On Fri, Oct 30, 2009 at 6:05 AM, sebastian.rohrer:+:basf.com <owner-chemistry- -ccl.net> wrote:

Hi all,
does anybody know a way to include c= hemical structures into R diagrams, eg. as axis labels or plot titles?
Thanks
Sebastian

--
Rajarshi Guha
NIH Chemical Genomics = Center
--0016e6d6410995551e047728973b-- From owner-chemistry@ccl.net Fri Oct 30 14:13:00 2009 From: "Rajarshi Guha rajarshi.guha-.-gmail.com" To: CCL Subject: CCL: SMILES to 2D mol/sdf files open source Message-Id: <-40567-091030132513-10981-ycqO2wT5vcc0PZbs5dROOQ%%server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Fri, 30 Oct 2009 13:24:57 -0400 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Rajarshi Guha [rajarshi.guha=gmail.com] On Oct 30, 2009, at 11:53 AM, Chido Mpamhanga chido.mpamhanga_ +_gmail.com wrote: > Hi all > > Does any one have an idea how best to generate 2D coodinates from > smiles, using open source programs... I have been generating them > using CDK via Knime > this works but I need them for images on my database. Ana when I > generate postscript files from these the resulting images are not > optimal. > Is there a nice way to optimise these or generate optimised ones? Do you want to generate just the 2D coordinates? Or also generate images of the structures? The CDK will do both (and you can save the images as PNG). You could also hit webservices such as http://toposome.chemistry.drexel.edu:6666/cdk/depict/200/200/c1cc(C(F)(F)(F))ccc1 ---------------------------------------------------- Rajarshi Guha | NIH Chemical Genomics Center http://www.rguha.net | http://ncgc.nih.gov ---------------------------------------------------- I live in my own little world... but it's OK, they like me there From owner-chemistry@ccl.net Fri Oct 30 14:55:01 2009 From: "Venable, Richard (NIH/NHLBI) E venabler__nhlbi.nih.gov" To: CCL Subject: CCL: Chemical structures in R Message-Id: <-40568-091030132709-12148-u9tGJiZjnb+6cnPNmzyCHA(!)server.ccl.net> X-Original-From: "Venable, Richard (NIH/NHLBI) [E]" Content-Language: en Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 30 Oct 2009 12:51:49 -0400 MIME-Version: 1.0 Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler{}nhlbi.nih.gov] In the past, I've found the xfig tool to be quite useful in combining plots= with chemical structures, importing both as .eps objects -- Rick Venable 5635 FL/T906 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-9314 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov On 10/30/09 6:05 AM, "sebastian.rohrer:+:basf.com" wrote: Hi all, does anybody know a way to include chemical structures into R diagrams, eg.= as axis labels or plot titles? Thanks Sebastian From owner-chemistry@ccl.net Fri Oct 30 15:23:01 2009 From: "Morad El-Hendawy m80elhendawy . yahoo.com" To: CCL Subject: CCL:G: AMBER calculation in Gaussian: missing parameters Message-Id: <-40569-091030135050-31448-tf95/L6URAONwJYYxRFMTw_-_server.ccl.net> X-Original-From: Morad El-Hendawy Content-Type: multipart/alternative; boundary="0-812559685-1256925038=:66619" Date: Fri, 30 Oct 2009 10:50:38 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Morad El-Hendawy [m80elhendawy===yahoo.com] --0-812559685-1256925038=:66619 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Lesley, As you know AMBER 94 or 95 is implemented in G03/09. In order to solve this= problem, you may use MOE suite or other one to complete the crossponding m= issing parameters. Another way, complete the missing parameters from AMBER = 99. Good luck=A0=20 ***************************************************************************= ***********************Morad M. El-Hendawy*********************************= *****************************************************************=A0If you = want a happy life, do four things:=A01- Contemplate and be thankful, 2- The past is gone forever, 3- Today all that you have, 4- Leave the future alone until it come.=A0********************************= ***************************************************************************= ******** --- On Fri, 10/30/09, Lesley Rutledge lesley.rutledge*o*uleth.ca wrote: > From: Lesley Rutledge lesley.rutledge*o*uleth.ca Subject: CCL:G: AMBER calculation in Gaussian: missing parameters To: "El-Hendawy, Morad Metwally " Date: Friday, October 30, 2009, 6:46 PM Sent to CCL by: "Lesley=A0 Rutledge" [lesley.rutledge[*]uleth.ca] Hello, I am trying to run an AMBER calculation in Gaussian where I have many water= molecules and a few Na+ ions to neutralize the charge of my protein-DNA sy= stem. When I run this calculation, I get the following error. Bondstretch undefined between atoms=A0 =A0 IP-HW Angle bend=A0 undefined between atoms=A0 =A0 IP-HW-OW Angle bend=A0 undefined between atoms=A0 =A0 HW-IP-HW I can't find any information about what I should do to fix this problem wit= h the sodium ions (IP atom type) and the water molecules in Gaussian.=20 I am aware that I could use 'HrmBnd1 IP HW' or 'HrmStr1 IP HW OW' to fix th= is, but I can't find any information about what parameters I would use in t= hese definitions. Also, I tried using 'NBonds IP 0' in my input file, but this resulted in th= e same error as above. Any help for this error would be greatly appreciated. Thanks, Lesley Rutledge Ph. D. student University of Lethbridge, Alberta, Canada -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A__________________________________________________=0ADo You Yahoo!?= =0ATired of spam? Yahoo! Mail has the best spam protection around =0Ahttp:= //mail.yahoo.com --0-812559685-1256925038=:66619 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Dear Lesley,
As you know AMBER 94 or 95 is= implemented in G03/09. In order to solve this problem, you may use MOE sui= te or other one to complete the crossponding missing parameters. Another wa= y, complete the missing parameters from AMBER 99.
Good luck

