From owner-chemistry@ccl.net Tue Jul 13 00:55:01 2010 From: "Vlad vvv900##anusf.anu.edu.au" To: CCL Subject: CCL: Generating image for small molecules: Message-Id: <-42270-100713004249-20966-EJ4m2V8823Mu+aqG9j+44A\a/server.ccl.net> X-Original-From: Vlad Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1251; format=flowed Date: Tue, 13 Jul 2010 14:42:38 +1000 MIME-Version: 1.0 Sent to CCL by: Vlad [vvv900,+,anusf.anu.edu.au] Dear Sangi, > Can someone suggest me freeware for generating good image files for > small molecules. You can use Jamberoo (http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html ) You have several options. 1) Save a picture in jpg or png format 2) For publication quality save your scene as a Povray input file and then use Povray (multi platform freeware) to generate high quality ray-traced image. 3) Save your molecular scene as a VRML file. You'll be able to embed it into the pdf document to obtain interactive 3d pdf document (some 3d pdf sample files are here: http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/manual/tutorials/3d-pdf/index.html ). Regards, Vlad From owner-chemistry@ccl.net Tue Jul 13 12:32:00 2010 From: "Jamin Krinsky jamink:_:berkeley.edu" To: CCL Subject: CCL:G: Generating image for small molecules: Message-Id: <-42271-100713120808-17481-k8H7I556PnWddTvRqKS7pQ%x%server.ccl.net> X-Original-From: Jamin Krinsky Content-Type: multipart/alternative; boundary=00c09fa54767ad0f9b048b471258 Date: Tue, 13 Jul 2010 09:07:58 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink[-]berkeley.edu] --00c09fa54767ad0f9b048b471258 Content-Type: text/plain; charset=ISO-8859-1 I would recommend VMD, it's free for all operating systems and while it is made for protein work you can do almost anything graphically. It accepts many coordinate file types (and cube files from Gaussian, for generating MO pictures). It also has an interface with POVRay (install that separately) although I've never used it. Regards, Jamin 2010/7/12 Vlad vvv900##anusf.anu.edu.au > > Sent to CCL by: Vlad [vvv900,+,anusf.anu.edu.au] > Dear Sangi, > > Can someone suggest me freeware for generating good image files for >> small molecules. >> > > You can use Jamberoo ( > http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html< > http://sf.anu.edu.au/%7Evvv900/cct/appl/jmoleditor/index.html>) > > You have several options. > > 1) Save a picture in jpg or png format > > 2) For publication quality save your scene as a Povray input file and then > use Povray (multi platform freeware) to generate high quality ray-traced > image. > > 3) Save your molecular scene as a VRML file. You'll be able to embed it > into the pdf document to obtain interactive 3d pdf document (some 3d pdf > sample files are here: > http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/manual/tutorials/3d-pdf/index.html< > http://sf.anu.edu.au/%7Evvv900/cct/appl/jmoleditor/manual/tutorials/3d-pdf/index.html > >). > > Regards, > Vladhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > -- Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink]~[berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu --00c09fa54767ad0f9b048b471258 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I would recommend VMD, it's free for all operating systems and while it= is made for protein work you can do almost anything graphically. It accept= s many coordinate file types (and cube files from Gaussian, for generating = MO pictures). It also has an interface with POVRay (install that separately= ) although I've never used it.
Regards,
Jamin

2010/7/12 Vlad vvv900##= anusf.anu.edu.au = <owner-chemistry]~[ccl.net&= gt;

Sent to CCL by: Vlad [vvv900,+,anusf.anu.edu.au]
Dear Sangi,

=A0Can someone suggest me freeware for generating good image files for
=A0small molecules.

You can use Jamberoo (http://sf.anu.edu.au/~vvv900/cct/app= l/jmoleditor/index.html <http://sf.anu.edu.au/%7Evv= v900/cct/appl/jmoleditor/index.html>)

You have several options.

1) Save a picture in jpg or png format

2) For publication quality save your scene as a Povray input file and then = use Povray (multi platform freeware) to generate high quality ray-traced im= age.

3) Save your molecular scene as a VRML file. You'll be able to embed it= into the pdf document to obtain interactive 3d pdf document (some 3d pdf s= ample files are here: http://sf.an= u.edu.au/~vvv900/cct/appl/jmoleditor/manual/tutorials/3d-pdf/index.html= <http://sf.anu.edu.au/%7Evvv90= 0/cct/appl/jmoleditor/manual/tutorials/3d-pdf/index.html>).

Regards,
Vlad



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY]~[ccl.net or use:
=A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST]~[ccl.net or use
=A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message
http://www.ccl.net/chemistry/sub_unsub.sh= tml

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

Job: http://www.ccl.n= et/jobs Conferences: http://server.ccl.net/chemistry/anno= uncements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 http= ://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/





--
Jamin L Krinsky, Ph.D.<= br>Molecular Graphics and Computation Facility
175 Tan Hall, University = of California, Berkeley, CA 94720
jamink]~[berkeley.edu, 510-643-0616
http://glab.cchem.berkeley.edu

