From owner-chemistry@ccl.net Fri Sep 11 00:06:00 2009
From: "Erik-Jan Ras Erik-Jan.Ras],[avantium.com" <owner-chemistry---server.ccl.net>
To: CCL
Subject: CCL: CAS number to Smile String
Message-Id: <-40220-090910144557-4036-/ZIpBpjBzjFIGCuJ/UCM1w---server.ccl.net>
X-Original-From: Erik-Jan Ras <Erik-Jan.Ras[]avantium.com>
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Date: Thu, 10 Sep 2009 20:13:04 +0200
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Sent to CCL by: Erik-Jan Ras [Erik-Jan.Ras!=!avantium.com]
One  method would be to use the SMILECAS database by Syracuse, which is sol=
d online for a few 100 dollars.

Alternatively, most of the SMILECAS database is implemented in the freely a=
vailable EPI Suite which can be found free of charge on the EPA website (ww=
w.epa.gov)

Hope this helps...

Regards,
Erik-Jan

________________________________________
> From: owner-chemistry+erikjan.ras=3D=3Davantium.com!A!ccl.net [owner-chemistr=
y+erikjan.ras=3D=3Davantium.com!A!ccl.net] On Behalf Of Chunhui Li baotogo200=
4#,#gmail.com [owner-chemistry!A!ccl.net]
Sent: Thursday, September 10, 2009 6:27 PM
To: Erik-Jan Ras
Subject: CCL: CAS number to Smile String

Sent to CCL by: "Chunhui  Li" [baotogo2004_._gmail.com]
Hi Dear ALl,

I want to generate smile strings for more than 100 chemicals. All I have is=
 the CAS number for each chemical. Is there any tools I can use to do this =
automatically?

Thanks in advance!



-=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis email (including its attached files and other content) is confidential=
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From owner-chemistry@ccl.net Fri Sep 11 02:21:00 2009
From: "Tapani Kinnunen takinnun-#-csc.fi" <owner-chemistry ~~ server.ccl.net>
To: CCL
Subject: CCL: ANNOUNCE: SOMA2 1.3 Magnesium Released
Message-Id: <-40221-090911021836-14714-DqdveY7D7AWtyZekbSnvtA ~~ server.ccl.net>
X-Original-From: "Tapani  Kinnunen" <takinnun~~csc.fi>
Date: Fri, 11 Sep 2009 02:18:32 -0400


Sent to CCL by: "Tapani  Kinnunen" [takinnun%%csc.fi]
SOMA2 is a WWW browser operated molecular modeling workflow environment. SOMA2 has been developed at CSC - IT Center for Science Ltd. SOMA2 1.3 Magnesium was released on 3rd of September 2009. SOMA2 Software is distributed under the terms of GNU General Public License (GPL). The source code package, documentation, etc. are available from:

http://www.csc.fi/soma

Version 1.3 Magnesium adds better support for modern WWW browsers and brings many usability enhancements along with other improvements. Direct link to release notes:

http://www.csc.fi/english/pages/soma/downloads/soma2/CHANGES.txt/view

Also a demo installation of SOMA2 1.3 Magnesium is available. This demo is a limited features installation where basic functionality of SOMA2 can be tried out. The demo requires no authentication and it is available from:

http://soma2demo.csc.fi

SOMA2 offers a full scale modeling environment from inputting molecular data to analysis of the results. System makes use of scientific applications installed in computing system. The SOMA2 environment enables an easy configuring of the scientific applications via a web interface. The scientific applications can also be seamlessly combined into an application workflow where several applications are automatically executed one after another. SOMA2 is designed so that integrating new tools and adaptation into local computing system is straightforward.

On behalf of SOMA2 developers,

Tapani Kinnunen
CSC - IT Center for Science Ltd.
P.O.BOX 405, FI-02101 Espoo, Finland
http://www.csc.fi


From owner-chemistry@ccl.net Fri Sep 11 06:02:01 2009
From: "Mudit Dixit dixitmuditk:-:gmail.com" <owner-chemistry^_^server.ccl.net>
To: CCL
Subject: CCL: Finding Primitive lattice vectors
Message-Id: <-40222-090911042907-17834-NJx3uyiC+XslUaCjNCuAkg^_^server.ccl.net>
X-Original-From: "Mudit  Dixit" <dixitmuditk(a)gmail.com>
Date: Fri, 11 Sep 2009 04:29:03 -0400


Sent to CCL by: "Mudit  Dixit" [dixitmuditk-x-gmail.com]
I want to generagte Primitive cell , I am doing it with Material Studio . I am not able to generate primitive cell lattice vectors . Please tell is there any software or way for doing this .
Or other way to generate Primitive cell from .cif file so that I can get the primitive cell lattice vectors also.

Thanks,
MD


From owner-chemistry@ccl.net Fri Sep 11 08:46:00 2009
From: "Srividya Madala madala.srividya3+/-gmail.com" <owner-chemistry,server.ccl.net>
To: CCL
Subject: CCL: Database for TB drugs ?
Message-Id: <-40223-090911005007-1643-NRYsRkm/Ng46QJeBdKGX1w,server.ccl.net>
X-Original-From: "Srividya  Madala" <madala.srividya3.,.gmail.com>
Date: Fri, 11 Sep 2009 00:50:02 -0400


Sent to CCL by: "Srividya  Madala" [madala.srividya3!^!gmail.com]
Is there any available database for TB drugs ?


