From owner-chemistry@ccl.net Wed Mar 16 04:04:00 2011 From: "vincent zoete vincent.zoete**gmail.com" To: CCL Subject: CCL: Multiple drawings for publication Message-Id: <-44144-110316035803-8568-AMnHvqgEBU7lD0WFLWn85w{}server.ccl.net> X-Original-From: vincent zoete Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 16 Mar 2011 08:57:54 +0100 MIME-Version: 1.0 Sent to CCL by: vincent zoete [vincent.zoete(-)gmail.com] Hello john, Another possibility could be to use molconvert from ChemAxon (free academic licence). It can draw molecules in 2D from different types of format. You can also get a 3D representation in stick. Outputs can be in jpeg, png, ppm, pdf, svg, msbmp, emf and pov. You can use it in command line, and so treat your 50 molecules using a single bash command. Possibly, if you are just interested in 2D drawings, openbabel could also do it in command line. Again, in case of 2D drawings only, you could have a try with 2Ddraw, > from BioSolvIT. It can draw batches of molecules, aligning them on a given scaffold to make the comparison easier. To add the numbers on a corner of a figure, you could use the "convert" tool on a linux machine. It allows adding a caption on a image, at a given position, using the -draw option: convert -pointsize 20 -fill black -draw 'text x,y "My caption here" ' image-without-caption.jpg image-with-caption.jpg where "x,y" gives the position of the text, "pointsize" gives the the fontsize and "fill" the font color. The advantages of this tool are that it is free and can be used in command line to treat batches of images using a command line. I hope this help. Have a nice day, Vincent Zoete www.click2drug.org On Tue, Mar 15, 2011 at 6:48 PM, John McKelvey jmmckel**gmail.com wrote: > > Sent to CCL by: John McKelvey [jmmckel=gmail.com] > Folks, > > I have a collection of ab 50 molecules in either cartesian or internal > coordinates for which I need stick figures.  There needs to be an > index in one corner for each molecule, i.e. 1,2 3 4,.. > > I would appreciate suggestions as how to do this. > > Many thanks, > > John > > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel~~gmail.com>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Wed Mar 16 08:18:01 2011 From: "Hans De Winter hans.dewinter!A!silicos.com" To: CCL Subject: CCL: Silicos announces the release of STRIPPER v1.0.4 Message-Id: <-44145-110316065140-24483-a30U/1Kgv52VGUT1SV7jBQ+*+server.ccl.net> X-Original-From: Hans De Winter Content-Type: multipart/alternative; boundary=Apple-Mail-14--157059912 Date: Wed, 16 Mar 2011 11:51:27 +0100 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Hans De Winter [hans.dewinter]=[silicos.com] --Apple-Mail-14--157059912 Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Content-Transfer-Encoding: 7bit Dear all, Silicos NV is pleased to announce the release of its newest open source program STRIPPER v1.0.4, built on top of the Open Babel 2.3.0 C+ + library. STRIPPER is a program to extract the core structures, also called scaffolds, from organic drug-like molecules by 'stripping' away the sidechains. The program incorporates a number of predefined scaffold- extraction algorithmes, including the scaffolds as described by: - Bemis & Murcko (J. Med. Chem. 1996, 39, 2887-2893) - Pollock, Coutsias, Wester & Oprea (J. Chem. Inf. Model. 2008, 48, 1304-1310) - Schuffenhauer, Ertl, Roggo, Wetzel & Koch (J. Chem. Inf. Model. 2007, 47, 47-58) [an interpretation of this work has been implemented in STRIPPER] STRIPPER can be downloaded from Silicos' website (www.silicos.com). The program is free software and one can redistribute and/or modify it under the terms of the GNU General Public License as published the Free Software Foundation version 2 of the License. Silicos NV is a Belgian service-based company providing services and tools in the fields of chemoinformatics, chemogenomics and database characterisation. Several other chemoinformatics tools have been brought into the open source domain by Silicos, including SIEVE, PHARAO, PIRAMID, and OBSPECTROPHORE, the latter being part of Open Babel 2.3. For more information about STRIPPER or any other tools, please contact Silicos at info : silicos.com. Kind regards, Hans De Winter CSO - Silicos NV --Apple-Mail-14--157059912 Content-Type: text/html; charset=US-ASCII Content-Transfer-Encoding: quoted-printable Dear = all,

Silicos NV is pleased to announce the release of = its newest open source program STRIPPER v1.0.4, built on top of the Open = Babel 2.3.0 C++ library.