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

Morad M. El-Hendawy

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

<= /strong> If you want a happy life, do four things:<= /div>

1- Contemplate and be thankful,
= 2- The past is gone f= orever,
3- Today all that you have,
4- Leave the future alone until it come. <= /font>
**********************= ***************************************************************************= ******************

=
--- On Fri, 10/30/09, Lesley Rutledge lesley.rutledge*o*uleth.ca = <owner-chemistry- -ccl.net> wrote:
=
From: Lesley Rutledge lesley.rutledge*o*uleth.ca <owner-chemistry- -cc= l.net>
Subject: CCL:G: AMBER calculation in Gaussian: missing paramet= ers
To: "El-Hendawy, Morad Metwally " <m80elhendawy- -yahoo.com= >
Date: Friday, October 30, 2009, 6:46 PM

Sent to CCL by: "Lesley Rutledge" [lesley.rutledge[*]uleth.ca]
Hello,

I am trying to run an AMBER = calculation in Gaussian where I have many water molecules and a few Na+ ion= s to neutralize the charge of my protein-DNA system.
When I run this cal= culation, I get the following error.

Bondstretch undefined between = atoms IP-HW
Angle bend undefined between atoms = IP-HW-OW
Angle bend undefined between atoms = HW-IP-HW

I can't find any information about what I should do to fix = this problem with the sodium ions (IP atom type) and the water molecules in= Gaussian.
I am aware that I could use 'HrmBnd1 IP HW' or 'HrmStr1 IP H= W OW' to fix this, but I can't find any information about what parameters I= would use in these definitions.
Also, I tried using 'NBonds IP 0' in my= input file, but this resulted in the same error as above.

Any help = for this error would be greatly appreciated.
Thanks,
Lesley Rutledge
Ph. D. student
University of Lethbridge, Alberta, Canada

-=3D This is automatically added to each message by the mailin= g script =3D-
To recover the email address of the author of the message,= please change
the strange characters on the top line to the - - sign. You= can also
E= -mail to subscribers: CHEMISTRY- -ccl.net or use:
&nbs= p; http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-m= ail to administrators: CHEMISTRY-REQUEST- -ccl.net or use
http://www.ccl.net/cgi-bin/ccl/send_ccl_message
<= br
http://www.ccl.net/chemi= stry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job= : http://www.ccl.net/= jobs
Conferences: http://server.ccl.net/chemistry/ann= ouncements/conferences/

Search Messages: http://www.ccl.ne= t/chemistry/searchccl/index.shtml

If your mail bounces from CCL = with 5.7.1 error, check:
http://www.ccl.net/spammers.txt
=
RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/

