thing. Kind Regards, Thomas Steinbrecher From chemistry-request@ccl.net Thu Aug 7 05:19:35 2003 Received: from ultra3000.if.sc.usp.br (ultra3000.if.sc.usp.br [143.107.228.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h779JSNG030992 for ; Thu, 7 Aug 2003 05:19:34 -0400 Received: from straits (straits.if.sc.usp.br [143.107.228.34]) by ultra3000.if.sc.usp.br (8.11.6/8.11.0) with ESMTP id h779DjH32740 for ; Thu, 7 Aug 2003 06:13:45 -0300 Message-ID: <002d01c35cc6$37813340$22e46b8f{at}if.sc.usp.br> From: "JOSE" To: Subject: About Dieletric constant Date: Thu, 7 Aug 2003 06:28:09 -0300 Someone had asked for a way of calculating the dielectric constant from first principle. I have found this link by accident today. To whom it is interesting, please have a look at NIST web site: http://physics.nist.gov/PhysRefData/FFast/Text1995/chap01.html __________________________________________________________________ Jose Ricardo Sabino ICQ#: 41252590 Current ICQ status: + More ways to contact me __________________________________________________________________ From chemistry-request@ccl.net Thu Aug 7 10:03:34 2003 Received: from dedalus.lcc.ufmg.br (dedalus.lcc.ufmg.br [150.164.65.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h77E3XNG005056 for ; Thu, 7 Aug 2003 10:03:34 -0400 Received: from dedalus.lcc.ufmg.br (loopback [127.0.0.1]) by dedalus.lcc.ufmg.br (8.12.8p1/8.12.8) with ESMTP id h77DoPxl036654; Thu, 7 Aug 2003 10:50:25 -0300 Received: from localhost (amolive@localhost) by dedalus.lcc.ufmg.br (8.12.8p1/8.12.8/Submit) with ESMTP id h77DoOUX036652; Thu, 7 Aug 2003 10:50:24 -0300 Date: Thu, 7 Aug 2003 10:50:24 -0300 (BSC) From: andre mauricio de oliveira X-X-Sender: amolive@dedalus To: Thomas Steinbrecher cc: chemistry.-at-.ccl.net Subject: Re: CCL:Tool for secondary structure prediction In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Dr. Steinbrecher, (1) Try www.expasy.org. (2) VEGA (freeware!) also has an interface w/ PREDICTOR suite. Both require sequence in FASTA format. Greets. On Thu, 7 Aug 2003, Thomas Steinbrecher wrote: > Dear CCLers, > > I am looking for a tool to predict secondary structure > elements for a protein of known sequence but without > 3D-structure. There are no homologues with known structure. > > Please point me to references for a program (ideally open > source/freeware) that can do such a thing. > > Kind Regards, > > Thomas Steinbrecher > > -= This is automatically added to each message by mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY.-at-.ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST.-at-.ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl.-at-.ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > Andre Mauricio de Oliveira VOICE +55-031-374-1325 +55-031-499-5765 FAX +55-031-499-5700 Laboratorio de QSAR e Modelagem Molecular Nucleo de Estudos em Quimica Medicinal (NEQUIM) NEQUIM's Homepage: http://www.qui.ufmg.br/~nequim Departamento de Quimica ICEx Federal University of Minas Gerais Av Antonio Carlos 6627 Pampulha ZIP CODE 31270-901 Belo Horizonte MG Brazil From chemistry-request@ccl.net Thu Aug 7 10:05:17 2003 Received: from dedalus.lcc.ufmg.br (dedalus.lcc.ufmg.br [150.164.65.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h77E5FNG005106 for ; Thu, 7 Aug 2003 10:05:17 -0400 Received: from dedalus.lcc.ufmg.br (loopback [127.0.0.1]) by dedalus.lcc.ufmg.br (8.12.8p1/8.12.8) with ESMTP id h77DqCxl035922; Thu, 7 Aug 2003 10:52:12 -0300 Received: from localhost (amolive@localhost) by dedalus.lcc.ufmg.br (8.12.8p1/8.12.8/Submit) with ESMTP id h77DqB4W035920; Thu, 7 Aug 2003 10:52:11 -0300 Date: Thu, 7 Aug 2003 10:52:10 -0300 (BSC) From: andre mauricio de oliveira X-X-Sender: amolive@dedalus To: jz7[at]duke.edu cc: chemistry[at]ccl.net Subject: Re: CCL:how to estimate the dielectric constant In-Reply-To: <1060117337.3f301b59aafc3[at]yefremov.acpub.duke.