STRIPPER is a program = to extract the core structures, also called scaffolds, from organic = drug-like molecules by 'stripping' away the sidechains. The program = incorporates a number of predefined scaffold-extraction algorithmes, = including the scaffolds as described by:

- = Bemis & Murcko (J. Med. Chem. 1996, 39, 2887-2893)
- = Pollock, Coutsias, Wester & Oprea (J. Chem. Inf. Model. 2008, 48, = 1304-1310)
- Schuffenhauer, Ertl, Roggo, Wetzel & Koch (J. = Chem. Inf. Model. 2007, 47, 47-58) [an interpretation of this work has = been implemented in STRIPPER]

STRIPPER can be = downloaded from Silicos' website (www.silicos.com). The program is = free software and one can redistribute and/or modify it under the terms of the GNU General Public License as published the Free Software Foundation version 2 of the = License.

Silicos NV is a Belgian = service-based company providing services and tools in the fields of = chemoinformatics, chemogenomics and database characterisation. Several = other chemoinformatics tools have been brought into the open source = domain by Silicos, including SIEVE, PHARAO, PIRAMID, and OBSPECTROPHORE, = the latter being part of Open Babel 2.3.

For = more information about STRIPPER or any other tools, please contact = Silicos at info : silicos.com.

Kind regards,

Hans De = Winter
CSO - Silicos = NV
= --Apple-Mail-14--157059912-- From owner-chemistry@ccl.net Wed Mar 16 08:52:00 2011 From: "Wolf Ihlenfeldt wdi|*|xemistry.com" To: CCL Subject: CCL: Multiple drawings for publication Message-Id: <-44146-110316083019-9969-NCClskVcKmBrfACOX/VCYA[-]server.ccl.net> X-Original-From: Wolf Ihlenfeldt Content-Type: multipart/alternative; boundary=000e0cd56ace9ccf80049e98b453 Date: Wed, 16 Mar 2011 13:30:09 +0100 MIME-Version: 1.0 Sent to CCL by: Wolf Ihlenfeldt [wdi[-]xemistry.com] --000e0cd56ace9ccf80049e98b453 Content-Type: text/plain; charset=UTF-8 On Wed, Mar 16, 2011 at 8:57 AM, vincent zoete vincent.zoete**gmail.com < owner-chemistry-,-ccl.net> wrote: > > Sent to CCL by: vincent zoete [vincent.zoete(-)gmail.com] > Hello john, > > > > Possibly, if you are just interested in 2D drawings, openbabel could > > also do it in command line. > > > I do not think anybody wants to use 2D layout software which cannot even plot simple cis/trans stereochemistry correctly for any serious purpose. When advising on tools, please take their maturity into account. There are *much* better 2D layouters available. But in any case, I think the question was clearly about 3D depictions. > > > > On Tue, Mar 15, 2011 at 6:48 PM, John McKelvey jmmckel**gmail.com > wrote: > > > > Sent to CCL by: John McKelvey [jmmckel=gmail.com] > > Folks, > > > > I have a collection of ab 50 molecules in either cartesian or internal > > coordinates for which I need stick figures. There needs to be an > > index in one corner for each molecule, i.e. 1,2 3 4,.. > > > > I would appreciate suggestions as how to do this. > > > > Many thanks, > > > > John > > > > -- > > John McKelvey > > 10819 Middleford Pl > > Ft Wayne, IN 46818 > > 260-489-2160 > > jmmckel~~gmail.com> > > > > > > -- Wolf-D. Ihlenfeldt, Xemistry GmbH www.xemistry.com --000e0cd56ace9ccf80049e98b453 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

On Wed, Mar 16, 2011 at 8:57 AM, vincent= zoete vincent.zoete**gmail.com <owner-chemistry-,-ccl= .net> wrote:

Sent to CCL by: vincent zoete [vincent.zoete(-)gmail.com]
Hello john,


> Possibly, if you are just interested in 2D drawings, openbabel could > also do it in command line.



I do not think anybody wants to use 2D layout sof= tware which=20 cannot even plot simple cis/trans stereochemistry correctly for any serious= purpose. When=20 advising on tools, please take their maturity into account. There are=20 *much* better 2D layouters available.

But in any case, I = think the question was clearly about 3D depictions.