_____________________________________= _____________
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best= spam protection around
http://mail.yahoo.com --0-812559685-1256925038=:66619-- From owner-chemistry@ccl.net Fri Oct 30 15:58:01 2009 From: "Wolf-D. Ihlenfeldt wdi/a\xemistry.com" To: CCL Subject: CCL: SMILES to 2D mol/sdf files open source Message-Id: <-40570-091030135927-6997-S1LT/g4zkYe2XbW9OVgVBw__server.ccl.net> X-Original-From: "Wolf-D. Ihlenfeldt" Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_001C_01CA598E.496B3030" Date: Fri, 30 Oct 2009 18:24:57 +0100 MIME-Version: 1.0 Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi[A]xemistry.com] This is a multi-part message in MIME format. ------=_NextPart_000_001C_01CA598E.496B3030 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable =20 Chido, =20 =20 If you are from academia, and are going to use these images for a = publicly available database, or only for an internal project without industry collaborators, I recommend you use Cactvs (www.xemistry.com, free for academics).=20 =20 The images from this software are probably the best in the industry - = see http://baoilleach.blogspot.com/2008/05/cheminformatics-toolkit-face-off.h= tml ) for a comparison with the competition, including CDK. The PubChem = images are also generated by this software. =20 The package is not open source, but you get access to a scripting environment which allows you to write your own scripts with minimum = effort on a very high level, so you do not need to re-invent the wheel. =20 As a bonus, Cactvs cannot just generate 2D atomic coordinates and render pixel images, but write directly lots of vector formats (including EPS, = PDF, SVG,WMF,EMF,PICT,MIF,SWF, all supported on any platform), so you do not = need to run your primary output through another converter software (and converting pixel images to EPS/PDF is always a bad idea anyways).=20 =20 If your application is a commercial project, you will need to purchase a license, but as a benefit, you get access to a very capable turnkey = batch depiction application and do not need to write a script yourself. =20 In case you prefer dynamic image generation on the fly, for example = with changing user-controlled depiction parameters, there is also a Web = CGI/FCGI depiction server application which can be fed with SMILES strings, = Molfiles and lots of other data formats. =20 =20 W. D. Ihlenfeldt Xemistry GmbH wdi##xemistry.com Phone: +49 6174 201455 / Fax +49 6174 209665 --- xemistry gmbh =96 Gesch=E4ftsf=FChrer/Managing Director: Dr. W. D. = Ihlenfeldt Address: Hainholzweg 11, D-61462 K=F6nigstein, Germany HR K=F6nigstein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719=20 =20 > From: owner-chemistry+wdi=3D=3Dxemistry.com##ccl.net [mailto:owner-chemistry+wdi=3D=3Dxemistry.com##ccl.net] On Behalf Of = Chido Mpamhanga chido.mpamhanga_+_gmail.com Sent: Friday, October 30, 2009 4:54 PM To: Ihlenfeldt, Wolf D Subject: CCL: SMILES to 2D mol/sdf files open source =20 Hi all=20 Does any one have an idea how best to generate 2D coodinates from = smiles, using open source programs... I have been generating them using CDK via Knime=20 this works but I need them for images on my database. Ana when I = generate postscript files from these the resulting images are not optimal.=20 Is there a nice way to optimise these or generate optimised ones? Thanks in advance... C ------=_NextPart_000_001C_01CA598E.496B3030 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Chido,

If you are from academia, and are going to use these = images for a publicly available database, or only for an internal project without = industry collaborators, I recommend you use Cactvs (www.xemistry.com, free for academics).

The images from this software are probably the best in = the industry - see http://baoilleach.blogspot.com/2008/05/cheminformatics-toolk= it-face-off.html) for a comparison with the competition, including CDK. The PubChem images = are also generated by this software.

The package is not open source, but you get access to a scripting environment which allows you to write your own scripts with = minimum effort on a very high level, so you do not need to re-invent the = wheel.

As a bonus, Cactvs cannot just generate 2D atomic = coordinates and render pixel images, but write directly lots of vector formats = (including EPS, PDF, SVG,WMF,EMF,PICT,MIF,SWF, all supported on any platform), so = you do not need to run your primary output =A0through another converter = software (and converting pixel images to EPS/PDF is always a bad idea anyways). =

If your application is a commercial project, you will = need to purchase a license, but as a benefit, you get access to a very capable = turnkey batch depiction application and do not need to write a script = yourself.

