From owner-chemistry@ccl.net Tue Mar 19 00:14:00 2013 From: "Vlad vvv900^-^anusf.anu.edu.au" To: CCL Subject: CCL:G: Regarding software for viewing gaussian output Message-Id: <-48432-130318220641-31060-Y8WHN/81gFPd8rEtlt5FkA|-|server.ccl.net> X-Original-From: Vlad Content-type: multipart/alternative; boundary="Boundary_(ID_abN3kSsWs/wwfwb8VDPScA)" Date: Tue, 19 Mar 2013 13:06:22 +1100 MIME-version: 1.0 Sent to CCL by: Vlad [vvv900-*-anusf.anu.edu.au] This is a multi-part message in MIME format. --Boundary_(ID_abN3kSsWs/wwfwb8VDPScA) Content-type: text/plain; CHARSET=US-ASCII; format=flowed Content-transfer-encoding: 7BIT Hi Avinash, > i need a software which i can use to open the gaussian output files > and draw different kind of structures of the molecules such as ball > and stick model and wireframe models and also what would be the best > method to get bond length and angles indicated or written on the > molecules structure. Try Jamberoo - http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html Regards, Vlad --Boundary_(ID_abN3kSsWs/wwfwb8VDPScA) Content-type: text/html; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Hi Avinash,

> i need a software which i can use to open the gaussian output files
> and draw different kind of structures of the molecules such as ball
> and stick model and wireframe models and also what would be the best
> method to get bond length and angles indicated or written on the
> molecules structure.

Try Jamberoo - http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html

Regards,
Vlad

--Boundary_(ID_abN3kSsWs/wwfwb8VDPScA)-- From owner-chemistry@ccl.net Tue Mar 19 11:18:01 2013 From: "Giuseppe Milano gmilano .. unisa.it" To: CCL Subject: CCL: NanomeetsBio+*+Nanomates May 2nd University of Salerno (ITALY) Message-Id: <-48433-130319103659-22972-m8lXXb/GjNTeJzAkirBL3w+*+server.ccl.net> X-Original-From: "Giuseppe Milano" Date: Tue, 19 Mar 2013 10:36:57 -0400 Sent to CCL by: "Giuseppe Milano" [gmilano * unisa.it] NanomeetsBio.+*+.Nanomates May 2nd University of Salerno (ITALY) This edition will be focused on the development and applications of state of the art and beyond molecular and atomic level computational techniques. The format will be very informal and the style of the talks will be in the middle between a school for PhD students/post-docs and a scientific workshop. The basic notions, together with interesting applications, of ab-initio, atomistic and coarse-graining techniques will be given by very distinguished speakers. List of Plenary Speakers: Wilfred F. van Gunsteren, ETH Zurich Title "Comparison of calculated and measured relative free energies of folding of protein mutants: a structural and thermodynamic analysis" Florian Mller-Plathe, TU Darmstadt Title "Scale-hopping in soft-matter simulation: Great successes and even greater challenges" Vincenzo Barone, Scuola Normale Superiore Pisa Title "TBA" There is no fee but registration is compulsory to help our organization. Abstracts for the afternoon poster session are very welcome especially from young PhD students, post-docs and researchers involved experimental, theoretical and computational works. Details and Registration Instructions at http://2nd_nanomeetsbio_at_nanomates.eventzilla.net Best Regards Giuseppe Milano From owner-chemistry@ccl.net Tue Mar 19 11:53:01 2013 From: "Andras Borosy andras.borosy|*|givaudan.com" To: CCL Subject: CCL: Visualisation of molecular networks Message-Id: <-48434-130319112830-32042-NNcuKTMm5Hn6Q/U/s6rWsg,,server.ccl.net> X-Original-From: Andras Borosy Content-Type: multipart/alternative; boundary="=_alternative 0054F242C1257B33_=" Date: Tue, 19 Mar 2013 16:28:21 +0100 MIME-Version: 1.0 Sent to CCL by: Andras Borosy [andras.borosy{}givaudan.com] This is a multipart message in MIME format. --=_alternative 0054F242C1257B33_= Content-Type: text/plain; charset="US-ASCII" Dear Mr. Zalevsky, Thank you. It seems that depicted molecular structures can not be displayed in the nodes. Best regards, Andras Borosy > From: "Arthur Zalevsky aozalevsky::gmail.com" To: "Borosy, Andras " , Date: 03/18/2013 11:45 PM Subject: CCL: Visualisation of molecular networks Sent by: owner-chemistry+andras.borosy==givaudan.com+*+ccl.net Sent to CCL by: Arthur Zalevsky [aozalevsky+*+gmail.com] Try to look at yEd: http://www.yworks.com/en/products_yed_about.html Cytoscape has GraphML export plugin and yEd works well with it. There are a couple of examples in gallery, already, which shows it's capabilities in the same task. http://www.yworks.com/en/products_yed_gallery.html yEd also has optional commercial support http://www.yworks.com/en/services.html Regards, Arthur Zalevsky 2013/3/18 Andras Borosy andras.borosy()givaudan.com : > Dear Colleagues, > > I would need a commercial application to display molecular networks (like > http://www.cytoscape.org/ but with a decent technical support). > > Might you suggest me some? > > Many thanks, > > Andras Borosyhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--=_alternative 0054F242C1257B33_= Content-Type: text/html; charset="US-ASCII" Dear Mr. Zalevsky,