From owner-chemistry@ccl.net Fri Sep 11 09:21:01 2009
From: "John ajitha Manjaly aji.john07,gmail.com" <owner-chemistry_._server.ccl.net>
To: CCL
Subject: CCL: the dynamic (or optical) dielectric constant of the solvent(EpsInf).
Message-Id: <-40224-090911004628-31068-lE52QOoe25jGYsmWvCtSBQ_._server.ccl.net>
X-Original-From: "John ajitha Manjaly" <aji.john07^^gmail.com>
Date: Fri, 11 Sep 2009 00:46:25 -0400


Sent to CCL by: "John ajitha Manjaly" [aji.john07(0)gmail.com]
Dear Friends,

It will be very useful for me to know about the calculation of the dynamic (or optical) dielectric constant(EpsInf)of a solvent(say methanol). Is there any DFT method to calculate the same? 

Thanking you,
Ajitha


From owner-chemistry@ccl.net Fri Sep 11 09:56:01 2009
From: "Sharan sara180681||gmail.com" <owner-chemistry%x%server.ccl.net>
To: CCL
Subject: CCL: Modelling in chemical industry
Message-Id: <-40225-090911074125-27147-GdiyXr9pQp5pkqF7kkQOjg%x%server.ccl.net>
X-Original-From: Sharan <sara180681],[gmail.com>
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Date: Fri, 11 Sep 2009 17:11:12 +0530
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Sent to CCL by: Sharan [sara180681###gmail.com]
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Dear Borosy
When i forwarded your question to my senior scientist,  who also a
biostatistician, his reply was "its too obvious", do u have something
different in mind???

with regard
saravanan.I
On Thu, Sep 10, 2009 at 6:33 PM, andras.borosy::givaudan.com <
owner-chemistry:+:ccl.net> wrote:

>
> Dear Colleagues,
>
> I am looking for a concise summary (survey, article or presentation) whic=
h
> shows why mathematical modelling is useful for the chemical industry.
>
> Many thank,
>
> Dr. Andr=E1s P=E9ter Borosy
> Scientific Modelling Expert
>
> Fragrance Research
> Givaudan Schweiz AG  -  Ueberlandstrasse 138  -  CH-8600  -  D=FCbendorf =
 -
>  Switzerland
> T:+41-44-824 2164  -  F:+41-44-8242926    -  http://www.givaudan.com




--=20
SARAVANAN.I
Jr. Scientist Chemoinformatics

http://www.linkedin.com/in/saravananilangovan

--001636ed690d05524104734bcbe5
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

<div>Dear Borosy<br></div>
<div>When i forwarded your question to my senior scientist,=A0 who also a b=
iostatistician, his reply was &quot;its too obvious&quot;, do u have someth=
ing different in mind???</div>
<div><br>with regard</div>
<div>saravanan.I<br></div>
<div class=3D"gmail_quote">On Thu, Sep 10, 2009 at 6:33 PM, andras.borosy::=
<a href=3D"http://givaudan.com">givaudan.com</a> <span dir=3D"ltr">&lt;<a h=
ref=3D"mailto:owner-chemistry:+:ccl.net">owner-chemistry:+:ccl.net</a>&gt;</spa=
n> wrote:<br>

<blockquote style=3D"BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex=
; PADDING-LEFT: 1ex" class=3D"gmail_quote"><br><font size=3D"2" face=3D"san=
s-serif">Dear Colleagues,</font> <br><br><font size=3D"2" face=3D"sans-seri=
f">I am looking for a concise summary (survey, article or presentation) whi=
ch shows why mathematical modelling is useful for the chemical industry.</f=
ont> <br>
<br><font size=3D"2" face=3D"sans-serif">Many thank,</font> <br><br><font s=
ize=3D"2" face=3D"sans-serif">Dr. Andr=E1s P=E9ter Borosy<br>Scientific Mod=
elling Expert<br><br>Fragrance Research<br>Givaudan Schweiz AG =A0- =A0Uebe=
rlandstrasse 138 =A0- =A0CH-8600 =A0- =A0D=FCbendorf =A0- =A0Switzerland<br=
>
T:+41-44-824 2164 =A0- =A0F:+41-44-8242926 =A0 =A0- =A0<a href=3D"http://ww=
w.givaudan.com/" target=3D"_blank">http://www.givaudan.com</a></font></bloc=
kquote></div><br><br clear=3D"all">
<div></div><br>-- <br>SARAVANAN.I <br>Jr. Scientist Chemoinformatics<br><br=
><a href=3D"http://www.linkedin.com/in/saravananilangovan">http://www.linke=
din.com/in/saravananilangovan</a><br>