In case you prefer dynamic image =A0generation on the = fly, for example with changing user-controlled depiction parameters, there is also a Web CGI/FCGI depiction server application which can be fed with SMILES = strings, Molfiles and lots of other data formats.

W. D. Ihlenfeldt
Xemistry GmbH
wdi##xemistry.com

Phone: +49 6174 201455 / Fax +49 6174 209665
---
xemistry gmbh – Gesch=E4ftsf=FChrer/Managing Director: Dr. W. D. = Ihlenfeldt
Address: Hainholzweg 11, D-61462 K=F6nigstein, Germany
HR K=F6nigstein B7522 : Ust/VAT ID DE215316329 : DUNS = 34-400-1719

From:= owner-chemistry+wdi=3D=3Dxemistry.com##ccl.net [mailto:owner-chemistry+wdi=3D=3Dxemistry.com##ccl.net] On Behalf Of = Chido Mpamhanga chido.mpamhanga_+_gmail.com
Sent: Friday, October 30, 2009 4:54 PM
To: Ihlenfeldt, Wolf D
Subject: CCL: SMILES to 2D mol/sdf files open = source

Hi all

Does any one have an idea how best to generate 2D coodinates from = smiles, using open source programs... I have been generating them using CDK via Knime =
this works but I need them for images on my database. Ana when I = generate postscript files from these the resulting images are not optimal.
Is there a nice way to optimise these or generate optimised ones?

Thanks in advance...

C

------=_NextPart_000_001C_01CA598E.496B3030-- From owner-chemistry@ccl.net Fri Oct 30 16:37:00 2009 From: "Agrafiotis, Dimitris K. PRDUS DAGRAFIO^its.jnj.com" To: CCL Subject: CCL: Chemical structures in R Message-Id: <-40571-091030122205-6636-nc+F6JSxqm54tP2/2VMurg|server.ccl.net> X-Original-From: "Agrafiotis, Dimitris K. [PRDUS]" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01CA5978.8DE824CD" Date: Fri, 30 Oct 2009 11:49:23 -0400 MIME-Version: 1.0 Sent to CCL by: "Agrafiotis, Dimitris K. [PRDUS]" [DAGRAFIO*its.jnj.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01CA5978.8DE824CD Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi Sebastian, =20 I don't have a solution to your specific R problem, but if you want to see some nice examples of this general functionality, you can look at our recent SAR map papers: =20 dx.doi.org/10.1021/ci900264n =20 and =20 dx.doi.org/10.1021/jm070845m =20 Kind regards, =20 ____________________________________________________=20 Dimitris Agrafiotis, Johnson & Johnson PRD, 665 Stockton Drive, Exton, PA 19341, (610) 458-6045, dagrafio=-=its.jnj.com, http://www.dimitris-agrafiotis.com =20 > From: owner-chemistry+dagrafio=3D=3Dprdus.jnj.com=-=ccl.net [mailto:owner-chemistry+dagrafio=3D=3Dprdus.jnj.com=-=ccl.net] On Behalf = Of sebastian.rohrer:+:basf.com Sent: Friday, October 30, 2009 6:05 AM To: Agrafiotis, Dimitris K. [PRDUS] Subject: CCL: Chemical structures in R =20 Hi all,=20 does anybody know a way to include chemical structures into R diagrams, eg. as axis labels or plot titles?=20 Thanks=20 Sebastian ------_=_NextPart_001_01CA5978.8DE824CD Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hi Sebastian,

I don’t have a solution to your specific R problem, but if you want = to see some nice examples of this general functionality, you can look at our = recent SAR map papers:

dx.doi.org/= 10.1021/ci900264n

and

dx.doi.org/= 10.1021/jm070845m

Kind regards,

___________= _________________________________________
Dimitris Agrafiotis, Johnson & Johnson PRD, 665 Stockton Drive, Exton, PA = 19341, (610) 458-6045, dagrafio=-=it= s.jnj.com, = http://www.dimitris-agrafiotis.com= =

From:= = owner-chemistry+dagrafio=3D=3Dprdus.jnj.com=-=ccl.net [mailto:owner-chemistry+dagrafio=3D=3Dprdus.jnj.com=-=ccl.net] On = Behalf Of sebastian.rohrer:+:basf.com
Sent: Friday, October 30, 2009 6:05 AM
To: Agrafiotis, Dimitris K. [PRDUS]
Subject: CCL: Chemical structures in R

Hi = all,

does anybody know a way to include chemical structures into R diagrams, eg. as axis = labels or plot titles?