Thank you. It seems that depicted molecular structures can not be displayed in the nodes.

Best regards,

Andras Borosy

From: "Arthur Zalevsky aozalevsky::gmail.com" <owner-chemistry+*+ccl.net>
To: "Borosy, Andras " <andras.borosy+*+givaudan.com>,
Date: 03/18/2013 11:45 PM
Subject: CCL: Visualisation of molecular networks
Sent by: owner-chemistry+andras.borosy==givaudan.com+*+ccl.net

Sent to CCL by: Arthur Zalevsky [aozalevsky+*+gmail.com] Try to look at yEd:http://www.yworks.com/en/products_yed_about.htmlCytoscape has GraphML export plugin and yEd works well with it. There are a couple of examples in gallery, already, which shows it's capabilities in the same task.http://www.yworks.com/en/products_yed_gallery.htmlyEd also has optional commercial supporthttp://www.yworks.com/en/services.htmlRegards, Arthur Zalevsky 2013/3/18 Andras Borosy andras.borosy()givaudan.com <owner-chemistry^-^ccl.net>: > Dear Colleagues, > > I would need a commercial application to display molecular networks (like >http://www.cytoscape.org/but with a decent technical support). > > Might you suggest me some? > > Many thanks, > > Andras Borosy 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.shtmlBefore posting, check wait time at:http://www.ccl.netJob:http://www.ccl.net/jobsConferences:http://server.ccl.net/chemistry/announcements/conferences/Search Messages:http://www.ccl.net/chemistry/searchccl/index.shtml http://www.ccl.net/spammers.txtRTFI:http://www.ccl.net/chemistry/aboutccl/instructions/
--=_alternative 0054F242C1257B33_=-- From owner-chemistry@ccl.net Tue Mar 19 12:28:00 2013 From: "Andras Borosy andras.borosy_+_givaudan.com" To: CCL Subject: CCL: Visualisation of molecular networks Message-Id: <-48435-130319113421-2151-yMqKILkVlE6HL8yvVutMMA^_^server.ccl.net> X-Original-From: Andras Borosy Content-Type: multipart/alternative; boundary="=_alternative 00557BC2C1257B33_=" Date: Tue, 19 Mar 2013 16:34:12 +0100 MIME-Version: 1.0 Sent to CCL by: Andras Borosy [andras.borosy a givaudan.com] This is a multipart message in MIME format. --=_alternative 00557BC2C1257B33_= Content-Type: text/plain; charset="US-ASCII" Dear Marc, It is really nice! How can I display depicted molecular structures in the nodes? Many thanks, Andras Borosy > From: "Marc Baaden baaden%smplinux.de" To: "Borosy, Andras " , Date: 03/18/2013 10:18 PM Subject: CCL: Visualisation of molecular networks Sent by: owner-chemistry+andras.borosy==givaudan.com]=[ccl.net Sent to CCL by: Marc Baaden [baaden]^[smplinux.de] Dear Andras, I am not sure I understand in what sense you mean commercial application, but if it's of any interest, our recently released UnityMol molecular viewer can read and visualize Cytoscape format in original ways (among other things). Technical support might be a bit more limited :) Please do see for yourself an example image of a network in toon rendering: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057990.g006/largerimage The software (Mac, Win, Linux, Source) can be obtained from http://unitymol.sourceforge.net and is described in more detail here: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057990 (Title: Game On, Science - How Video Game Technology May Help Biologists Tackle Visualization Challenges) Best, Marc owner-chemistry:+:ccl.net said: >>Dear Colleagues, >>I would need a commercial application to display molecular networks >>(like http://www.cytoscape.org/ but with a decent technical support). >>Might you suggest me some? >>Many thanks, >>Andras Borosy -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baaden:+:smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--=_alternative 00557BC2C1257B33_= Content-Type: text/html; charset="US-ASCII" Dear Marc,

