From owner-chemistry@ccl.net Fri Oct 27 00:28:00 2006
From: "Jeff Hammond jhammond.:.uchicago.edu" <owner-chemistry]_[server.ccl.net>
To: CCL
Subject: CCL:G: HyperChem
Message-Id: <-32876-061027002610-15016-HGhDA9FU0WDpUE+4hnELzg]_[server.ccl.net>
X-Original-From: Jeff Hammond <jhammond-*-uchicago.edu>
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Sent to CCL by: Jeff Hammond [jhammond.[-].uchicago.edu]
Brock,

I don't know what it is about Hyperchem that you find most appealing, 
but given the vast array of very powerful free software available today, 
I can't imagine why you would pay for any chemistry code.  It would be a 
far better use of money to buy hardware instead.

If you want ab initio quantum chemistry or DFT, check out NWChem, 
GAMESS, PSI or Dalton.  NWChem also does MD and MM if that's your need. 
  If you like pretty pictures, Molden and MacMolPlot are great for 
viewing orbitals and ECCE is a powerful graphical interface to NWChem, 
Gaussian and GAMESS-UK.

I'm sure I've left out some great free software, so perhaps other 
members of this list can share their favorites.

Jeff

Brock Askew chemguy1985*o*hotmail.com wrote:
> Sent to CCL by: "Brock  Askew" [chemguy1985 .. hotmail.com]
> I am thinking of buying HyperChem for the Mac.
> 
> Does any one have an openion about this product or any of Hypercubes other products or services before I pruchase the software?
> 
> Thank you for your advice.
> 
> Brock


From owner-chemistry@ccl.net Fri Oct 27 09:51:01 2006
From: "Maurizzio m.argonni::gmail.com" <owner-chemistry]~[server.ccl.net>
To: CCL
Subject: CCL: Kurt Thorn's Alanine Scanning Database
Message-Id: <-32877-061026233907-25999-F5J5nz2XhaVy5a71LFwYFQ]~[server.ccl.net>
X-Original-From: Maurizzio <m.argonni-x-gmail.com>
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Sent to CCL by: Maurizzio [m.argonni . gmail.com]
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Hello,

Does anyone have any info on the fate of Kurt Thorn's Alanine Scanning
Database?
The link to it is dead as of a couple of weeks ago. I could not connect to
any of his
lab web pages either.

Are there any other databases listing alanine scanning results?

Any info is greatly appreciated.

Thanks,

Maurizzio

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<div>Hello,</div>
<div>&nbsp;</div>
<div>Does anyone have any info on the fate of Kurt Thorn's Alanine Scanning Database?</div>
<div>The link to it is dead as of a couple of weeks ago. I could not connect to any of his</div>
<div>lab web pages either.</div>
<div>&nbsp;</div>
<div>Are there any other databases listing alanine scanning results?</div>
<div>&nbsp;</div>
<div>Any info is greatly appreciated.</div>
<div>&nbsp;</div>
<div>Thanks,</div>
<div>&nbsp;</div>
<div>Maurizzio</div>
<div>&nbsp;</div>

------=_Part_26349_3374588.1161916487091--


From owner-chemistry@ccl.net Fri Oct 27 10:25:01 2006
From: "John McKelvey jmmckel^^attglobal.net" <owner-chemistry^_^server.ccl.net>
To: CCL
Subject: CCL:G: HyperChem
Message-Id: <-32878-061027075850-19572-giWUCTk6E8jPt53X4PjtiQ^_^server.ccl.net>
X-Original-From: John McKelvey <jmmckel**attglobal.net>
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Date: Fri, 27 Oct 2006 07:54:19 -0400
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Sent to CCL by: John McKelvey [jmmckel!A!attglobal.net]
Don't forget ORCA.. a great mixture of semiempirical, ab initio, and 
DFT.  Very efficient, good documentation. 