Thanks=

Sebastian

------_=_NextPart_001_01CA5978.8DE824CD-- From owner-chemistry@ccl.net Fri Oct 30 17:08:00 2009 From: "=?ISO-8859-1?Q?Horacio_P=E9rez-S=E1nchez?= horacio.sanchez/a\kit.edu" To: CCL Subject: CCL: SMILES to 2D mol/sdf files open source Message-Id: <-40572-091030134957-30759-qqHXYKBQ6c4gMdSaXqlvww]-[server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Horacio_P=E9rez-S=E1nchez?= Content-Type: multipart/alternative; boundary="------------000008020004090704020402" Date: Fri, 30 Oct 2009 18:17:46 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Horacio_P=E9rez-S=E1nchez?= [horacio.sanchez[A]kit.edu] This is a multi-part message in MIME format. --------------000008020004090704020402 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit chemaxon's standardize Chido Mpamhanga chido.mpamhanga_+_gmail.com schrieb: > > Hi all > > Does any one have an idea how best to generate 2D coodinates from > smiles, using open source programs... I have been generating them > using CDK via Knime > this works but I need them for images on my database. Ana when I > generate postscript files from these the resulting images are not > optimal. > Is there a nice way to optimise these or generate optimised ones? > > Thanks in advance... > > C > -- ====================================================== Dr. Horacio P�rez-S�nchez Karlsruhe Institute of Technology Institut f�r Nanotechnologie, Building 640-Room 223 Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany Tel: + 49 724 782 6884 Fax: + 49 724 782 8282 horacio.sanchez ~~ kit.edu http://www.kit.edu http://www.int.kit.edu/english/index.php http://www.fzk.de/biostruct ====================================================== (Message transmitted on 100% recycled electrons) --------------000008020004090704020402 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit chemaxon's standardize

Chido Mpamhanga chido.mpamhanga_+_gmail.com schrieb:

Hi all

Does any one have an idea how best to generate 2D coodinates from smiles, using open source programs... I have been generating them using CDK via Knime
this works but I need them for images on my database. Ana when I generate postscript files from these the resulting images are not optimal.
Is there a nice way to optimise these or generate optimised ones?

Thanks in advance...

C

-- 
======================================================
Dr. Horacio Pérez-Sánchez

Karlsruhe Institute of Technology
Institut für Nanotechnologie, Building 640-Room 223
Hermann-von-Helmholtz-Platz 1
76344 Eggenstein-Leopoldshafen
Germany

Tel: + 49 724 782 6884
Fax: + 49 724 782 8282

horacio.sanchez ~~ kit.edu  
 
http://www.kit.edu
http://www.int.kit.edu/english/index.php      
http://www.fzk.de/biostruct

======================================================

(Message transmitted on 100% recycled electrons)

--------------000008020004090704020402-- From owner-chemistry@ccl.net Fri Oct 30 17:43:01 2009 From: "Morad El-Hendawy m80elhendawy(0)yahoo.com" To: CCL Subject: CCL: Chemical structures in R Message-Id: <-40573-091030151509-1361-l9dfurI4W3mgSAt2ug0olQ:+:server.ccl.net> X-Original-From: Morad El-Hendawy Content-Type: multipart/alternative; boundary="0-555861144-1256926496=:78433" Date: Fri, 30 Oct 2009 11:14:56 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Morad El-Hendawy [m80elhendawy]^[yahoo.com] --0-555861144-1256926496=:78433 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Sebastian, It is easy way to add chemical structure on the xy plot. Origin 7 program c= an do that; just plot your curve using it. Afterwards copy your structure f= rom Paint=A0 then past on the workspace of origin. Good luck ***************************************************************************= ***********************Morad M. El-Hendawy=A0******************************= ********************************************************************=A0If y= ou want a happy life, do four things:=A01- Contemplate and be thankful, 2- The past is gone forever, 3- Today all that you have, 4- Leave the future alone until it come.=A0********************************= ***************************************************************************= ******** --- On Fri, 10/30/09, sebastian.rohrer:+:basf.com = wrote: > From: sebastian.rohrer:+:basf.com Subject: CCL: Chemical structures in R To: "El-Hendawy, Morad Metwally " Date: Friday, October 30, 2009, 12:05 PM =0AHi all,=0Adoes anybody know a way to include chemical=0Astructures into = R diagrams, eg. as axis labels or plot titles?=0AThanks=0ASebastian=0A=0A= =0A --0-555861144-1256926496=:78433 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Dear Sebastia= n,
It is easy way to add chemical structure on the xy plot. Origin 7 program can do that; ju= st plot your curve using it. Afterwards copy your structure from Paint the= n past on the workspace of origin.
Good luck