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Dr. Duke, Try ACD's freeware ChemSketch 5.0 (www.acd.com). Best wishes. On Tue, 5 Aug 2003 jz7[at]duke.edu wrote: > Hi there, > > Would someone please suggest what calculation method can estimate the > dielectric constant for a specific compound? The literature don't have > dielectric constant for it. > > Thanks a lot! > > > -= This is automatically added to each message by mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY[at]ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST[at]ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl[at]ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > Andre Mauricio de Oliveira VOICE +55-031-374-1325 +55-031-499-5765 FAX +55-031-499-5700 Laboratorio de QSAR e Modelagem Molecular Nucleo de Estudos em Quimica Medicinal (NEQUIM) NEQUIM's Homepage: http://www.qui.ufmg.br/~nequim Departamento de Quimica ICEx Federal University of Minas Gerais Av Antonio Carlos 6627 Pampulha ZIP CODE 31270-901 Belo Horizonte MG Brazil From chemistry-request@ccl.net Thu Aug 7 12:47:23 2003 Received: from ntsmtp01.usc.edu (chl179129.usc.edu [128.125.179.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h77GlMNG009140 for ; Thu, 7 Aug 2003 12:47:23 -0400 Received: by NTSMTP01 with Internet Mail Service (5.5.2653.19) id ; Thu, 7 Aug 2003 09:47:30 -0700 Message-ID: <73564B8DE398D61180500008C75D7E49033E5D42@NTMAIL03> From: "Pandey, Jaya" To: "'chemistry[at]ccl.net'" Subject: Improving the structure from PDB Date: Thu, 7 Aug 2003 09:47:24 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain Dear All, I am dowmloading a secondary structure from PDB for publication purpose but I do not get a good quality image, can someone advice any software where it can be improved or worked on to look better? Also, my docking results from BiGGER needs to be improved, how can I do that? Please advice, Thanks, Jaya From chemistry-request@ccl.net Thu Aug 7 13:30:38 2003 Received: from yakko.cimav.edu.mx (yakko.cimav.ecustomer.mx [148.223.46.2] (may be forged)) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h77HUaNG009883 for ; Thu, 7 Aug 2003 13:30:37 -0400 Received: from yakko (localhost [127.0.0.1]) by localhost.cimav.edu.mx (Postfix) with ESMTP id 49DAF7611B for ; Thu, 7 Aug 2003 11:30:37 -0600 (MDT) Received: from localhost ([127.0.0.1]) by yakko.cimav.edu.mx (MailMonitor for SMTP v1.2.2 ) ; Thu, 7 Aug 2003 11:30:37 -0600 (MDT) Received: from laquicom02 (byron.cimav.edu.mx [148.223.46.1]) by yakko.cimav.edu.mx (Postfix) with SMTP id 8C0B57611A for ; Thu, 7 Aug 2003 11:30:36 -0600 (MDT) Message-ID: <002a01c35d09$9d6a63f0$8400000a@laquicom02> From: "Dr. Daniel Glossman-Mitnik" To: Subject: summary for program for superimposing (small) molecules and new question Date: Thu, 7 Aug 2003 12:30:34 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0027_01C35CDF.B3015FE0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 Disposition-Notification-To: "Dr. Daniel Glossman-Mitnik" X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 This is a multi-part message in MIME format. ------=_NextPart_000_0027_01C35CDF.B3015FE0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear netters: I have received quite a lot of answers to my query about=20 Windows programs to superimpose molecules and calculate the RMSD. Below is the summary of answers I've received. Thanks a lot to everybody!!!! I have not tried yet all the=20 suggestions, but I found that QMol on the free side, and Hyperchem and CaChe on the non-free side can do the job quite easily. Before I present the summary, I was to ask the (neccessary) follow-up question: In your experience, when a comparison of an experimental molecular structure (i.e. X-rays) and its=20 calculated (Gaussian) counterpart is done, which will be the treshold RMSD value which can be considered acceptable ? Thanks in advance Dr. Daniel Glossman-Mitnik ********************************************************************** > From Jim Kress: gOpenMol http://www.csc.fi/~laaksone/gopenmol/gopenmol.html and Tinker =20 http://dasher.wustl.edu/tinker/ can do this. *********************************************************************** > From Ataualpa Albert Carmo Braga: Hi Daniel, Look for molden (http://www.caos.kun.nl/~schaft/molden/windowsnt95.html) See you, Ataualpa. *********************************************************************** > From Ray Merewheter: if you only want to do it once or just a few times, you