From owner-chemistry@ccl.net Mon Feb 8 09:08:01 2010 From: "rinu iyer rinuiyer|a|gmail.com" To: CCL Subject: CCL:G: G03 Geometry Optimization Fails Message-Id: <-41208-100206130453-17223-eJX8e3k/uaMacvxBZLCB/g_-_server.ccl.net> X-Original-From: rinu iyer Content-Type: multipart/alternative; boundary=00504502e9a9645cab047ef1a964 Date: Sat, 6 Feb 2010 22:41:40 +0530 MIME-Version: 1.0 Sent to CCL by: rinu iyer [rinuiyer_._gmail.com] --00504502e9a9645cab047ef1a964 Content-Type: text/plain; charset=ISO-8859-1 this is due to syntax error.Maximum number of optimization steps is twice the number of variables to be optimized. Try increasing the value by specifying OPT=(*MaxCycle*=*N*) in .inp file, where *N *is the number of optimization steps (see *OPT *keyword). Alternatively, try to start optimization from different geometry.. -- K.R.Ramya Research fellow IIndian Institute of Science Education & Research(IISER) Central Tower, Sai Trinity Building, Sutarwadi Road, Pashan, Pune 411021, INDIA --00504502e9a9645cab047ef1a964 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

this is due to syntax error.Maximum number of optimization steps is= twice the number of variables to be optimized. Try increasing the value by specifying OPT=3D(MaxC= ycle=3DN) in .inp file, where N is the number of= optimization steps=A0(see OPT keyword). = Alternatively, try to start optimization from different geometry..