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

Morad M. El-Hendawy

******= ***************************************************************************= *****************
If you = want a happy life, do four things:

1- Contemplate and be thankful,
2- The past is gone forever,
3= - Today all that you have,
4- Leave the future alone until it come.
******= ***************************************************************************= **********************************

--- On Fri, 10/30/09, sebastian.rohrer:+:basf.com <owner-chemistry-x-ccl.net> wrote:

From: sebastian.rohrer:+:basf.com <owner-chemistry-x-ccl.net>
Subject: CC= L: Chemical structures in R
To: "El-Hendawy, Morad Metwally " &l= t;m80elhendawy-x-yahoo.com>
Date: Friday, October 30, 2009, 12:05 PM
=0A
Hi all= ,=0A
does anybody know a way t= o include chemical=0Astructures into R diagrams, eg. as axis labels or plot= titles?=0A
Thanks=0A
Sebastian

=0A=0A --0-555861144-1256926496=:78433-- From owner-chemistry@ccl.net Fri Oct 30 18:18:00 2009 From: "John McKelvey jmmckel^^^gmail.com" To: CCL Subject: CCL:G: Be a bit cautious... Message-Id: <-40574-091030180502-14714-Eb/uImp1s5tFeD/dUP9sFA^-^server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=0016368e2b7f8e3a5804772e372b Date: Fri, 30 Oct 2009 18:04:51 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel__gmail.com] --0016368e2b7f8e3a5804772e372b Content-Type: text/plain; charset=ISO-8859-1 Folks, I have a dilemma: Significantly results depending on the compiler. All copies of source are identical and compiled for real*8 (double precision for 32 bits), and all answers are independent of optimization level. The gfortran is the latest available download version. ( I chose it because it is available across several OS's) The g77 came with RHEL. The calculation involved reading output from a G03 log file where Mulliken populations were computed from selected printed open shell MO's and printed AO overlaps. [log file numbers had 5-6 significant figuresafter decimal] Again, all calculations done in the special program were done in real*8, and results are independent of optimization level. Compiler Answer Hardware, OS 1) Linux Intel compiler (ifort) ~16 AMD64 opteron RHEL4 (~=Centos 4) 2) Linux g77 compiler ~10 " 3) Windows Digital Corp compiler ~16 Intel P4 Windows2000 4) Windows gfortran compiler ~10 " 5) Linux gfortran " ~10 Xeon Centos 5.3 (~= RHEL5.3) Thoughts? Thanks! John -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel],[gmail.com -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel],[gmail.com --0016368e2b7f8e3a5804772e372b Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Folks,

I have a dilemma: Significantly results depending on the comp= iler.

All copies of source are identical and compiled for real*8 (do= uble precision for 32 bits), and all answers are independent of optimizatio= n level.=A0 The gfortran is the latest available download version. ( I chos= e it because it is available across several OS's)=A0 The g77 came with = RHEL.=A0

The calculation involved reading output from a G03 log file where Mulli= ken populations were computed from selected printed open shell MO's and= printed AO overlaps. [log file numbers had 5-6 significant figuresafter de= cimal]=A0 Again, all calculations done in the special program were done in = real*8, and results are independent of optimization level.=A0

=A0 =A0 =A0 =A0 =A0=A0 Compiler =A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Answer=A0=A0=A0=A0=A0 Hardwar= e, OS
1) Linux Intel compiler (ifort) =A0 =A0 =A0 =A0 =A0=A0 ~16=A0=A0 A= MD64 opteron=A0 RHEL4 (~=3DCentos 4)
2) Linux g77 compiler=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0 ~10 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 "
3) Windows Digital C= orp compiler=A0=A0=A0 ~16=A0=A0=A0 Intel P4=A0 Windows2000
4) Windows gf= ortran=A0 compiler =A0=A0=A0=A0=A0=A0=A0 ~10 =A0=A0=A0 =A0 " =A0=A0=A0= =A0
5) Linux=A0=A0=A0=A0=A0 gfortran=A0=A0=A0=A0=A0=A0=A0 "=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ~10=A0=A0=A0=A0=A0 Xeon=A0=A0=A0=A0=A0= Centos 5.3 (~=3D RHEL5.3)

Thoughts?

