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
**********= ************************************************************
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