--00c09fa54767ad0f9b048b471258-- From owner-chemistry@ccl.net Tue Jul 13 14:59:01 2010 From: "Adegboyega Akinsiku aoakinsiku{=}gmail.com" To: CCL Subject: CCL: Gar2Ped, Research Assistant Message-Id: <-42272-100713143755-5387-ZrLmDcMZjY0vZYu6Ha7ppw]^[server.ccl.net> X-Original-From: Adegboyega Akinsiku Content-Type: multipart/alternative; boundary=000e0cd4854e753aeb048b492a33 Date: Tue, 13 Jul 2010 14:37:47 -0400 MIME-Version: 1.0 Sent to CCL by: Adegboyega Akinsiku [aoakinsiku,+,gmail.com] --000e0cd4854e753aeb048b492a33 Content-Type: text/plain; charset=ISO-8859-1 Good Afternoon, My name is Adegboyega Akinsiku and I am a current Junior Computer Engineering Major at Howard University. I recently downloaded the Gar2Ped program (http://www.ccl.net/cca/software/SOURCES/FORTRAN/gar2ped/index.shtml) to use for a current research project in which I am conducting. Since downloading the program I have had a hard time getting it to Compile and just wondering if their is anyone who will be able to assist me with compiling the program. Any form of information will be greatly appreciated. Thank You, Ade -- Adegboyega Akinsiku Department of Electrical and Computer Engineering Howard University 2300 Sixth Street NW | Washington DC (T) 240.421.3673 (E) aoakinsiku_-_gmail.com --000e0cd4854e753aeb048b492a33 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Good Afternoon,

My name is Adegboyega Akinsiku and I am a current Junior Computer
Engineering Major at Howard University. I recently downloaded the
Gar2Ped program
(http://www.ccl.net/cca/software/SOURCES/FORTRAN/gar= 2ped/index.shtml) to
use for a current research project in which I am conducting. =A0Since
downloading the program I have had a hard time getting it to Compile and just wondering if their is anyone who will be able to assist me with
compiling the program. Any form of information will be greatly appreciated.=

Thank You,

Ade

--
Adegboyega Akinsiku
Department of Electr= ical and Computer Engineering
Howard University
2300 Sixth Street NW = | Washington DC
(T) 240.421.3673
(E) aoakinsiku_-_gmail.com


--000e0cd4854e753aeb048b492a33-- From owner-chemistry@ccl.net Tue Jul 13 16:23:00 2010 From: "Jason Swails jason.swails{=}gmail.com" To: CCL Subject: CCL: Gar2Ped, Research Assistant Message-Id: <-42273-100713161915-25683-OEzXQysQi+6tTPYIvgvH5Q++server.ccl.net> X-Original-From: Jason Swails Content-Type: multipart/alternative; boundary=0016e68eef98e60fa6048b4a9431 Date: Tue, 13 Jul 2010 16:19:08 -0400 MIME-Version: 1.0 Sent to CCL by: Jason Swails [jason.swails]|[gmail.com] --0016e68eef98e60fa6048b4a9431 Content-Type: text/plain; charset=ISO-8859-1 Hello, What compiler are you trying to use to build it? gfortran doesn't like a lot of the f77-specific syntax that has kind of fallen by the wayside. You'll have to manually fix the source code to play nice with gfortran by getting rid of stuff that it complains about (and replacing it by the stuff that works) to use that compiler. I've compiled it successfully with both ifort and g77 without any modifications, so make sure the makefile specifies either of those 2 (and you'll obviously have to install one of those compilers). I believe pgf77 will also work... Hope this helps, Jason On Tue, Jul 13, 2010 at 2:37 PM, Adegboyega Akinsiku aoakinsiku{=}gmail.com wrote: > Good Afternoon, > > My name is Adegboyega Akinsiku and I am a current Junior Computer > Engineering Major at Howard University. I recently downloaded the > Gar2Ped program > (http://www.ccl.net/cca/software/SOURCES/FORTRAN/gar2ped/index.shtml) to > use for a current research project in which I am conducting. Since > downloading the program I have had a hard time getting it to Compile and > just wondering if their is anyone who will be able to assist me with > compiling the program. Any form of information will be greatly appreciated. > > Thank You, > > Ade > > -- > Adegboyega Akinsiku > Department of Electrical and Computer Engineering > Howard University > 2300 Sixth Street NW | Washington DC > (T) 240.421.3673 > (E) aoakinsiku .. gmail.com > > > -- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Graduate Student 352-392-4032 --0016e68eef98e60fa6048b4a9431 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello,

What compiler are you trying to use to build it?=A0 gfortran = doesn't like a lot of the f77-specific syntax that has kind of fallen b= y the wayside.=A0 You'll have to manually fix the source code to play n= ice with gfortran by getting rid of stuff that it complains about (and repl= acing it by the stuff that works) to use that compiler.=A0 I've compile= d it successfully with both ifort and g77 without any modifications, so mak= e sure the makefile specifies either of those 2 (and you'll obviously h= ave to install one of those compilers).=A0 I believe pgf77 will also work..= .

Hope this helps,
Jason

On Tue, Jul= 13, 2010 at 2:37 PM, Adegboyega Akinsiku aoakinsiku{=3D}gmail.com <owner-chemistry{}ccl.net> wrote:
Good Afternoon,
My name is Adegboyega Akinsiku and I am a current Junior Computer
Engineering Major at Howard University. I recently downloaded the
Gar2Ped program
(http://www.ccl.net/cca/software/SOURCES/FORTRAN/gar= 2ped/index.shtml) to
use for a current research project in which I am conducting. =A0Since
downloading the program I have had a hard time getting it to Compile and just wondering if their is anyone who will be able to assist me with
compiling the program. Any form of information will be greatly appreciated.=

Thank You,

Ade

--
Adegboyega Akinsiku=
Department of Electrical and Computer Engineering
Howard University<= br>2300 Sixth Street NW | Washington DC
(T) 240.421.3673
(E) aoakinsiku .. gmail.c= om





--
Jason M. Swails<= br>Quantum Theory Project,
University of Florida
Ph.D. Graduate Stude= nt
352-392-4032
--0016e68eef98e60fa6048b4a9431--