John McKelvey

Jeff Hammond jhammond.:.uchicago.edu wrote:

>Sent to CCL by: Jeff Hammond [jhammond.-$-.uchicago.edu]
>Brock,
>
>I don't know what it is about Hyperchem that you find most appealing, 
>but given the vast array of very powerful free software available today, 
>I can't imagine why you would pay for any chemistry code.  It would be a 
>far better use of money to buy hardware instead.
>
>If you want ab initio quantum chemistry or DFT, check out NWChem, 
>GAMESS, PSI or Dalton.  NWChem also does MD and MM if that's your need. 
>  If you like pretty pictures, Molden and MacMolPlot are great for 
>viewing orbitals and ECCE is a powerful graphical interface to NWChem, 
>Gaussian and GAMESS-UK.
>
>I'm sure I've left out some great free software, so perhaps other 
>members of this list can share their favorites.
>
>Jeff
>
>Brock Askew chemguy1985*o*hotmail.com wrote:
>  
>
>>Sent to CCL by: "Brock  Askew" [chemguy1985 .. hotmail.com]
>>I am thinking of buying HyperChem for the Mac.
>>
>>Does any one have an openion about this product or any of Hypercubes other products or services before I pruchase the software?
>>
>>Thank you for your advice.
>>
>>Brock>
>
>
>
>
>  
>


From owner-chemistry@ccl.net Fri Oct 27 11:18:00 2006
From: "John Daily john.daily . colorado.edu" <owner-chemistry=-=server.ccl.net>
To: CCL
Subject: CCL: HyperChem
Message-Id: <-32879-061027093653-27800-UNz+KR17sMLIntVQnihedw=-=server.ccl.net>
X-Original-From: John Daily <john.daily() colorado.edu>
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Date: Fri, 27 Oct 2006 06:57:42 -0600
Mime-Version: 1.0 (Apple Message framework v752.2)


Sent to CCL by: John Daily [john.daily_+_colorado.edu]
Brock,

Hyperchem is a program that is quite useful for learning about  
molecular modeling methods. It has a very user friendly windows  
interface that makes it easy to draw and manipulate structures. It  
offers a number of molecular mechanics force fields, as well as semi- 
empirical, ab initio and DFT methods. You can perform single point  
calculations, geometry optimizations, vibratiional anaylysis, and  
visualize orbitals. In addition you can carry out molecular dynamics,  
monte carlo and Langevin calculations. In principle you can interface  
with the Hyperchem engines from other programing languages including  
Excel. It also comes with an extensive structure database. Because of  
this, I have been using Hyperchem for teaching as the student edition  
is quite affordable. And I still use it to build and optimize  
structures for the first time.

Having said all that, it is not particularly good at any one thing  
(other than building), nor is it well suited for large calculations.  
Hence, the comments about why use it when there are so many good free  
programs out there. For example, I use the Tinker suite of programs  
for molecular dynamics.

Thus, if you are a beginner, and can afford the program, it might be  
a good place to start. But eventually you will move to other more  
specialized programs, many of which are free.

Note that there are also some other multifunctional commercial codes  
available.

John







On Oct 26, 2006, at 9:51 PM, Brock Askew chemguy1985*o*hotmail.com  
wrote:

> Sent to CCL by: "Brock  Askew" [chemguy1985 .. hotmail.com]
> I am thinking of buying HyperChem for the Mac.
>
> Does any one have an openion about this product or any of  
> Hypercubes other products or services before I pruchase the software?
>
> Thank you for your advice.
>
> Brock
>
>
>
> -= This is automatically added to each message by the mailing  
> script =-
> To recover the email address of the author of the message, please  
> change> Conferences: http://server.ccl.net/chemistry/announcements/ 
> conferences/
>
> Search Messages: http://www.ccl.net/htdig  (login: ccl, Password:  
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From owner-chemistry@ccl.net Fri Oct 27 13:45:01 2006
From: "Sabri Alkis alkis^-^ufl.edu" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL: Dlpoly calculation of angular momentum
Message-Id: <-32880-061027134259-1367-bzQCqE8FTruU3rS6kyKiyQ^server.ccl.net>
X-Original-From: "Sabri  Alkis" <alkis#ufl.edu>
Date: Fri, 27 Oct 2006 13:42:58 -0400