On Tue, Mar 15, 2011 at 6:48 PM, John McKelvey jmmckel**gmail.com
<owner-chemistry[a]ccl.net<= /a>> wrote:
>
> Sent to CCL by: John McKelvey [jmmckel=3Dgmail.com]
> Folks,
>
> I have a collection of ab 50 molecules in either cartesian or internal=
> coordinates for which I need stick figures. =C2=A0There needs to be an=
> index in one corner for each molecule, i.e. 1,2 3 4,..
>
> I would appreciate suggestions as how to do this.
>
> Many thanks,
>
> John
>
> --
> John McKelvey
> 10819 Middleford Pl
> Ft Wayne, IN 46818
> 260-489-2160
> jmmckel~~gmail.com&= gt; =C2=A0 =C2=A0 =C2=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message<= /a>> =C2=A0 =C2=A0 =C2=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_mess= age> =C2=A0 =C2=A0 =C2=A0http://www.ccl.net/chemistry/sub_unsub.shtm= l> =C2=A0 =C2=A0 =C2=A0http://www.ccl.net/spammers.txt>
>
>




--
Wolf-D. Ihlenfeldt, Xem= istry GmbH
www.xem= istry.com

--000e0cd56ace9ccf80049e98b453-- From owner-chemistry@ccl.net Wed Mar 16 12:37:01 2011 From: "vincent zoete vincent.zoete{:}gmail.com" To: CCL Subject: CCL: Multiple drawings for publication Message-Id: <-44147-110316123559-25669-0DuEHBEuDS/k+8Zll9rz2A-*-server.ccl.net> X-Original-From: vincent zoete Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 16 Mar 2011 17:35:51 +0100 MIME-Version: 1.0 Sent to CCL by: vincent zoete [vincent.zoete---gmail.com] >> > Possibly, if you are just interested in 2D drawings, openbabel could >> > also do it in command line. >> >> > > There are *much* better 2D layouters available. > Although I like using this open source tool, it's true that you may have problems in 2D drawings using openbabel for some molecules. So, let's just mention molconvert as in my previous message, and of course the tools of http://www.xemistry.com/, for example. Obviously, this is by far not a comprehensive list, and I hope others will forgive me not to mention them. To go back to the original message. If you are just interested in images of molecules in 3D, a combination of molconvert (or others) and of the "convert" command of the Imagemagick library (http://www.imagemagick.org/script/convert.php) both used in command lines could make it for large batches of molecules. Cordially, Vincent From owner-chemistry@ccl.net Wed Mar 16 14:23:00 2011 From: "Guenter Grethe ggrethe##att.net" To: CCL Subject: CCL: Reminder - CINF-FIZ Scholarships Message-Id: <-44148-110316134543-32237-zu4sT5gMHf7xNDLVJDjdwA%server.ccl.net> X-Original-From: "Guenter Grethe" Date: Wed, 16 Mar 2011 13:45:41 -0400 Sent to CCL by: "Guenter Grethe" [ggrethe_+_att.net] 2011 CINF Scholarship for Scientific Excellence Sponsored by FIZ Chemie Berlin The scholarship program of the Division of Chemical Information (CINF) of the American Chemical Society (ACS) funded by FIZ Chemie Berlin is designed to reward graduate and postdoctoral students in chemical information and related sciences for scientific excellence and to foster their involvement in CINF. Up to three scholarships valued at $1,000 each will be presented at the 242th ACS National Meeting in Denver, CO, August 28 September 1, 2011. Applicants must be enrolled at a certified college or university, and they will present a poster during the Welcoming Reception of the division on Sunday evening at the National Meeting. Additionally, they will have the option to also show their poster at the Sci-Mix session on Monday night. Abstracts for the poster must be submitted electronically through PACS, the abstract submission system of ACS. To apply, please inform the Chair of the selection committee, Guenter Grethe at ggrethe**att.net, that you are applying for a scholarship. Submit your abstract to http://abstracts.acs.org using your ACS ID. If you do not have an ACS ID, follow the registration instructions and submit your abstract for CINF Scholarship for Scientific Excellence. The deadline for submitting an abstract to PACS is April 1, 2011. Additionally, please send a 2,000-word abstract describing the work to be presented in electronic form to the Chair of the selection committee by June30, 2010. Any questions related to applying for one of the scholarships should be directed to the same e-mail address. Winners will be chosen based on contents, presentation and relevance of the poster and they will be announced during the reception. The contents shall reflect upon the students work and describe research in the field of cheminformatics and related sciences. Winning posters will be marked Winner of FIZ Chemie-CINF Scholarship for Scientific Excellence at the poster session. Guenter Grethe