--001636ed690d05524104734bcbe5--


From owner-chemistry@ccl.net Fri Sep 11 11:32:01 2009
From: "Bryan Bishop kanzure],[gmail.com" <owner-chemistry:_:server.ccl.net>
To: CCL
Subject: CCL: Free and open source retrosynthesis software project
Message-Id: <-40226-090911112904-5692-V2267wV0La1Y2XS/+vxTUA:_:server.ccl.net>
X-Original-From: Bryan Bishop <kanzure[*]gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Date: Fri, 11 Sep 2009 10:28:50 -0500
MIME-Version: 1.0


Sent to CCL by: Bryan Bishop [kanzure^gmail.com]
Hello all,

A few days ago I mentioned some work that I am doing on an open source
and free retrosynthetic analysis engine. A few people offered to help,
and the response was fantastic. Right now the main hold up in
development is getting access to a chemical reaction database in some
common, standard format. Typing in this information by hand for the
hundreds of thousands of reaction mechanisms is inappropriate. Maybe
there are alternative solutions. Once this challenge is solved, and I
can test what little code I do have without being embarrassed for my
eternal well-being, I'll be sure to send everyone a link and some
instructions on how to get it working with the least hassle.

Btw, someone recomended the Route Designer paper. I came across that a
few months ago and recommend it as well. However, the authors were not
very responsive to my inquiries, and it seems like that research may
end up in a black hole. :-(

- Bryan
http://heybryan.org/
1 512 203 0507


From owner-chemistry@ccl.net Fri Sep 11 13:06:00 2009
From: "Bryan Bishop kanzure(a)gmail.com" <owner-chemistry%x%server.ccl.net>
To: CCL
Subject: CCL: Free and open source retrosynthesis software project
Message-Id: <-40227-090911130254-5520-gckD6xZjvny/y/GQs9Dd1g%x%server.ccl.net>
X-Original-From: Bryan Bishop <kanzure---gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Date: Fri, 11 Sep 2009 12:02:41 -0500
MIME-Version: 1.0


Sent to CCL by: Bryan Bishop [kanzure(-)gmail.com]
On Fri, Sep 11, 2009 at 10:28 AM, Bryan Bishop <kanzure__gmail.com> wrote:
> Btw, someone recomended the Route Designer paper. I came across that a
> few months ago and recommend it as well. However, the authors were not
> very responsive to my inquiries, and it seems like that research may
> end up in a black hole. :-(

Orr and I just had a quick chat about this actually, and I suppose
> from the perspective of academia or commercial projects, Route
Designer is not a black hole. From the perspective of an open source
project, things look different, but apparently Route Designer is alive
and kicking, just not kicking in the direction that I need it to.

- Bryan
http://heybryan.org/
1 512 203 0507


From owner-chemistry@ccl.net Fri Sep 11 13:40:00 2009
From: "Andrew Orry andy^^molsoft.com" <owner-chemistry|a|server.ccl.net>
To: CCL
Subject: CCL: Chemical reactions and mol2 files
Message-Id: <-40228-090911130614-6408-oXzDuC+a2Jt7AxBtoXpaWA|a|server.ccl.net>
X-Original-From: Andrew Orry <andy(-)molsoft.com>
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Date: Fri, 11 Sep 2009 10:01:49 -0700
MIME-Version: 1.0


Sent to CCL by: Andrew Orry [andy]-[molsoft.com]
ICM-Chemist ( http://www.molsoft.com/icm-chemist.html ) allows you to 
enumerate a chemical library by a reaction see: 
http://www.molsoft.com/gui/reactions.html

You can also do a simple "search-and-replace" chemical group procedure 
on a set of chemicals in MOL2 format.

Werner K werner.schroedinger^googlemail.com wrote:
> Sent to CCL by: "Werner  K" [werner.schroedinger,,googlemail.com]
> Hi,
>
> I have a file in MOL2 format with around 10000 molecules. I want to perform chemical reactions on them (for instance change all -OH to -COOH) and get the results in MOL2 format with the corresponding new 3D coordinates for the new functional groups, etc.
>
> What is the best software for this purpose?
>
> Thanks
>
> W>
>   


-- 
Andrew Orry Ph.D.
Senior Scientist
MolSoft LLC
3366 North Torrey Pines Court
Suite 300
La Jolla, CA 92037
U S A

Phone: (858) 625-2000 (x108)
Fax: (858) 625-2888
www.molsoft.com
Latest ICM News: www.molsoft.com/news.html


From owner-chemistry@ccl.net Fri Sep 11 14:53:01 2009
From: "Philip J. McHale pmchale[A]cambridgesoft.com" <owner-chemistry ~~ server.ccl.net>
To: CCL
Subject: CCL: 2010 Herman Skolnik Award Winner Announced
Message-Id: <-40229-090911144526-32045-YsBwly2nDp4veJJX1xNvHA ~~ server.ccl.net>
X-Original-From: "Philip J. McHale" <pmchale^cambridgesoft.com>
Date: Fri, 11 Sep 2009 14:45:23 -0400


Sent to CCL by: "Philip J. McHale" [pmchale[]cambridgesoft.com]
Anton (Tony) J. Hopfinger, Distinguished Research Professor of Pharmacy, University of New Mexico, Professor Emeritus of Medicinal Chemistry and Pharmacognosy, University of Illinois, and co-Founder and Chief Science Officer of The Chem21 Group, Inc. is the recipient of the 2010 Herman Skolnik Award presented by the ACS Division of Chemical Information (CINF). The award recognizes outstanding contributions to and achievements in the theory and practice of chemical information science and related disciplines. The prize consists of a $3,000 honorarium and a plaque.