Sent to CCL by: "Sabri  Alkis" [alkis * ufl.edu]
Dear all,

I put a cluster of 55 atoms on top of alkanthiol molecule surface . The cluster is moving as a nano ball and I wanna calculate the angular momentum of this cluster with respect to time. The problem is, there is a periodic boundary and the cluster is  moving outside the boundary. The HISTORY file gives me the coordinates inside the box, so I can never know where the actual coordinates of the cluster are. How can I calculate the angular momentum of my cluster? need help...

best wishes,

Sabri..


From owner-chemistry@ccl.net Fri Oct 27 15:28:01 2006
From: "Konstantin Kudin konstantin_kudin_-_yahoo.com" <owner-chemistry,server.ccl.net>
To: CCL
Subject: CCL: GROMACS & AMBER scaling on Linux clusters
Message-Id: <-32881-061027152303-9365-/W6zokgh1+wZ8/FT8mSVJw,server.ccl.net>
X-Original-From: Konstantin Kudin <konstantin_kudin(a)yahoo.com>
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Date: Fri, 27 Oct 2006 11:22:56 -0700 (PDT)
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Sent to CCL by: Konstantin Kudin [konstantin_kudin_-_yahoo.com]


--- "Andrew Emerson a.emerson-$-cineca.it" <owner-chemistry[a]ccl.net>
wrote:
> I
> have had some experience with Gromacs and a  simulation of a protein
> in water  scales well upto about 16 processors on an IBM SP machine,
> but scales poorly on a  Linux/Xeon cluster (not quite sure why there
> is such a difference). 

 This issue of poor MPI scaling on Linux clusters with Gigabit does
come up from time to time. And the problem appears for a variety of
different codes, that all however have something in common.
 
 Specifically, many of these codes use FFTs for electrostatics. Then,
parallel FFTs make substantial use of the MPI "alltoall" routine, where
 every processor sends the data to every other processor. In worse
cases "alltoall" is implemented as a bunch of "isend+irecv". And that
is where the issue is. The performance of most of the ethernet switches
seems to degrade significantly for more than just a few cpus.

 Below is the "skampi" test for 64k packets with OpenMPI 1.1 which
actually has one of the better "alltoall" implementations. The
unproportional increase in the communication time is what is killing
the parallel FFTs. Better interconnects do not choke like that.

 Kostya


#############
64k packets

(choking at 15 cpus, see 2nd column)
#/*[a]insyncol_MPI_Alltoall-nodes-long-SM.ski*/
       2     275.1      1.6      8     275.1      1.6      8
       3    1890.2     31.3      8    1890.2     31.3      8
       4    3467.1     85.0      8    3467.1     85.0      8
       5    5843.9     66.3      8    5843.9     66.3      8
       6    8720.9    110.6      8    8720.9    110.6      8
       7    9598.8     99.6      7    9598.8     99.6      7
       8   11757.9    256.4      6   11757.9    256.4      6
       9   13428.2    166.4      8   13428.2    166.4      8
      10   14623.4    176.2      8   14623.4    176.2      8
      11   16689.4    171.9      4   16689.4    171.9      4
      12   18941.4    502.9      5   18941.4    502.9      5
      13   20105.2     99.0      8   20105.2     99.0      8
      14   22731.1    155.0      2   22731.1    155.0      2
      15  123939.7  49248.4      8  123939.7  49248.4      8
      16  142048.0  43888.8      8  142048.0  43888.8      8

 When this "alltoall" is implemented as disjoint operations, the
choking effect kicks in much earlier:

(choking at 6 cpus, see 2nd column)
#/*[a]insyncol_MPI_Alltoall_Isend_Irecv-nodes-long-SM.ski*/
       2     247.4      0.8      8     247.4      0.8      8
       3    1861.8     10.1      8    1861.8     10.1      8
       4    3158.4     24.5      8    3158.4     24.5      8
       5    4270.0     75.0      2    4270.0     75.0      2
       6  225351.5  12504.5      2  225351.5  12504.5      2
       7  228399.5  14770.5      2  228399.5  14770.5      2
       8  247087.5  14448.4      2  247087.5  14448.4      2
       9  243806.7   3878.9      8  243806.7   3878.9      8
      10  248353.0   6640.9      2  248353.0   6640.9      2
      11  267541.5   5210.1      8  267541.5   5210.1      8
      12  286600.1   1665.1      2  286600.1   1665.1      2
      13  277546.5   4208.1      8  277546.5   4208.1      8
      14  364208.9  98276.9      2  364208.9  98276.9      2
      15  392139.0 101163.9      2  392139.0 101163.9      2
      16  367182.1  97711.0      2  367182.1  97711.0      2


__________________________________________________
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From owner-chemistry@ccl.net Fri Oct 27 16:38:01 2006
From: "Phil Hultin hultin++cc.umanitoba.ca" <owner-chemistry:server.ccl.net>
To: CCL
Subject: CCL:G: Hyperchem and other "easy" software
Message-Id: <-32882-061027152444-9523-o+NvvOKiLTeair8dvFt/Jg:server.ccl.net>
X-Original-From: "Phil Hultin" <hultin::cc.umanitoba.ca>
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Sent to CCL by: "Phil Hultin" [hultin _ cc.umanitoba.ca]
This is a multi-part message in MIME format.

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I agree with the statement that Hyperchem's primary advantage is easy use,
and its weakness is in the actual implementation of theoretical models.

 

If you want a user-friendly interface with good computational tools, Spartan
is probably a better choice and is in the same price range as Hyperchem.
Even so, Spartan is by no means an ideal computational code.

 

The big problems with MOST computational freeware are 1) poor documentation
and 2) cryptic command line interfaces.  While there are very nice freeware
visualization tools (eg Rasmol, Molekel, Molden, SwissView) the range of
tools for creating starting structures for computations is much more
limited, and primarily addresses the peptide and nucleic acid communities
(eg VMD/Molefacture).  I have also found that several programs that claim to
be able to save structure files in a given format actually create files that
are not readable by other programs - either because the drawing program uses
a "dialect" of the file format, or the computational program does.  Yes, you
can use sometimes use OpenBabel to get around this, but the frustration
factor grows with every step you have to go through to get a usable
structure input file.

 

There is a need for a simple, reliable and FREE option for general structure
drawing that can save in a variety of formats.  The Marvin package from
ChemAxon approaches this goal but it is still not quite what I have in mind.
Such a program would create absolutely canonical 3-D structure files in MOL,
XYZ (simple Cartesian and TINKER formats), PDB (both ATOM and HETATM/CONECT
variants), and unique SMILES.  The Dundee PRODRG server on the web can do
this but is not as convenient as a local program on one's own workstation or
PC.

 

It would also be able to make input files for the common computational
codes: Gaussian, GAMESS, MOPAC.  I know that GaussView can do this for
Gaussian but GaussView is not free - in fact it is rather expensive.  It is
not essential that this Freeware have all the options for these computations
as buttons or menus, but if it can set up the structure of the file
including the coordinate sets, and then give a command line for the user to
type in the route section etc. that would be very convenient.  If it had
some tools for creating z-matrices that would be a nice touch but is not as
important as it once was.

 

Ok, so I have described what I want for Christmas.  Any altruistic
programmers out there?