can sort the=20 output coordinate files in Excel by x, y, and z and then brute force=20 the alignment of any difficult atoms and do your own RMS. pdb format=20 is particularly easy to understand. *************************************************************************= **** > From Jason D. Gans: Hello, Qmol, available from the CCL software repository http://www.ccl.net/cca/software/MS-WIN95-NT/qmol/index.shtml can superimpose molecules and compute RMS deviation. Regards, Jason Gans B division Los Alamos National Lab *************************************************************************= ******* > From Brian Bennion: Hi VMD will do this fairly easily and is free www.ks.uiuc.edu/Research/VMD Brian *************************************************************************= ******** > From Olalla Nieto Faza: I don't know whether it can be used for small molecules as well, but SwissPDB viewer (you can download it from the Expasy.org server)=20 can make structure alignments of proteins and give you the RMS. Hope it helps, Regards *************************************************************************= ************* > From Dr. Richard L. Wood: Hi Dr. Glossman-Mitnik=20 I assume the two molecules are the same. If so, couldn't you=20 open the files in MS Excel and calculate the RMSD that way?=20 Hope this helps.=20 Richard=20 *************************************************************************= ************** > From Nicolas Saettel: Hi, I would be very interested too. So far the only workaround I found was = to=20 reorder the Zmatrix in Molden and put all the xyz coordinates in 1 = file... but=20 no RMS deviation! Cordially Nicolas Saettel *************************************************************************= ******************** > From Elmar Gerwalin: Hello Daniel, "quatfit" does what you need. It gives the RMS-deviation of 2 structures. It's a simple C-Programm that should be installable on any platform with = a=20 C-Compiler. (I'm using it on LINUX without problems) You may find it using "google" or another search engine. I append the src-code to my mail in case you can't find it. Hope that helps. Bye Elmar *************************************************************************= ************************* > From Giulio Vistoli: Dear Daniel Our VEGA program (http://www.ddl.unimi.it) is able to superimpose two o = more=20 molecules defining the opportune match atoms (with a graphical = interface) Best regards Giulio Vistoli *************************************************************************= **************************** > From Juan Alexander Padron: Dear Dr. Glossman-Mitnik: I would extremelly apreciate if you could send me the replies to your question about this topic, because I am interested in the same problem (actually I am programming something like it and I need to know what have been done). A propo, I think that DS viewer pro from Accelrys do the trick (specially with the DS ViewerPro Molecular Overlay module) but it is quite expensive (around 600 USD for the program, one copy, plus the cost of the module). Best Regards, -- Juan Alexander Padr=F3n Garc=EDa, PhD Student Laboratorio de Qu=EDmica Computacional y Te=F3rica Facultad de Qu=EDmica Universidad de la Habana e-mail: padrongj[at]fq.uh.cu, alex2473[at]yahoo.es http://www.fq.uh.cu/investigacion/lqct/index.htm *************************************************************************= ************************ > From Andr=E1s Borosy: Dear Dr Glossman-Mitnik, Try the Windows version of MOE from CCG or MOLOC (www.moloc.ch)! Best wishes, Andr=E1s Borosy ********************************************************************** Dr. Daniel Glossman-Mitnik Centro de Investigaci=F3n en Materiales Avanzados (CIMAV) LAQUICOM - Laboratorio de Qu=EDmica Computacional Miguel de Cervantes 120 - Comp. Ind. Chihuahua Chihuahua, Chih. 31109 - MEXICO Tel.: (52) 614 4391151 FAX: (52) 614 4391112 E-mail: daniel.glossman[at]cimav.edu.mx glossman[at]hotmail.com dglossman[at]yahoo.com ********************************************************************** ------=_NextPart_000_0027_01C35CDF.B3015FE0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear netters:
 