--
K.R.Ramya
Research fellow
IIndian Institute of Science Edu= cation & Research(IISER)
Central Tower, Sai Trinity Building, Sutarw= adi Road, Pashan,
Pune 411021, INDIA
--00504502e9a9645cab047ef1a964-- From owner-chemistry@ccl.net Mon Feb 8 09:43:01 2010 From: "Alberto Pasamontes alberto.pasamontes===shirotafoods.com" To: CCL Subject: CCL: software to create a pharmacophore Message-Id: <-41209-100208064010-12845-EtOfFtEPOf9Aegy1B/lwfw ~ server.ccl.net> X-Original-From: "Alberto Pasamontes" Date: Mon, 8 Feb 2010 06:40:06 -0500 Sent to CCL by: "Alberto Pasamontes" [alberto.pasamontes(-)shirotafoods.com] Dear Colleagues, I'm looking for a software that allows me to create a pharmacophore from a PDB file (protein-ligand).Could you help me? Alberto From owner-chemistry@ccl.net Mon Feb 8 10:18:00 2010 From: "krishna chary salikolimi kittuiit009|gmail.com" To: CCL Subject: CCL: request for any suggessions about the free base porphyrin spectra Message-Id: <-41210-100208002304-10314-BR6X87U/eLpg9dU572fApA=server.ccl.net> X-Original-From: "krishna chary salikolimi" Date: Mon, 8 Feb 2010 00:23:00 -0500 Sent to CCL by: "krishna chary salikolimi" [kittuiit009!^!gmail.com] Dear all CCLers, I tried to get the electronic spectra of free base porphyrin at 380-400nm in ADF SCM (Amsterdam Density Functional) software software, i am getting only around 330-355nm.i didn't currect keywords to get right spectra..i tried different keywords. Right now iam working on ALTERNATE PORPHYRINS which may explore the properties of porphyrins, I need currect keywords to get right spectra of "FREE BASE PORPHYRINS". I c'dnot get much information from journals about the keywords used in ADF jobs. Could anyone give me some hints to solve the problem? Thank you in advance. From owner-chemistry@ccl.net Mon Feb 8 11:42:00 2010 From: "pascal boulet pascal.boulet(0)univ-provence.fr" To: CCL Subject: CCL: request for any suggessions about the free base porphyrin spectra Message-Id: <-41211-100208113518-26247-BiL21x1fDol12XcdN5tYxQ++server.ccl.net> X-Original-From: pascal boulet Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 08 Feb 2010 17:34:57 +0100 MIME-Version: 1.0 Sent to CCL by: pascal boulet [pascal.boulet!A!univ-provence.fr] -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Krishna, Well, not too bad, after all, especially if you used "usual" XC-potentials! 380-400nm -> 3.10-3.26 eV 330-355nm -> 3.49-3.87 eV The difference is about 0.5-0.6 eV, which is usually expected. Have you tried some special XC potentials baring correct asymptotic behaviour (like LB94, GRACLB, SAOP)? It could help, but there is no garantee. Hope this help, Pascal krishna chary salikolimi kittuiit009|gmail.com a écrit : > Sent to CCL by: "krishna chary salikolimi" > [kittuiit009!^!gmail.com] Dear all CCLers, I tried to get the > electronic spectra of free base porphyrin at 380-400nm in ADF SCM > (Amsterdam Density Functional) software software, i am getting only > around 330-355nm.i didn't currect keywords to get right spectra..i > tried different keywords. > > Right now iam working on ALTERNATE PORPHYRINS which may explore the > properties of porphyrins, I need currect keywords to get right > spectra of "FREE BASE PORPHYRINS". I c'dnot get much information > from journals about the keywords used in ADF jobs. > > Could anyone give me some hints to solve the problem? Thank you in > advance. > > > > -= This is automatically added to each message by the mailing > script =- 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 look up the X-Original-From: line in the > mail header.http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > - -- Dr. pascal Boulet, computational chemist Laboratoire Chimie Provence, UMR 6264 University of Aix-Marseille I Avenue Escadrille Normandie-Niemen 13397 Marseille Cedex 20 France ********** Tel. (+33) (0)491.63.71.17 Fax. (+33) (0)491.63.71.11 ********** http://www.lc-provence.fr http://allos.up.univ-mrs.fr/boulet %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iEYEARECAAYFAktwPS8ACgkQNLjdBN1V75mj/ACeLdg/utR/X0wL5T0q0cWZPDoH O48AoIx/1jswQnYkFroKWsup1a9OnbVQ =gOJh -----END PGP SIGNATURE----- From owner-chemistry@ccl.net Mon Feb 8 12:17:01 2010 From: "=?ISO-8859-15?Q?Horacio_P=E9rez-S=E1nchez?= horacio.sanchez:-:kit.edu" To: CCL Subject: CCL: software to create a pharmacophore Message-Id: <-41212-100208114904-31758-QO7nW/TN2E2pZaIukKysoQ##server.ccl.net> X-Original-From: =?ISO-8859-15?Q?Horacio_P=E9rez-S=E1nchez?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Mon, 08 Feb 2010 17:18:08 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-15?Q?Horacio_P=E9rez-S=E1nchez?= [horacio.sanchez[A]kit.edu] There are several options like: - Molecular Operating Environment - Discovery Studio Apart from that I would recommend you Ligand Scout. It can even create pharmacophore models for MOE and DS, and it can perform also Virtual Screening. Its rather ease to use and user friendly. Good Luck Horacio Am 08/02/10 12:40, schrieb Alberto Pasamontes alberto.pasamontes===shirotafoods.com: > Sent to CCL by: "Alberto Pasamontes" [alberto.pasamontes(-)shirotafoods.com] > Dear Colleagues, > I'm looking for a software that allows me to create a pharmacophore from a PDB file (protein-ligand).Could you help me? > > Alberto> > > > -- ====================================================== 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) From owner-chemistry@ccl.net Mon Feb 8 12:52:01 2010 From: "Rajarshi Guha rajarshi.guha]*[gmail.com" To: CCL Subject: CCL: Converting Sybyl SLN queries to SMARTS Message-Id: <-41213-100208114921-32067-GFR7IfsmgSo561jOhS5xdg a server.ccl.net> X-Original-From: Rajarshi Guha Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 8 Feb 2010 10:46:05 -0500 MIME-Version: 1.0 Sent to CCL by: Rajarshi Guha [rajarshi.guha .. gmail.com] Hi, does anybody know of a tool (or has code) that can convert a Sybyl SLN query to a SMARTS pattern? Thanks, -- Rajarshi Guha NIH Chemical Genomics Center From owner-chemistry@ccl.net Mon Feb 8 13:27:00 2010 From: "Sangeetha Subramaniam srdshigella.:.gmail.com" To: CCL Subject: CCL: software to create a pharmacophore Message-Id: <-41214-100208113947-27290-Aiu6IRbELAkuJ+RLU1Gbfw a server.ccl.net> X-Original-From: Sangeetha Subramaniam Content-Type: multipart/alternative; boundary=0050450169f38eb8b5047f18b8e1 Date: Mon, 8 Feb 2010 21:17:19 +0530 MIME-Version: 1.0 Sent to CCL by: Sangeetha Subramaniam [srdshigella . gmail.com] --0050450169f38eb8b5047f18b8e1 Content-Type: text/plain; charset=ISO-8859-1 Hi Alberto, Have a look at Ligandscout. http://www.inteligand.com/ligandscout/ Best wishes Sangeetha. On Mon, Feb 8, 2010 at 5:10 PM, Alberto Pasamontes alberto.pasamontes=== shirotafoods.com wrote: > > Sent to CCL by: "Alberto Pasamontes" [alberto.pasamontes(-) > shirotafoods.com] > Dear Colleagues, > I'm looking for a software that allows me to create a pharmacophore from a > PDB file (protein-ligand).Could you help me? > > Alberto> > > --0050450169f38eb8b5047f18b8e1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Alberto,