 

Dr. Philip G. Hultin

Professor of Chemistry,

University of Manitoba

Winnipeg, MB

R3T 2N2

 <mailto:hultin^cc.umanitoba.ca> hultin^cc.umanitoba.ca

 <http://umanitoba.ca/chemistry/people/hultin>
http://umanitoba.ca/chemistry/people/hultin

 


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<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>I agree with the statement that Hyperchem&#8217;s =
primary
advantage is easy use, and its weakness is in the actual implementation =
of
theoretical models.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>If you want a user-friendly interface with good
computational tools, Spartan is probably a better choice and is in the =
same
price range as Hyperchem. &nbsp;Even so, Spartan is by no means an ideal
computational code.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>The big problems with MOST computational freeware are =
1)
poor documentation and 2) cryptic command line interfaces.&nbsp; While =
there
are very nice freeware visualization tools (eg Rasmol, Molekel, Molden,
SwissView) the range of tools for creating starting structures for =
computations
is much more limited, and primarily addresses the peptide and nucleic =
acid
communities (eg VMD/Molefacture). &nbsp;I have also found that several =
programs
that claim to be able to save structure files in a given format actually =
create
files that are not readable by other programs &#8211; either because the
drawing program uses a &#8220;dialect&#8221; of the file format, or the
computational program does.&nbsp; Yes, you can use sometimes use =
OpenBabel to
get around this, but the frustration factor grows with every step you =
have to
go through to get a usable structure input =
file.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>There is a need for a simple, reliable and FREE =
option for general
structure drawing that can save in a variety of formats. &nbsp;The =
Marvin
package from ChemAxon approaches this goal but it is still not quite =
what I
have in mind.&nbsp; Such a program would create absolutely canonical 3-D
structure files in MOL, XYZ (simple Cartesian and TINKER formats), PDB =
(both ATOM
and HETATM/CONECT variants), and unique SMILES.&nbsp; The Dundee PRODRG =
server
on the web can do this but is not as convenient as a local program on =
one&#8217;s
own workstation or PC.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>It would also be able to make input files for the =
common
computational codes: Gaussian, GAMESS, MOPAC. &nbsp;I know that =
GaussView can
do this for Gaussian but GaussView is not free &#8211; in fact it is =
rather
expensive.&nbsp; It is not essential that this Freeware have all the =
options
for these computations as buttons or menus, but if it can set up the =
structure
of the file including the coordinate sets, and then give a command line =
for the
user to type in the route section etc. that would be very convenient. =
&nbsp;If
it had some tools for creating z-matrices that would be a nice touch but =
is not
as important as it once was.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Ok, so I have described what I want for =
Christmas.&nbsp; Any
altruistic programmers out there?<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Dr. Philip G. Hultin<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Professor of Chemistry,<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><ns0:place w:insAuthor=3D"Philip Hultin"
 w:insDate=3D"2006-10-27T13:25:00Z" w:endInsAuthor=3D"Philip Hultin"
 w:endInsDate=3D"2006-10-27T13:25:00Z"><ns0:PlaceType =
w:insAuthor=3D"Philip Hultin"
  w:insDate=3D"2006-10-27T13:25:00Z" w:endInsAuthor=3D"Philip Hultin"
  w:endInsDate=3D"2006-10-27T13:25:00Z"><st1:place =
w:st=3D"on"><st1:PlaceType
   w:st=3D"on">University</st1:PlaceType></ns0:PlaceType></st1:place> of =
<ns0:PlaceName
  w:insAuthor=3D"Philip Hultin" w:insDate=3D"2006-10-27T13:25:00Z"
  w:endInsAuthor=3D"Philip Hultin" =
w:endInsDate=3D"2006-10-27T13:25:00Z"><st1:PlaceName
  =
w:st=3D"on">Manitoba</st1:PlaceName></ns0:PlaceName></ns0:place><o:p></o:=
p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><ns0:place w:insAuthor=3D"Philip Hultin"
 w:insDate=3D"2006-10-27T13:25:00Z" w:endInsAuthor=3D"Philip Hultin"
 w:endInsDate=3D"2006-10-27T13:25:00Z"><ns0:City w:insAuthor=3D"Philip =
Hultin"
  w:insDate=3D"2006-10-27T13:25:00Z" w:endInsAuthor=3D"Philip Hultin"
  w:endInsDate=3D"2006-10-27T13:25:00Z">Winnipeg</ns0:City>, <ns0:State
  w:insAuthor=3D"Philip Hultin" w:insDate=3D"2006-10-27T13:25:00Z"
  w:endInsAuthor=3D"Philip Hultin" =
w:endInsDate=3D"2006-10-27T13:25:00Z">MB</ns0:State></ns0:place><o:p></o:=
p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DFR-CA =
style=3D'font-size:
10.0pt;font-family:Arial'>R3T 2N2<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><a href=3D"mailto:hultin^cc.umanitoba.ca"><span =
lang=3DFR-CA>hultin^cc.umanitoba.ca</span></a></span></font><font
size=3D2 face=3DArial><span lang=3DFR-CA =
style=3D'font-size:10.0pt;font-family:Arial'><o:p></o:p></span></font></p=
>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><a =
href=3D"http://umanitoba.ca/chemistry/people/hultin"><span
lang=3DFR-CA>http://umanitoba.ca/chemistry/people/hultin</span></a></span=
></font><font
size=3D2 face=3DArial><span lang=3DFR-CA =
style=3D'font-size:10.0pt;font-family:Arial'><o:p></o:p></span></font></p=
>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
lang=3DFR-CA
style=3D'font-size:12.0pt'><o:p>&nbsp;</o:p></span></font></p>