I have received quite a lot of answers = to my query=20 about
Windows programs to superimpose = molecules and=20 calculate
the RMSD. Below is the summary of = answers I've=20 received.
Thanks a lot to everybody!!!! I have = not tried yet=20 all the
suggestions, but I found that QMol on = the free=20 side, and
Hyperchem and CaChe on the non-free = side can do=20 the
job quite easily.
 
Before I present the summary, I was to = ask the=20 (neccessary)
follow-up question:  In your = experience, when=20 a comparison
of an experimental molecular structure = (i.e.=20 X-rays) and its
calculated (Gaussian) counterpart is done, which will be the
treshold RMSD value which can be = considered=20 acceptable ?
 
Thanks in advance
 
          &nbs= p;            = ;          =20 Dr. Daniel Glossman-Mitnik
 
 
****************************************************************= ******
From Jim Kress:
 
gOpenMol
  http://www.cs= c.fi/~laaksone/gopenmol/gopenmol.html
 
and
 
Tinker 
http://dasher.wustl.edu/tinker/<= /A>
 
can do this.
 
****************************************************************= *******
From Ataualpa Albert Carmo = Braga:
 
Hi=20 Daniel,

Look for molden (http://www.caos.kun.nl/~schaft/molden/windowsnt95.html)

See=20 you,

Ataualpa.
 
****************************************************************= *******
From Ray Merewheter:
 
if you=20 only want to do it once or just a few times, you can sort the=20
output=20 coordinate files in Excel by x, y, and z and then brute force=20
the=20 alignment of any difficult atoms and do your own RMS.  pdb format=20
is=20 particularly easy to understand.
 
****************************************************************= *************
 
From Jason D. Gans:
 
Hello,

Qmol, available from = the CCL=20 software repository

http://www.ccl.net/cca/software/MS-WIN95-NT/qmol/index.shtml

can superimpose molecules and compute RMS=20 deviation.

Regards,

Jason Gans

B division
Los = Alamos=20 National Lab
 
****************************************************************= ****************
 
From Brian Bennion:
 
Hi

VMD will do this fairly = easily and is=20 free
www.ks.uiuc.edu/Research/VMD

Brian
****************************************************************= *****************
From Olalla Nieto Faza:
 
I don't know whether it can be used for small molecules as well,=20 but
SwissPDB viewer (you can download it from  the Expasy.org = server)=20
can make structure alignments of proteins and give you the = RMS.
Hope it=20 helps,
Regards
****************************************************************= **********************
 
From Dr. Richard L. Wood:
 
Hi Dr. Glossman-Mitnik=20

I assume the two molecules are the same.  If so, couldn't you =
open=20 the files in MS Excel and calculate the RMSD that way?=20

Hope this helps.=20

Richard

****************************************************************= ***********************
From Nicolas Saettel:
 
Hi,
I would be very interested too. So far the only workaround I = found was to=20
reorder the Zmatrix in Molden and put all the xyz coordinates = in 1=20 file... but
no RMS deviation!
Cordially
Nicolas Saettel
 
****************************************************************= *****************************
From Elmar Gerwalin:
 
Hello Daniel,

"quatfit" does what you need.
It gives the=20 RMS-deviation of 2 structures.
It's a simple C-Programm that should = be=20 installable on any platform with a
C-Compiler. (I'm using it on = LINUX=20 without problems)

You may find it using "google" or another = search=20 engine.

I append the src-code to my mail in case you can't find=20 it.

Hope that helps.
Bye
Elmar

****************************************************************= **********************************
 
From Giulio Vistoli:
 
Dear Daniel
 
Our VEGA program (http://www.ddl.unimi.it) is able to = superimpose two o more
molecules defining the opportune match = atoms (with=20 a graphical interface)
 
Best regards
 
Giulio Vistoli
 
 
****************************************************************= *************************************
 
From Juan Alexander Padron:
 
Dear Dr. Glossman-Mitnik:

I = would=20 extremelly apreciate if you could send me the replies to = your
question about=20 this topic, because I am interested in the same problem
(actually I = am=20 programming something like it and I need to know what
have been = done). A=20 propo, I think that DS viewer pro from Accelrys do
the trick = (specially with=20 the DS ViewerPro Molecular Overlay module) but
it is quite expensive = (around=20 600 USD for the program, one copy, plus
the cost of the = module).

Best=20 Regards,

--
Juan Alexander Padr=F3n Garc=EDa, PhD = Student
Laboratorio=20 de Qu=EDmica Computacional y Te=F3rica
Facultad de = Qu=EDmica
Universidad de la=20 Habana
e-mail: padrongj[at]fq.uh.cu, alex2473[at]yahoo.es
http://www.fq.uh.cu/investigacion/lqct/index.htm
<= /FONT>
****************************************************************= *********************************
 
From Andr=E1s Borosy:
 
 
Dear Dr = Glossman-Mitnik,


Try the=20 Windows version of MOE from CCG or MOLOC (www.moloc.ch)!