Have a look at Ligandscout.

http://www.inteligand.com/ligandscout/
Best wishes
Sangeetha.

On Mon, F= eb 8, 2010 at 5:10 PM, Alberto Pasamontes alberto.pasamontes=3D=3D=3Dshirotafoods.com <owner-chemistry^ccl.net> wrote:

Sent to CCL by: "Alberto =A0Pasamontes" [alberto.pasamontes(-)shirotafoods.com] Dear Colleagues,
I'm looking for a software that allows me to create a pharmacophore fro= m a PDB file (protein-ligand).Could you help me?

Alberto



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY^ccl.n= et or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEM= ISTRY-REQUEST^ccl.net or use
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml

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

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0h= ttp://www.ccl.net/spammers.txt

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






--0050450169f38eb8b5047f18b8e1-- From owner-chemistry@ccl.net Mon Feb 8 14:02:01 2010 From: "Need47 need47]-[gmail.com" To: CCL Subject: CCL: software to create a pharmacophore Message-Id: <-41215-100208122705-22740-cf67UhEWWKfZFmkMc4eHiw-*-server.ccl.net> X-Original-From: Need47 Content-Type: multipart/alternative; boundary=001636e1e82ee1b0fb047f1950f7 Date: Mon, 8 Feb 2010 11:30:14 -0500 MIME-Version: 1.0 Sent to CCL by: Need47 [need47 * gmail.com] --001636e1e82ee1b0fb047f1950f7 Content-Type: text/plain; charset=ISO-8859-1 Hi, Alberto You may try LigandScout Thanks, Jay On Mon, Feb 8, 2010 at 6:40 AM, Alberto Pasamontes alberto.pasamontes=== shirotafoods.com wrote: > > Sent to CCL by: "Alberto Pasamontes" [alberto.pasamontes(-) > shirotafoods.com] > Dear Colleagues, > I'm looking for a software that allows me to create a pharmacophore from a > PDB file (protein-ligand).Could you help me? > > Alberto> > > > --001636e1e82ee1b0fb047f1950f7 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi, Alberto

You may try LigandScout

=
Thanks,

Jay

On Mon, Feb 8, 2010 at 6:40 AM, Alberto Pasamontes alberto.pasamontes=3D= =3D=3Dshirotafoods.com <owner-chemistry(0)ccl.ne= t> wrote:

Sent to CCL by: "Alberto =A0Pasamontes" [alberto.pasamontes(-)shirotafoods.com] Dear Colleagues,
I'm looking for a software that allows me to create a pharmacophore fro= m a PDB file (protein-ligand).Could you help me?

Alberto



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY(0)ccl.n= et or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEM= ISTRY-REQUEST(0)ccl.net or use
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml

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

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0h= ttp://www.ccl.net/spammers.txt