</div>

</body>

</html>

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From owner-chemistry@ccl.net Fri Oct 27 17:13:00 2006
From: "Joseph Han jhh3851^yahoo.com" <owner-chemistry.@.server.ccl.net>
To: CCL
Subject: CCL: Req for information regarding CHEOPS software
Message-Id: <-32883-061027162704-5641-Wb9qQF+T547Z07J+/KPpew.@.server.ccl.net>
X-Original-From: Joseph Han <jhh3851]^[yahoo.com>
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Date: Fri, 27 Oct 2006 13:26:58 -0700 (PDT)
MIME-Version: 1.0


Sent to CCL by: Joseph Han [jhh3851^yahoo.com]
Has anybody used the Cheops software for polymer model synthesis and analysis
developed by Millionzillion software? 
(http://www.millionzillion.com/MZSoftHome/index_1.htm, http://www.mzchem.com)

The software looks interesting; however, none of the links appear current.

Thanks.

Joseph


From owner-chemistry@ccl.net Fri Oct 27 17:47:01 2006
From: "Scott G Flicker sflicker2#%#earthlink.net" <owner-chemistry]=[server.ccl.net>
To: CCL
Subject: CCL: Information on Reaction Similarity Searching
Message-Id: <-32884-061027153539-23938-WJyp07eESrReU0/9qS5pmg]=[server.ccl.net>
X-Original-From: "Scott G Flicker" <sflicker2(!)earthlink.net>
Date: Fri, 27 Oct 2006 15:35:39 -0400


Sent to CCL by: "Scott G Flicker" [sflicker2[A]earthlink.net]
I am looking for information on algorithms to conduct Reaction Similarity Searches against a chemical structure & reaction database. I have control over the database so I could add indexes etc if necessary.

Thanks


From owner-chemistry@ccl.net Fri Oct 27 18:23:00 2006
From: "Roy Jensen rjensen||consol.ca" <owner-chemistry{:}server.ccl.net>
To: CCL
Subject: CCL: HyperChem question...
Message-Id: <-32885-061027125113-22222-rcnfnP8Q9IyCn7cjmJ7ZKA{:}server.ccl.net>
X-Original-From: "Roy Jensen" <rjensen++consol.ca>
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Date: Fri, 27 Oct 2006 11:09:13 -0500 (CDT)
MIME-Version: 1.0


Sent to CCL by: "Roy Jensen" [rjensen]*[consol.ca]

For those who have 7.5 installed on their computer...

Can you generate a 'translucent surface'?
(Under COMPUTE:PLOT MOLECULAR GRAPHS:ISOSURFACE RENDERING)

I can generate any other type of surface once the energy is calculated,
but 'translucent surface' is always greyed out. This is frustrating as it
is the only option that shows both the molecule and, for example,
electrostatic potential.

Thanks,
Roy Jensen