Tony Hopfinger is recognized as a pioneer and major contributor in the fields of quantitative structure activity relationship (QSAR) and quantitative structure property relationship (QSPR) techniques employing three and higher dimensional levels of information derived from modeling and simulation. Tony has addressed chemical information and modeling problems in the pharmaceutical, polymer and materials sciences, in both industry and academia, and he is generally acknowledged as having fathered the development of QSPR modeling in polymer and materials science, including coining the acronym QSPR. The breadth of his interests and the applicability of the techniques he has developed are reflected in the topics covered in some of his recent papers, including drug discovery, ADME-Tox property prediction, nanotoxicity, cheminformatic descriptors and molecular similarity analysis.

Tony has made many contributions to the field of cheminformatics through publication, teaching, mentoring, advising and organizing. He has authored or co-authored more than 270 peer-reviewed (and highly cited) papers and delivered almost 360 invited lectures. He has served on many journal editorial boards and has been an associate editor the Journal of Chemical Information and Modeling (previously Journal of Chemical Information and Computer Science) for the past 16 years. He has been a member of government and industrial advisory boards, and he chaired a Gordon Research Conference on Quantitative Structure Activity-Relationships in Biology. He has coordinated and taught at short courses in North and South America and Europe; more than 50 computational scientists earned their Ph.D. degrees under Tonys mentoring; and he has also provided advanced training to more than 70 postdoctoral students.

Tony Hopfinger received a B.S. in Math and Physics from the University of Wisconsin in 1966, and a Ph.D. in Biophysical Chemistry from Case Western Reserve University in 1969. He started his career in 1969 as an NIH Postdoctoral Fellow, Department of Biological Chemistry, Harvard Medical School, and from there moved to Case Western Reserve University in 1970 as Assistant Professor of Macromolecular Science. He held increasingly senior positions at Case Western, eventually becoming Professor of Macromolecular Science in 1978 and Director, Research Computing Laboratory in 1979. In 1981 he moved from academia to industry, joining G.D. Searle (now part of Pfizer) as Director, Department of Drug Design, and later Director, Department of Medicinal Chemistry. Tony maintained links with academia, holding several adjunct and visiting professorships, and in his spare time founded, or co-founded, a number of software and pharmaceutical companies including Intersoft, ChemLab, Receptor Laboratories and DNACodes. He returned to academia in 1985 and was Professor of Bioengineering, Chemistry and Medicinal Chemistry, University of Illinois at Chicago until 2005. Since then he divides his time as Distinguished Research Professor of Pharmacy, University of New Mexico, Chief Science Officer of The Chem21 Group, Inc.  and Professor Emeritus of Medicinal Chemistry and Pharmacognosy, University of Illinois.

Tony Hopfinger is highly respected by all of his colleagues worldwide and this Award is a well-deserved recognition of the outstanding career of an unstinting and generous pioneer and practitioner of cheminformatics.  


Phil McHale
Chair, CINF Awards Committee
pmchale|cambridgesoft.com


From owner-chemistry@ccl.net Fri Sep 11 15:29:01 2009
From: "Zork Zou zorkzou#%#gmail.com" <owner-chemistry:server.ccl.net>
To: CCL
Subject: CCL: Finding Primitive lattice vectors
Message-Id: <-40230-090911141540-16173-WCu6x8M5IuXGs45+uZ/D9A:server.ccl.net>
X-Original-From: Zork Zou <zorkzou ~ gmail.com>
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Date: Fri, 11 Sep 2009 12:01:11 -0500
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Sent to CCL by: Zork Zou [zorkzou.::.gmail.com]
--00163642722861b2f5047350436a
Content-Type: text/plain; charset=ISO-8859-1

Hi Mudit,

To my known, several free programs can do it.

FINDSYM. It is downloadable or can be used online.
http://stokes.byu.edu/findsym.html

SGROUP. The updated version of SGROUP can be found in WIEN2k, if you have
it.
http://cpc.cs.qub.ac.uk/summaries/ADON_v1_0.html

Wenli

On Fri, Sep 11, 2009 at 3:29 AM, Mudit Dixit dixitmuditk:-:gmail.com <
owner-chemistry::ccl.net> wrote:

>
> Sent to CCL by: "Mudit  Dixit" [dixitmuditk-x-gmail.com]
> I want to generagte Primitive cell , I am doing it with Material Studio . I
> am not able to generate primitive cell lattice vectors . Please tell is
> there any software or way for doing this .
> Or other way to generate Primitive cell from .cif file so that I can get
> the primitive cell lattice vectors also.
>
> Thanks,
> MD>
>
>