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




--001636e1e82ee1b0fb047f1950f7-- From owner-chemistry@ccl.net Mon Feb 8 14:37:01 2010 From: "Govender, Penny pennyg~!~uj.ac.za" To: CCL Subject: CCL: software to create a pharmacophore Message-Id: <-41216-100208115909-4228-qb1yJAWj7Rhgb94hGf3L3w _ server.ccl.net> X-Original-From: "Govender, Penny" Content-Language: en-US Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Mon, 8 Feb 2010 18:20:58 +0200 MIME-Version: 1.0 Sent to CCL by: "Govender, Penny" [pennyg|,|uj.ac.za] Hi There Did you check Accelrys-Discovery Studio? Ms Penny Govender (AMRSC) Lecturer: Organic Chemistry University of Johannesburg Department of Chemical Technology Doornfontein Campus (w) 011-5596555 (fax) 011-5596425 (c) 0845002689 pennyg_-_uj.ac.za Louis Pasteur "There are no such things as applied sciences, only applicati= ons of science" -----Original Message----- > From: owner-chemistry+pennyg=3D=3Duj.ac.za_-_ccl.net [mailto:owner-chemistry+= pennyg=3D=3Duj.ac.za_-_ccl.net] On Behalf Of Alberto Pasamontes alberto.pasam= ontes=3D=3D=3Dshirotafoods.com Sent: 08 February 2010 01:40 PM To: Govender, Penny Subject: CCL: software to create a pharmacophore Sent to CCL by: "Alberto Pasamontes" [alberto.pasamontes(-)shirotafoods.co= m] Dear Colleagues, I'm looking for a software that allows me to create a pharmacophore from a = PDB file (protein-ligand).Could you help me? Alberto -=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 and all contents are subject to the following disclaimer: http://www.uj.ac.za/UJ_email_legal_disclaimer.htm From owner-chemistry@ccl.net Mon Feb 8 18:16:00 2010 From: "Shikha Varma SVarma{}accelrys.com" To: CCL Subject: CCL: software to create a pharmacophore Message-Id: <-41217-100208181153-6087-cAKo4cL0exNZdJx2Vyy2nQ!^!server.ccl.net> X-Original-From: Shikha Varma Content-Language: en-US Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Mon, 8 Feb 2010 14:41:22 -0800 MIME-Version: 1.0 Sent to CCL by: Shikha Varma [SVarma::accelrys.com] Hi Alberto, In fact, the FREE visualizer of Discovery Studio, the DSVisualizer, allows = you to manually perceive and generate a pharmacophore model! A hidden gem = of the software. For more details on DSVisualizer capabilities, you can loo= k at this page: http://accelrys.com/products/datasheets/ds-visualizer-0809.= pdf And you can also download the free Visualizer here:=20 http://accelrys.com/products/discovery-studio/visualization/index.html All the subsequent work with pharmacophore can be done in Discovery Studio. Regards, Shikha -----Original Message----- > From: owner-chemistry+shikha=3D=3Daccelrys.com]|[ccl.net [mailto:owner-chemis= try+shikha=3D=3Daccelrys.com]|[ccl.net] On Behalf Of Govender, Penny pennyg~!= ~uj.ac.za Sent: Monday, February 08, 2010 8:21 AM To: Shikha Varma Subject: CCL: software to create a pharmacophore Sent to CCL by: "Govender, Penny" [pennyg|,|uj.ac.za] Hi There Did you check Accelrys-Discovery Studio? Ms Penny Govender (AMRSC) Lecturer: Organic Chemistry University of Johannesburg Department of Chemical Technology Doornfontein Campus (w) 011-5596555 (fax) 011-5596425 (c) 0845002689 pennyg]*[uj.ac.za Louis Pasteur "There are no such things as applied sciences, only applicati= ons of science" -----Original Message----- > From: owner-chemistry+pennyg=3D=3Duj.ac.za]*[ccl.net [mailto:owner-chemis= try+pennyg=3D=3Duj.ac.za]*[ccl.net] On Behalf Of Alberto Pasamontes alberto= .pasamontes=3D=3D=3Dshirotafoods.com Sent: 08 February 2010 01:40 PM To: Govender, Penny Subject: CCL: software to create a pharmacophore Sent to CCL by: "Alberto Pasamontes" [alberto.pasamontes(-)shirotafoods.co= m] Dear Colleagues, I'm looking for a software that allows me to create a pharmacophore from a = PDB file (protein-ligand).Could you help me? Alberto -=3D This is automatically added to each message by the mailing script =3D-=http://www.ccl.net/chemistry= /sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis email and all contents = are subject to the following disclaimer: http://www.uj.ac.za/UJ_email_legal_disclaimer.htm -=3Dis is automatically added to each message by the mailing script =3Dhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Feb 8 19:28:00 2010 From: "Wolf-D. Ihlenfeldt wdi:+:xemistry.com" To: CCL Subject: CCL: AW: Converting Sybyl SLN queries to SMARTS Message-Id: <-41218-100208183111-18104-71PbPOnRvbArXKVTXhle1w]-[server.ccl.net> X-Original-From: "Wolf-D. Ihlenfeldt" Content-Language: de Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 8 Feb 2010 23:29:14 +0100 MIME-Version: 1.0 Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi__xemistry.com] Cactvs (to a certain degree). Can you please send me some sample data so that I can check? > -----Urspr=FCngliche Nachricht----- > Von: owner-chemistry+wdi=3D=3Dxemistry.com++ccl.net [mailto:owner- > chemistry+wdi=3D=3Dxemistry.com++ccl.net] Im Auftrag von Rajarshi Guha > rajarshi.guha]*[gmail.com > Gesendet: Montag, 8. Februar 2010 16:46 > An: Ihlenfeldt, Wolf D > Betreff: CCL: Converting Sybyl SLN queries to SMARTS >=20 >=20 > Sent to CCL by: Rajarshi Guha [rajarshi.guha .. gmail.com] > Hi, does anybody know of a tool (or has code) that can convert a Sybyl > SLN query to a SMARTS pattern? >=20 > Thanks, >=20 > -- > Rajarshi Guha > NIH Chemical Genomics Center >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please > change>=20>=20>=20>=20>=20> Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20 From owner-chemistry@ccl.net Mon Feb 8 21:46:00 2010 From: "rocky walden rocky.walden19+/-gmail.com" To: CCL Subject: CCL: software to create a pharmacophore Message-Id: <-41219-100208214346-10818-pa7anqTfydlIpDF1z2N/dA]=[server.ccl.net> X-Original-From: rocky walden Content-Type: multipart/alternative; boundary=001636c92c8954b8b8047f21e2a1 Date: Tue, 9 Feb 2010 08:13:34 +0530 MIME-Version: 1.0 Sent to CCL by: rocky walden [rocky.walden19*|*gmail.com] --001636c92c8954b8b8047f21e2a1 Content-Type: text/plain; charset=ISO-8859-1 Dear Alberto, For pharmacophore you cna try with PHASE form Schrodinger, Ligand scout form Intelligand, you can also use MOE and Discovery studios (Acclerys) tools. Happy Pharmocophore creation. Rocky On Mon, Feb 8, 2010 at 5:10 PM, Alberto Pasamontes alberto.pasamontes=== shirotafoods.com wrote: > > Sent to CCL by: "Alberto Pasamontes" [alberto.pasamontes(-) > shirotafoods.com] > Dear Colleagues, > I'm looking for a software that allows me to create a pharmacophore from a > PDB file (protein-ligand).Could you help me? > > Alberto> > > --001636c92c8954b8b8047f21e2a1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Alberto,
=A0=A0=A0 For pharmacophore you cna try with=A0 PHASE form= Schrodinger, Ligand scout form Intelligand, you can also use MOE and Disco= very studios (Acclerys) tools.
=A0
Happy Pharmocophore creation.
<= br>Rocky