Best=20 wishes,

Andr=E1s Borosy

****************************************************************= ******
Dr.=20 Daniel Glossman-Mitnik
Centro de Investigaci=F3n en Materiales = Avanzados=20 (CIMAV)
LAQUICOM - Laboratorio de Qu=EDmica Computacional
Miguel = de=20 Cervantes 120 - Comp. Ind. Chihuahua
Chihuahua, Chih. 31109 - = MEXICO
Tel.:=20 (52) 614 4391151
FAX: (52) 614 4391112
E-mail: daniel.glossman[at]cimav.edu.mx=
           = ;=20 glossman[at]hotmail.com
 &n= bsp;         =20 dglossman[at]yahoo.com
**********= ************************************************************
= ------=_NextPart_000_0027_01C35CDF.B3015FE0-- From chemistry-request@ccl.net Thu Aug 7 15:57:40 2003 Received: from postoffice.mail.cornell.edu (postoffice.mail.cornell.edu [132.236.56.7]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h77JveNG013687 for ; Thu, 7 Aug 2003 15:57:40 -0400 Received: from cornell.edu (cs666981-224.satx.rr.com [66.69.81.224]) by postoffice.mail.cornell.edu (8.9.3p2/8.9.3) with ESMTP id PAA27013; Thu, 7 Aug 2003 15:57:39 -0400 (EDT) Message-ID: <3F32AF2F.110FE643-.at.-cornell.edu> Date: Thu, 07 Aug 2003 14:57:35 -0500 From: "Dr. Richard L. Wood" Organization: Cornell University X-Mailer: Mozilla 4.5 [en]C-CCK-MCD {TLC;RETAIL} (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: "Dr. Daniel Glossman-Mitnik" CC: chemistry-.at.-ccl.net Subject: Re: CCL:summary for program for superimposing (small) molecules and new question References: <002a01c35d09$9d6a63f0$8400000a@laquicom02> Content-Type: multipart/alternative; boundary="------------735E08B5D339FC9B98749EAE" --------------735E08B5D339FC9B98749EAE Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I have a question as to how the program QMol calculates the RMSD of two structures. I used Excel to calculate the RMSD for two different conformations of the same molecule and compared the result that I get using QMol, and I get two different values, and I am wondering why that is. In Excel, I calculated the distances between the same two atoms in the two conformations, squared them, added them up, then divided by the number of atoms. After this, take the square root to get the RMSD. It looks to me like QMol does something different. Thanks in advance, Richard > From Jason D. Gans: Hello, > > Qmol, available from the CCL software repository > > http://www.ccl.net/cca/software/MS-WIN95-NT/qmol/index.shtml > > can superimpose molecules and compute RMS deviation. > > Regards, > > Jason Gans > > B division > Los Alamos National Lab -- Richard L. Wood, Ph. D. Physical/Computational Chemist --------------735E08B5D339FC9B98749EAE Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit I have a question as to how the program QMol calculates the RMSD of two structures.

I used Excel to calculate the RMSD for two different conformations of the same molecule and compared the result that I get using QMol, and I get two different values, and I am wondering why that is.

In Excel, I calculated the distances between the same two atoms in the two conformations, squared them, added them up, then divided by the number of atoms.
After this, take the square root to get the RMSD.

It looks to me like QMol does something different.

Thanks in advance,
Richard
 

From Jason D. Gans: Hello,

Qmol, available from the CCL software repository

http://www.ccl.net/cca/software/MS-WIN95-NT/qmol/index.shtml

can superimpose molecules and compute RMS deviation.