--00163642722861b2f5047350436a
Content-Type: text/html; charset=ISO-8859-1
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<div>Hi Mudit,</div>
<div>=A0</div>
<div>To my known, several free=A0programs can do it.</div>
<div>=A0</div>
<div>FINDSYM. It is downloadable or can be used online.</div>
<div><a href=3D"http://stokes.byu.edu/findsym.html">http://stokes.byu.edu/f=
indsym.html</a></div>
<div><br>SGROUP. The updated version of SGROUP can be found in WIEN2k, if y=
ou have it.</div>
<div><a href=3D"http://cpc.cs.qub.ac.uk/summaries/ADON_v1_0.html">http://cp=
c.cs.qub.ac.uk/summaries/ADON_v1_0.html</a></div>
<div>=A0</div>
<div>Wenli<br></div>
<div>=A0</div>
<div class=3D"gmail_quote">On Fri, Sep 11, 2009 at 3:29 AM, Mudit Dixit dix=
itmuditk:-:<a href=3D"http://gmail.com">gmail.com</a> <span dir=3D"ltr">&lt=
;<a href=3D"mailto:owner-chemistry::ccl.net">owner-chemistry::ccl.net</a>&gt;=
</span> wrote:<br>

<blockquote style=3D"BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex=
; PADDING-LEFT: 1ex" class=3D"gmail_quote"><br>Sent to CCL by: &quot;Mudit =
=A0Dixit&quot; [<a href=3D"http://dixitmuditk-x-gmail.com/" target=3D"_blan=
k">dixitmuditk-x-gmail.com</a>]<br>
I want to generagte Primitive cell , I am doing it with Material Studio . I=
 am not able to generate primitive cell lattice vectors . Please tell is th=
ere any software or way for doing this .<br>Or other way to generate Primit=
ive cell from .cif file so that I can get the primitive cell lattice vector=
s also.<br>
<br>Thanks,<br>MD<br><br><br><br>-=3D This is automatically added to each m=
essage by the mailing script =3D-<br>To recover the email address of the au=
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><br><br></blockquote></div><br>

--00163642722861b2f5047350436a--


From owner-chemistry@ccl.net Fri Sep 11 16:15:01 2009
From: "N. Sukumar nagams(!)rpi.edu" <owner-chemistry[a]server.ccl.net>
To: CCL
Subject: CCL: Modelling in chemical industry
Message-Id: <-40231-090911160836-14157-OH3oD4NwFSmlcnXP0Y2nxQ[a]server.ccl.net>
X-Original-From: "N. Sukumar" <nagams-$-rpi.edu>
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Sent to CCL by: "N. Sukumar" [nagams]_[rpi.edu]
Too obvious to some perhaps (especially to those of us who are invested
in the technology). But Nicholls has argued (J. Comput.-Aided Mol. Des.
2008, 22:239–255; DOI: 10.1007/s10822-008-9170-2) "Why is the modeling
field so poor at the most basic elements of evaluation? ... An extreme
view is that we are poor at evaluations because we simply do not matter
very much. If large fortunes were won or lost on the results from
computational techniques there would be immense debate as to how to
analyze and compare methods, on what we know and exactly when we know it. 
There would be double blind, prospective and rigorously reviewed studies
of a scale and depth unknown in our field but common in, for instance,
clinical trials. In short, there would be standards."

(Don't direct your flames at me :-)

Dr. N. Sukumar
Rensselaer Exploratory Center for Cheminformatics Research
http://reccr.chem.rpi.edu/ 
==============Original message text===============
On Fri, 11 Sep 2009 7:41:12 EDT "Sharan sara180681||gmail.com" wrote:

Dear Borosy
When i forwarded your question to my senior scientist,  who also a
biostatistician, his reply was "its too obvious", do u have something
different in mind???

with regard
saravanan.I
On Thu, Sep 10, 2009 at 6:33 PM, andras.borosy::givaudan.com <
owner-chemistry!A!ccl.net> wrote:

>
> Dear Colleagues,
>
> I am looking for a concise summary (survey, article or presentation) which
> shows why mathematical modelling is useful for the chemical industry.
>
> Many thank,
>
> Dr. András Péter Borosy
> Scientific Modelling Expert
>
> Fragrance Research
> Givaudan Schweiz AG  -  Ueberlandstrasse 138  -  CH-8600  -  Dübendorf  -
>  Switzerland
> T:+41-44-824 2164  -  F:+41-44-8242926    -  http://www.givaudan.com



-- 
SARAVANAN.I
Jr. Scientist Chemoinformatics

http://www.linkedin.com/in/saravananilangovan===========End of original message text===========


From owner-chemistry@ccl.net Fri Sep 11 19:33:00 2009
From: "Joe Leonard jleonard42{:}gmail.com" <owner-chemistry]_[server.ccl.net>
To: CCL
Subject: CCL: Thanks to all...
Message-Id: <-40232-090911192424-32096-QEJdciRoC8MpcnAohxxw3A]_[server.ccl.net>
X-Original-From: Joe Leonard <jleonard42() gmail.com>
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Sent to CCL by: Joe Leonard [jleonard42+*+gmail.com]

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... who helped me out with the Mac/X11 problem.  The concensus was  
that I should download the latest stable X-server from XQuartz.  I did  
(2.4.0) and it seems to have cleared up the window/stability issues I  
was having with X11 under Leopard (10.5).  It did not, however, deal  
with the 8- vs. 16-bit buffer problems we're seeing - things that  
cause the mac to look worse than similar PC's or Linux machines...