On Mon, Feb 8, 2010 at 5:10 PM, Alberto Pasa= montes alberto.pasamontes=3D=3D=3Dshiro= tafoods.com <owner-chemistry^-^ccl.net> wrote:

Sent to CCL by: "Alberto =A0Pasamontes" [alberto.pasamontes(-)shirotafoods.com] Dear Colleagues,
I'm looking for a software that allows me to create a pharmacophore fro= m a PDB file (protein-ligand).Could you help me?

Alberto



-=3D This is automatically added to each message by the mailing script =3D-=

--001636c92c8954b8b8047f21e2a1-- From owner-chemistry@ccl.net Mon Feb 8 23:19:01 2010 From: "MQO.Carlos Javier Nunez Aguero carlosjavierna|-|gmail.com" To: CCL Subject: CCL: software to list chi1 angles Message-Id: <-41220-100208185705-4336-iYM6M3jSg3Kpik6ydboLbQ(_)server.ccl.net> X-Original-From: "MQO.Carlos Javier Nunez Aguero" Content-Type: multipart/alternative; boundary=001636e0ba031ec648047f1e3a8e Date: Mon, 8 Feb 2010 16:21:47 -0600 MIME-Version: 1.0 Sent to CCL by: "MQO.Carlos Javier Nunez Aguero" [carlosjavierna||gmail.com] --001636e0ba031ec648047f1e3a8e Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi, With VADAR: http://redpoll.pharmacy.ualberta.ca/vadar/ My 2cents, Carlos Javier El 7 de febrero de 2010 10:59, Elaine Meng meng[#]cgl.ucsf.edu < owner-chemistry~~ccl.net> escribi=F3: > > Sent to CCL by: "Elaine Meng" [meng*o*cgl.ucsf.edu] > Hi Reynier, > In Chimera, you could do this by > > (a) opening the protein structure ("File... Open" or "File... Fetch by ID= ") > (b) choosing "Tools... Depiction... Render by Attribute" > (c) from the Render dialog, choosing "File... Save Attributes" > (d) in that file save dialog, specify saving Attribute: of "residues" > (instead of "atoms") named "chi1", output filename and location > > That gives a plain text file with contents like: > > attribute: chi1 > recipient: residues > :1.A 155.14827579618091 > :2.A 173.65904867904251 > :3.A 161.03647418613772 > :4.A -61.545841796253114 > [... etc.] > > Chimera is free for noncommercial use. For info and download see > http://www.cgl.ucsf.edu/chimera/index.html > > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --001636e0ba031ec648047f1e3a8e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,