It is really nice!

How can I display depicted molecular structures in the nodes?

Many thanks,

Andras Borosy

From: "Marc Baaden baaden%smplinux.de" <owner-chemistry]=[ccl.net>
To: "Borosy, Andras " <andras.borosy]=[givaudan.com>,
Date: 03/18/2013 10:18 PM
Subject: CCL: Visualisation of molecular networks
Sent by: owner-chemistry+andras.borosy==givaudan.com]=[ccl.net

Sent to CCL by: Marc Baaden [baaden]^[smplinux.de] Dear Andras, I am not sure I understand in what sense you mean commercial application, but if it's of any interest, our recently released UnityMol molecular viewer can read and visualize Cytoscape format in original ways (among other things). Technical support might be a bit more limited :) Please do see for yourself an example image of a network in toon rendering:http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057990.g006/largerimageThe software (Mac, Win, Linux, Source) can be obtained fromhttp://unitymol.sourceforge.netand is described in more detail here:http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057990(Title: Game On, Science - How Video Game Technology May Help Biologists Tackle Visualization Challenges) Best, Marc owner-chemistry:+:ccl.net said: >>Dear Colleagues, >>I would need a commercial application to display molecular networks >>(like http://www.cytoscape.org/but with a decent technical support). >>Might you suggest me some? >>Many thanks, >>Andras Borosy -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Parismailto:baaden:+:smplinux.de - http://www.baaden.ibpc.frFAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 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.shtmlBefore posting, check wait time at:http://www.ccl.netJob:http://www.ccl.net/jobsConferences:http://server.ccl.net/chemistry/announcements/conferences/Search Messages:http://www.ccl.net/chemistry/searchccl/index.shtml http://www.ccl.net/spammers.txtRTFI:http://www.ccl.net/chemistry/aboutccl/instructions/
--=_alternative 00557BC2C1257B33_=-- From owner-chemistry@ccl.net Tue Mar 19 14:06:00 2013 From: "baaden(!)smplinux.de" To: CCL Subject: CCL: Visualisation of molecular networks Message-Id: <-48436-130319135220-17561-RZCF51FZ6O/rBzJkAXRXQQ[#]server.ccl.net> X-Original-From: baaden,+,smplinux.de Content-Type: text/plain; charset=us-ascii Date: Tue, 19 Mar 2013 18:54:59 +0100 Mime-Version: 1.0 Sent to CCL by: baaden]|[smplinux.de Dear Andras, If I understand you correctly, what you would like is that each node is a molecular structure, and not just a sphere? Currently, this is not implemented. In the version that is available, the cytoscape network is read, for each node a sphere is drawn, and the connections are made using hyperballs. One can click on the nodes to see the information > from the cytoscape xml file. You can move the nodes in the z-direction to create more contrast, or change the graphical aspects. That's about all that is implemented. Two demo files are provided (xgmml extension; for example galFiltered.sif.xgmml). If you open one of those, the network will automatically be displayed. You can rearrange it manually to some limited extent, if you activate interactive mode and choose Drag/Spring values appropriately. The node information can be displayed by activating the "Atom info" option. The graphical aspects can be altered by using the textures, colors, radii, shrink and scale options. I am sorry that there is currently not more functionality available for molecular networks. Marc owner-chemistry|,|ccl.net said: >>Dear Marc, >>It is really nice! >>How can I display depicted molecular structures in the nodes? >>Many thanks, >>Andras Borosy >>The software (Mac, Win, Linux, Source) can be obtained from >>http://unitymol.sourceforge.net -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baaden|,|smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217