Our current lead for this is some commented out code in the XQuartz  
source that seems to have disabled some 16-bit functionality while  
trying to eliminate other problems.  This seems to have appeared  
between 10.5.6 and 10.5.7 - and I recall blogs commenting on Leopard X  
performance being worse than Tiger's.

We are still trying to understand this problem so that we can file a  
bug with the appropriate party :-).  In case anybody wants to play at  
home, the best thing would be to find machines (particularly macbook  
pro's) running early versions of Leopard - the lazy people who aren't  
into (or can't for some reason) upgrade their software.  Run glxinfo  
in a Terminal window and send it to me - this will help narrow down  
this issue.  If we can truly find the downgrade, we will know exactly  
what to submit, blah blah blah.

It's not a big deal, as it seems related to anti-aliasing.  It's just  
frustrating to have worse performance on my machine (the mac) than  
those I have at work - I paid for the home machine :-).

Joe Leonard
jleonard42:-:gmail.com
--
Elves are tall and fair and use bows, dwarves are small and dark and  
vote Labour.


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<html><body style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; =
-webkit-line-break: after-white-space; ">... who helped me out with the =
Mac/X11 problem. &nbsp;The concensus was that I should download the =
latest stable X-server from <a =
href=3D"http://xquartz.macosforge.org/trac/wiki">XQuartz</a>. &nbsp;I =
did (2.4.0) and it seems to have cleared up the window/stability issues =
I was having with X11 under Leopard (10.5). &nbsp;It did not, however, =
deal with the 8- vs. 16-bit buffer problems we're seeing - things that =
cause the mac to look worse than similar PC's or Linux =
machines...<div><br></div><div>Our current lead for this is some =
commented out code in the XQuartz source that seems to have disabled =
some 16-bit functionality while trying to eliminate other problems. =
&nbsp;This seems to have appeared between 10.5.6 and 10.5.7 - and I =
recall blogs commenting on Leopard X performance being worse than =
Tiger's.</div><div><br></div><div>We are still trying to understand this =
problem so that we can file a bug with the appropriate party :-). =
&nbsp;In case anybody wants to play at home, the best thing would be to =
find machines (particularly macbook pro's) running early versions of =
Leopard - the lazy people who aren't into (or can't for some reason) =
upgrade their software. &nbsp;Run glxinfo in a Terminal window and send =
it to me - this will help narrow down this issue. &nbsp;If we can truly =
find the downgrade, we will know exactly what to submit, blah blah =
blah.</div><div><br></div><div>It's not a big deal, as it seems related =
to anti-aliasing. &nbsp;It's just frustrating to have worse performance =
on my machine (the mac) than those I have at work - I paid for the home =
machine :-).</div><div><br></div><div>Joe Leonard</div><div><a =
href=3D"mailto:jleonard42:-:gmail.com">jleonard42:-:gmail.com</a><br><div =
apple-content-edited=3D"true"> <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"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"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"word-wrap: =
break-word; -webkit-nbsp-mode: space; -webkit-line-break: =
after-white-space; ">--</div><div style=3D"word-wrap: break-word; =
-webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div =
style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; =
-webkit-line-break: after-white-space; ">Elves are tall and fair and use =
bows, dwarves are small and dark and =
vote&nbsp;Labour.</div></div></span></div></span></div></span></div> =
</div><br></div></body></html>=

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From owner-chemistry@ccl.net Fri Sep 11 21:59:01 2009
From: "Kadir Diri kadir*visual1.chem.pitt.edu" <owner-chemistry,,server.ccl.net>
To: CCL
Subject: CCL: ezDyson: A new program for photoelectron cross sections
Message-Id: <-40233-090911215729-5377-QC0C/v7tn3S2AwXa3ct9Jw,,server.ccl.net>
X-Original-From: Kadir Diri <kadir() visual1.chem.pitt.edu>
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Date: Fri, 11 Sep 2009 18:57:18 -0700
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Sent to CCL by: Kadir Diri [kadir:-:visual1.chem.pitt.edu]
Dear Colleagues,

Apologies for cross posting...

A new program for calculating absolute and differential cross
sections of photoelectrons is available for download:
http://iopenshell.usc.edu/downloads/ezdyson/

ezDyson requires Dyson orbitals computed by an ab initio program
and is based on a simple model that involves the dipole and sudden
ionization approximations, and neglects the interaction between the
outgoing electron and the ionized core.

A general xml input format allows for easy customizations and interfacing
with different ab initio programs.

Enjoy!
kadir

 


----------
Kadir Diri, PhD
Research Scientist
Department of Chemistry and iOpenShell Center
SSC #401
University of Southern California
Los Angeles, CA 90089-0482
--------------------------

Relativistic correction to Murphy's law:
Whether things can go wrong or not, depends on your frame of reference.