With VADAR:
http://redpoll.pharmacy.ualberta.ca/vadar/

My 2cents,
Carlos Javier







=
El 7 de febrero de 2010 10:59, Elaine Meng meng[= #]cgl.ucsf.edu <owner-chemistry~~ccl.net> escribi=F3:

Sent to CCL by: "Elaine =A0Meng" [meng*o*cgl.ucsf.edu]
Hi Reynier,
In Chimera, you could do this by

(a) opening the protein structure ("File... Open" or "File..= . Fetch by ID")
(b) choosing "Tools... Depiction... Render by Attribute"
(c) from the Render dialog, choosing "File... Save Attributes" (d) in that file save dialog, specify saving Attribute: of "residues&q= uot; (instead of "atoms") named "chi1", output filename= and location

That gives a plain text file with contents like:

attribute: chi1
recipient: residues
=A0 =A0 =A0 :1.A =A0 =A0155.14827579618091
=A0 =A0 =A0 :2.A =A0 =A0173.65904867904251
=A0 =A0 =A0 :3.A =A0 =A0161.03647418613772
=A0 =A0 =A0 :4.A =A0 =A0-61.545841796253114
[... etc.]

Chimera is free for noncommercial use. For info and download see
ht= tp://www.cgl.ucsf.edu/chimera/index.html

Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY~~ccl.n= et or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEM= ISTRY-REQUEST~~ccl.net or use
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml

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

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0h= ttp://www.ccl.net/spammers.txt

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



--001636e0ba031ec648047f1e3a8e-- From owner-chemistry@ccl.net Mon Feb 8 23:56:01 2010 From: "Shikha Varma-O Brien shikha_+_accelrys.com" To: CCL Subject: CCL: Announcing Accelrys Discovery Studio Open Hour - Supporting our users! Message-Id: <-41221-100208183453-20446-5bfWgs+2+qaXZkfLGqB96A++server.ccl.net> X-Original-From: "Shikha Varma-O Brien" Date: Mon, 8 Feb 2010 18:34:49 -0500 Sent to CCL by: "Shikha Varma-O Brien" [shikha[]accelrys.com] Dear colleagues, At Accelrys we take great pride in providing the best scientific support to our users where scientists can call in and/or write to our outstanding Support team at any time: http://accelrys.com/services/support.html In addition, we have just launched a new mechanism to help scientists around the world with support on Discovery Studio through the New Discovery Studio Open Hour! Discovery Studio Open Hour is an open session hosted by an Accelrys scientist to answer any questions or queries you might have with regard to Discovery Studio. These sessions are completely open and FREE to attend and do not require any previous registration at all. Drop in anytime and stay as long as you like. These sessions are open for 1 hour and you can drop in for 10 minutes or you can stay for the entire hour. Any questions, queries or comments are welcome or you can see a new script or custom protocol being shown by one of our expert scientists. The sessions are LIVE with demos covering science, scripts, protcols, tips and tricks and more! Have a question about the FREE DSVisualizer. This might be the best forum to get started or ask questions. Take advantage of these sessions!! Sessions are hosted every second Tuesday of each month in 2010. (Jan 12, Feb 9, March 9, April 13, May 11, June 8, July 13, Aug 10, Sept 14, Oct 12, Nov 9, Dec 14). Add the dates to your calendar for a future appointment with an Accelrys scientist. Please visit the following website for web-ex and teleconference details: http://accelrys.com/products/discovery-studio/ds-open-hour.html Best regards, Shikha Varma-O'Brien, Ph.D. Director, LS Modeling & Simulations Accelrys, Inc.