Thanks!

John

--
John McKelvey
10819 Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel],[gmail.com

--
John McKelvey
10819 Middle= ford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel],[gmail.com
--0016368e2b7f8e3a5804772e372b-- From owner-chemistry@ccl.net Fri Oct 30 19:11:00 2009 From: "Markus Sitzmann sitzmann[*]helix.nih.gov" To: CCL Subject: CCL: SMILES to 2D mol/sdf files open source Message-Id: <-40575-091030161622-22883-DOKVGB+aveaRdBMiOQ+3lA]^[server.ccl.net> X-Original-From: Markus Sitzmann Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 30 Oct 2009 15:43:01 -0400 MIME-Version: 1.0 Sent to CCL by: Markus Sitzmann [sitzmann*_*helix.nih.gov] Sorry, I forgot to mention, it accepts also arbitrary SMILES strings as input format: http://cactus.nci.nih.gov/chemical/structure/C1CCCC1(=O)/image Markus Chido Mpamhanga chido.mpamhanga_+_gmail.com wrote: > Hi all > > Does any one have an idea how best to generate 2D coodinates from > smiles, using open source programs... I have been generating them using > CDK via Knime > this works but I need them for images on my database. Ana when I > generate postscript files from these the resulting images are not optimal. > Is there a nice way to optimise these or generate optimised ones? > > Thanks in advance... > > C > -- Markus Sitzmann, Ph.D. Laboratory of Medicinal Chemistry Center for Cancer Research National Cancer Institute National Institutes of Health 376 Boyles St Frederick, MD 21702, USA 301-846-5974 (office) 301-846-6033 (fax) sitzmann%x%helix.nih.gov http://www.linkedin.com/pub/1/7b8/342 http://www.xing.com/profile/Markus_Sitzmann From owner-chemistry@ccl.net Fri Oct 30 19:45:01 2009 From: "Markus Sitzmann sitzmann.:.helix.nih.gov" To: CCL Subject: CCL: SMILES to 2D mol/sdf files open source Message-Id: <-40576-091030160627-13598-BbgGIWqRr2KLrAsDdmnSfQ(!)server.ccl.net> X-Original-From: Markus Sitzmann Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 30 Oct 2009 15:34:31 -0400 MIME-Version: 1.0 Sent to CCL by: Markus Sitzmann [sitzmann{=}helix.nih.gov] Hi, similar to what Rajarshi suggests you might use our "NCICADD Chemical Identifier Resolver". The generation of a structure images is quite simple with this service: http://cactus.nci.nih.gov/chemical/structure/aspirin/image http://cactus.nci.nih.gov/chemical/structure/InChIKey=LFQSCWFLJHTTHZ-UHFFFAOYSA-N/image?format=png http://cactus.nci.nih.gov/chemical/structure/taxol/image?format=png&width=800&height=500 All possible options for image generation are described here: http://cactus.nci.nih.gov/blog/?p=136 You can also request many different file formats containing 2D coordinates (generated by chemoinformatic toolkit Cactvs): http://cactus.nci.nih.gov/chemical/structure/aspirin/file?format=sdf A description of all file format options is available here: http://cactus.nci.nih.gov/blog/?p=68 Markus Chido Mpamhanga chido.mpamhanga_+_gmail.com wrote: > Hi all > > Does any one have an idea how best to generate 2D coodinates from > smiles, using open source programs... I have been generating them using > CDK via Knime > this works but I need them for images on my database. Ana when I > generate postscript files from these the resulting images are not optimal. > Is there a nice way to optimise these or generate optimised ones? > > Thanks in advance... > > C > -- Markus Sitzmann, Ph.D. Laboratory of Medicinal Chemistry Center for Cancer Research National Cancer Institute National Institutes of Health 376 Boyles St Frederick, MD 21702, USA 301-846-5974 (office) 301-846-6033 (fax) sitzmann],[helix.nih.gov http://www.linkedin.com/pub/1/7b8/342 http://www.xing.com/profile/Markus_Sitzmann