From owner-chemistry@ccl.net Fri Sep 11 23:49:01 2009
From: "David A. Mannock dmannock**ualberta.ca" <owner-chemistry%a%server.ccl.net>
To: CCL
Subject: CCL: CAS number to Smile String
Message-Id: <-40234-090911184701-29255-qH/fEtcguGbk5YqyfhQIQg%a%server.ccl.net>
X-Original-From: "David A. Mannock" <dmannock[A]ualberta.ca>
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Date: Fri, 11 Sep 2009 16:46:18 -0600
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Sent to CCL by: "David A. Mannock" [dmannock++ualberta.ca]
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Don't forget that there are both simple and complex Smile string 
formats. The later allow for chirality, whereas the former do not. Dave

At 06:11 PM 10/09/2009, you wrote:
>There are a series of ChemSPider web services to use if you wish to 
>avail yourself of them. The services are listed online here: 
><http://www.chemspider.com/Search.asmx>http://www.chemspider.com/Search.asmx
>
>In terms of internet-based quality there are significant issues when 
>it comes to registry numbers. For example, take a simple element 
>like Carbon. CAS's own website declares the CAS registry number as 
>7440-44-0: 
><http://www.commonchemistry.org/search.aspx?terms=carbon>http://www.commonchemistry.org/search.aspx?terms=carbon
>
>A search on PubChem will give two hits: methane and progesterone: 
><http://www.ncbi.nlm.nih.gov/sites/entrez?db=pccompound&term=7440-44-0>http://www.ncbi.nlm.nih.gov/sites/entrez?db=pccompound&term=7440-44-0
>
>Some of these issues have proliferated into databases utilizing 
>PubChem as the seed set so a search on the NCI database also gives 
>methane: 
><http://cactus.nci.nih.gov/chemical/structure/7440-44-0/file?format=sdf>http://cactus.nci.nih.gov/chemical/structure/7440-44-0/file?format=sdf 
>
>
>There is no easy way to curate and validate CAS registry numbers as 
>it requires access to the CAS Registry to validate so only 
>investigative work and diligence can improve this situation and the 
>majority of databases are not resourced to curate the data. It is 
>also not allowable to use SciFinder to validate Registry Numbers as 
>stated here 
><http://en.wikipedia.org/wiki/Wikipedia_talk:WikiProject_Chemistry/CAS_validation>http://en.wikipedia.org/wiki/Wikipedia_talk:WikiProject_Chemistry/CAS_validation 
>
>
>Those databases with the resources and mission to curate do get it 
>right and I recommend ChEBI as an example: 
><http://www.ebi.ac.uk/ebisearch/search.ebi?db=smallMolecules&t=7440-44-0>http://www.ebi.ac.uk/ebisearch/search.ebi?db=smallMolecules&t=7440-44-0
>
>Please note that many of the identifiers in ChemSPider, including 
>CAS numbers, have been curated and validated by curators and by the 
>public (crowdsourced curation). While the database is far from 
>perfect we have put considerable effort into validating the data.
>
>Feel free to contact us if you need help.
>
>[]
>Antony Williams, VP Strategic Development
>ChemSpider, Royal Society of Chemistry
>US Office: 904 Tamaras Circle, Wake Forest, NC-27587
>
>Phone: +1 (919) 201-1516
>Fax: +1 (919) 300-5321
>
>From: owner-chemistry+wdi==xemistry.com-,-ccl.net 
>[mailto:owner-chemistry+wdi==xemistry.com-,-ccl.net] On Behalf Of 
>Rajarshi Guha rajarshi.guha+*+gmail.com
>Sent: Thursday, September 10, 2009 7:30 PM
>To: Ihlenfeldt, Wolf D
>Subject: CCL: CAS number to Smile String
>
>
>On Thu, Sep 10, 2009 at 12:27 PM, Chunhui Li 
>baotogo2004#,#<http://gmail.com>gmail.com 
><<mailto:owner-chemistry]=cl.net>owner-chemistry]=cl.net> wrote:
>
>Sent to CCL by: "Chunhui  Li" [baotogo2004_._<http://gmail.com>gmail.com]
>Hi Dear ALl,
>
>I want to generate smile strings for more than 100 chemicals. All I 
>have is the CAS number for each chemical. Is there any tools I can 
>use to do this automatically?
>
>One way to get it is to use the PubChem synonym tables - this is 
>obviously not a comprehensive solution as it doesn't contain the 
>entire CAS registry.
>
>There's a simple REST interface (based on a mirror of PubChem at 
>IU). For example, given a CAS for aspirin visit
>
><http://toposome.chemistry.drexel.edu/~rguha/rest/db/pubchem/cas2smi/69-46-5>http://toposome.chemistry.drexel.edu/~rguha/rest/db/pubchem/cas2smi/69-46-5
>
>and you get back the SMILES for it. In general, replace the CAS at 
>the end of the URL to whatever you want
>
>
>
>--
>Rajarshi Guha
>NIH Chemical Genomics Center
>