Regards,

Jason Gans

B division
Los Alamos National Lab 


--
Richard L. Wood, Ph. D.
Physical/Computational Chemist
 
  --------------735E08B5D339FC9B98749EAE-- From chemistry-request@ccl.net Thu Aug 7 15:30:51 2003 Received: from mailrelay.mdli.com ([208.200.221.8]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h77JUmNG012708 for ; Thu, 7 Aug 2003 15:30:51 -0400 Received: from puffin.mdli.com (puffin.mdli.com [172.16.1.12]) by mailrelay.mdli.com (Postfix) with ESMTP id 693D1B5F20; Thu, 7 Aug 2003 12:30:47 -0700 (PDT) Received: from exch-sl02.mdli.com by puffin.mdli.com (980427.SGI.8.8.8/BCH1.0) id MAA24777; Thu, 7 Aug 2003 12:30:45 -0700 (PDT) Received: by exch-sl02.mdli.com with Internet Mail Service (5.5.2653.19) id ; Thu, 7 Aug 2003 12:30:45 -0700 Message-ID: From: Doug Henry To: "'andre mauricio de oliveira'" , Thomas Steinbrecher Cc: chemistry_at_ccl.net Subject: RE: Tool for secondary structure prediction Date: Thu, 7 Aug 2003 12:30:43 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Another is PSIPRED: http://bioinf.cs.ucl.ac.uk/psipred/ -----Original Message----- From: andre mauricio de oliveira [mailto:amolive_at_dedalus.lcc.ufmg.br] Sent: Thursday, August 07, 2003 6:50 AM To: Thomas Steinbrecher Cc: chemistry_at_ccl.net Subject: CCL:Tool for secondary structure prediction Dear Dr. Steinbrecher, (1) Try www.expasy.org. (2) VEGA (freeware!) also has an interface w/ PREDICTOR suite. Both require sequence in FASTA format. Greets. On Thu, 7 Aug 2003, Thomas Steinbrecher wrote: > Dear CCLers, > > I am looking for a tool to predict secondary structure > elements for a protein of known sequence but without > 3D-structure. There are no homologues with known structure. > > Please point me to references for a program (ideally open > source/freeware) that can do such a thing. > > Kind Regards, > > Thomas Steinbrecher > > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST_at_ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > > > > > > Andre Mauricio de Oliveira VOICE +55-031-374-1325 +55-031-499-5765 FAX +55-031-499-5700 Laboratorio de QSAR e Modelagem Molecular Nucleo de Estudos em Quimica Medicinal (NEQUIM) NEQUIM's Homepage: http://www.qui.ufmg.br/~nequim Departamento de Quimica ICEx Federal University of Minas Gerais Av Antonio Carlos 6627 Pampulha ZIP CODE 31270-901 Belo Horizonte MG Brazil -= This is automatically added to each message by mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY_at_ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST_at_ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jkl_at_ccl.net (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Thu Aug 7 16:52:31 2003 Received: from hal.netbox.cz (hal.netbox.cz [212.96.166.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h77KqVNG015803 for ; Thu, 7 Aug 2003 16:52:31 -0400 Received: from chemi.muni.cz (r10s01p08.home.nbox.cz [213.211.37.34]) by hal.netbox.cz (Postfix) with ESMTP id B66EB171D44; Thu, 7 Aug 2003 22:52:40 +0200 (CEST) Message-ID: <3F32BBF3.1060002=at=chemi.muni.cz> Date: Thu, 07 Aug 2003 22:52:03 +0200 From: Lubos Vrbka Reply-To: shnek=at=chemi.muni.cz Organization: NCBR User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.4) Gecko/20030624 X-Accept-Language: en-us, en MIME-Version: 1.0 To: "Dr. Richard L. Wood" Cc: chemistry=at=ccl.net, daniel.glossman=at=cimav.edu.mx Subject: Re: CCL:summary for program for superimposing (small) molecules and new question References: <002a01c35d09$9d6a63f0$8400000a@laquicom02> <3F32AF2F.110FE643=at=cornell.edu> In-Reply-To: <3F32AF2F.110FE643=at=cornell.edu> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dr. Richard L. Wood wrote: > I have a question as to how the program QMol calculates the RMSD of two > structures. > > I used Excel to calculate the RMSD for two different conformations of > the same molecule and compared the result that I get using QMol, and I > get two different values, and I am wondering why that is. > > In Excel, I calculated the distances between the same two atoms in the > two conformations, squared them, added them up, then divided by the > number of atoms. > After this, take the square root to get the RMSD. > > It looks to me like QMol does something different. isn't it possible that QMol produces for example mass-weighted RMS or something similar? i can remember having similar problems (i.e. different values of the RMSD on the same set of structures) with some other programs (e.g. amber/ptraj, amber/carnal and vmd). maybe qmol could be some kind of similar case... regards, lubos -- ################################################# Mgr. Lubos Vrbka National Centre for Biomolecular Research Masaryk university, Brno, Czech Republic shnek=at=chemi.muni.cz http://www.chemi.muni.cz/~shnek tel. +420 541 129 508 #################################################