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<html>
<body>
Don't forget that there are both simple and complex Smile string formats.
The later allow for chirality, whereas the former do not. Dave<br><br>
At 06:11 PM 10/09/2009, you wrote:<br>
<blockquote type=cite class=cite cite="">There are a series of ChemSPider
web services to use if you wish to avail yourself of them. The services
are listed online here:
<a href="http://www.chemspider.com/Search.asmx">
http://www.chemspider.com/Search.asmx</a><br>
&nbsp;<br>
In terms of internet-based quality there are significant issues when it
comes to registry numbers. For example, take a simple element like
Carbon. CAS’s own website declares the CAS registry number as 7440-44-0:
<a href="http://www.commonchemistry.org/search.aspx?terms=carbon">
http://www.commonchemistry.org/search.aspx?terms=carbon</a><br>
&nbsp;<br>
A search on PubChem will give two hits: methane and progesterone:
<a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pccompound&amp;term=7440-44-0">
http://www.ncbi.nlm.nih.gov/sites/entrez?db=pccompound&amp;term=7440-44-0</a>
<br>
&nbsp;<br>
Some of these issues have proliferated into databases utilizing PubChem
as the seed set so a search on the NCI database also gives methane:
<a href="http://cactus.nci.nih.gov/chemical/structure/7440-44-0/file?format=sdf">
http://cactus.nci.nih.gov/chemical/structure/7440-44-0/file?format=sdf</a>
 <br>
&nbsp;<br>
There is no easy way to curate and validate CAS registry numbers as it
requires access to the CAS Registry to validate so only investigative
work and diligence can improve this situation and the majority of
databases are not resourced to curate the data. It is also not allowable
to use SciFinder to validate Registry Numbers as stated here
<a href="http://en.wikipedia.org/wiki/Wikipedia_talk:WikiProject_Chemistry/CAS_validation">
http://en.wikipedia.org/wiki/Wikipedia_talk:WikiProject_Chemistry/CAS_validation</a>
 <br>
&nbsp;<br>
Those databases with the resources and mission to curate do get it right
and I recommend ChEBI as an example:
<a href="http://www.ebi.ac.uk/ebisearch/search.ebi?db=smallMolecules&amp;t=7440-44-0">
http://www.ebi.ac.uk/ebisearch/search.ebi?db=smallMolecules&amp;t=7440-44-0</a>
<br>
&nbsp;<br>
Please note that many of the identifiers in ChemSPider, including CAS
numbers, have been curated and validated by curators and by the public
(crowdsourced curation). While the database is far from perfect we have
put considerable effort into validating the data.<br>
&nbsp;<br>
Feel free to contact us if you need help.<br>
&nbsp;<br>
<img src="cid:7.1.0.9.0.20090911164445.010d00f8]![ualberta.ca.1" width=134 height=134 alt="[]">
<b>Antony Williams, VP Strategic Development</b><br>
<b>ChemSpider, Royal Society of Chemistry<br>
</b>US Office: 904 Tamaras Circle, Wake Forest, NC-27587<br>
&nbsp;<br>
<b>Phone:</b> +1 (919) 201-1516<br>
<b>Fax:</b> +1 (919) 300-5321<br>
&nbsp;<br>
<b>From:</b> owner-chemistry+wdi==xemistry.com-,-ccl.net
[<a href="mailto:owner-chemistry+wdi==xemistry.com-,-ccl.net" eudora="autourl">
mailto:owner-chemistry+wdi==xemistry.com-,-ccl.net</a>] <b>On Behalf Of
</b>Rajarshi Guha rajarshi.guha+*+gmail.com<br>
<b>Sent:</b> Thursday, September 10, 2009 7:30 PM<br>
<b>To:</b> Ihlenfeldt, Wolf D <br>
<b>Subject:</b> CCL: CAS number to Smile String<br>
&nbsp;<br>
&nbsp;<br>
On Thu, Sep 10, 2009 at 12:27 PM, Chunhui Li
baotogo2004#,#<a href="http://gmail.com">gmail.com</a>
&lt;<a href="mailto:owner-chemistry]=cl.net">owner-chemistry]=cl.net</a>
&gt; wrote:<br><br>
Sent to CCL by: &quot;Chunhui&nbsp; Li&quot;
[baotogo2004_._<a href="http://gmail.com">gmail.com</a>]<br>
Hi Dear ALl,<br><br>
I want to generate smile strings for more than 100 chemicals. All I have
is the CAS number for each chemical. Is there any tools I can use to do
this automatically?<br><br>
One way to get it is to use the PubChem synonym tables - this is
obviously not a comprehensive solution as it doesn't contain the entire
CAS registry.<br><br>
There's a simple REST interface (based on a mirror of PubChem at IU). For
example, given a CAS for aspirin visit<br><br>
<a href="http://toposome.chemistry.drexel.edu/~rguha/rest/db/pubchem/cas2smi/69-46-5">
http://toposome.chemistry.drexel.edu/~rguha/rest/db/pubchem/cas2smi/69-46-5</a>
<br><br>
and you get back the SMILES for it. In general, replace the CAS at the
end of the URL to whatever you want<br><br>
<br><br>
-- <br>
Rajarshi Guha<br>
NIH Chemical Genomics Center<br><br>
</blockquote></body>
</html>

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