From owner-chemistry@ccl.net Wed Dec 21 01:24:00 2011 From: "Arnout RD Voet arnout.voet~~riken.jp" To: CCL Subject: CCL: superposition of pdb files from discontiguous selection Message-Id: <-46063-111220193513-3715-9blRTthdKrhL5CmIgEtDLQ[-]server.ccl.net> X-Original-From: "Arnout RD Voet" Date: Tue, 20 Dec 2011 19:35:12 -0500 Sent to CCL by: "Arnout RD Voet" [arnout.voet(~)riken.jp] Dear all, I am trying to find a program that allows me the superposition of pdb files according to a discontiguous selection: I would like to superpose like this: residues x1 x2 x3 ... onto residues a1 a2 a3 ... respectively and y1 y2 y3 ... onto residues b1 b2 b3 ... respectively and z1 z2 z3 ... onto residues c1 c2 c3 ... respectively and .... in which x y z are part of the first pdb file and a b c of the second the amino acid sequences also are not conserved within these files Can somebody please direct me to a tool that allows this? kindest regards Arnout Voet Riken, jp From owner-chemistry@ccl.net Wed Dec 21 02:01:00 2011 From: "=?ISO-8859-1?Q?Jordi_Vill=E0_i_Freixa?= jordi.villafreixa(!)gmail.com" To: CCL Subject: CCL: superposition of pdb files from discontiguous selection Message-Id: <-46064-111221015904-24904-j8LhIwsaWJR8Ye3vxRJRdg%a%server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Jordi_Vill=E0_i_Freixa?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 21 Dec 2011 07:58:58 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Jordi_Vill=E0_i_Freixa?= [jordi.villafreixa%x%gmail.com] I think that XAM is the program you look for, although I cannot find the link to it 2011/12/21 Arnout RD Voet arnout.voet~~riken.jp : > > Sent to CCL by: "Arnout RD Voet" [arnout.voet(~)riken.jp] > Dear all, > > I am trying to find a program that allows me the superposition of pdb files according to a discontiguous selection: > I would like to superpose like this: > residues x1 x2 x3 ... onto residues a1 a2 a3 ... respectively > and      y1 y2 y3 ... onto residues b1 b2 b3 ... respectively > and      z1 z2 z3 ... onto residues c1 c2 c3 ... respectively > and      .... > in which x y z are part of the first pdb file and a b c of the second > the amino acid sequences also are not conserved within these files > > Can somebody please direct me to a tool that allows this? > > kindest regards > Arnout Voet > Riken, jp>      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> > -- Jordi Villà i Freixa Computational Biochemistry and Biophysics lab Research Program on Biomedical Informatics (GRIB) - IMIM/UPF Parc de Recerca Biomèdica de Barcelona C/ Doctor Aiguader, 88; 08003 Barcelona (Spain) Tel: +34 93 316 0504 // Fax: +34 93 316 0550 e-mail: jordi.villa!A!upf.edu http://cbbl.imim.es http://www.ascidea.com From owner-chemistry@ccl.net Wed Dec 21 04:16:01 2011 From: "Peng Yun ericyunp]|[gmail.com" To: CCL Subject: CCL:G: About Spin Density of Molecular Orbitals Message-Id: <-46065-111221041443-24627-IbHNnayGGD5WxZHRsL75lQ a server.ccl.net> X-Original-From: "Peng Yun" Date: Wed, 21 Dec 2011 04:14:42 -0500 Sent to CCL by: "Peng Yun" [ericyunp===gmail.com] Is there any methods that I can get the spin dendity data of a spicific molecular orbital from Gaussian 09 output file or any keywords can do this? Thank you for your help. Best regards! Peng Yun ericyunp,+,gmail.com From owner-chemistry@ccl.net Wed Dec 21 04:50:00 2011 From: "Michel Petitjean petitjean.chiral^gmail.com" To: CCL Subject: CCL: superposition of pdb files from discontiguous selection Message-Id: <-46066-111221041405-24478-eqbexNY9/giggKLUfHlBDg,+,server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 21 Dec 2011 10:13:59 +0100 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral:gmail.com] Dear Arnout, I may recommend the following procedure: (1) Extract the C-alphas of the two proteins by the grep ' CA ' command, and put them in a new file. (2) Add the key words HEADER and END twice in order to separate the two C-alphas sets in the new file. (3) Reorder the two sets in the file such that in the the first set the C-alphas are x1,x2,x3, y1,y2,y3,z1,z2,z3, then comes the rest of the C-alphas of the first set, and similarly in the second set you have a1,a2,a3,b1,b2,b3,c1,c2,c3, then the rest of the C-alphas of the second set. (4) Run the freeware ARMS (see URL on my webpage below); assuming that you have 9 pairs as in your example, set on the line IMOL1, IMOL2, IAT1, IAT2, LENGTH, CUT-OFF DIST, TRANSL the following input data: 1,2,1,1,9,5.0,y (5) If needed, retain the optimal rotation/translation output by ARMS and apply it to the full second protein (the translated and rotated C-alphas of the second protein are written by ARMS). That should solve your problem. Pls. contact me if you need more information about ARMS. Best, Michel. Michel Petitjean MTi, INSERM UMR-S 973, University Paris 7, 35 rue Helene Brion, 75205 Paris Cedex 13, France. Phone: +331 5727 8434; Fax: +331 5727 8372 E-mail: petitjean.chiral~~gmail.com (preferred), michel.petitjean~~univ-paris-diderot.fr http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html 2011/12/21 Arnout RD Voet arnout.voet~~riken.jp : > > Sent to CCL by: "Arnout RD Voet" [arnout.voet(~)riken.jp] > Dear all, > > I am trying to find a program that allows me the superposition of pdb files according to a discontiguous selection: > I would like to superpose like this: > residues x1 x2 x3 ... onto residues a1 a2 a3 ... respectively > and      y1 y2 y3 ... onto residues b1 b2 b3 ... respectively > and      z1 z2 z3 ... onto residues c1 c2 c3 ... respectively > and      .... > in which x y z are part of the first pdb file and a b c of the second > the amino acid sequences also are not conserved within these files > > Can somebody please direct me to a tool that allows this? > > kindest regards > Arnout Voet > Riken, jp > From owner-chemistry@ccl.net Wed Dec 21 08:09:01 2011 From: "Giovanni Allegretta g.allegretta,+,inwind.it" To: CCL Subject: CCL: Fullerene interaction with organic molecule in G03 with Gaussview Message-Id: <-46067-111221053125-19536-VHboCs/mhQEb1YM7a1hs/Q(-)server.ccl.net> X-Original-From: "Giovanni Allegretta" Date: Wed, 21 Dec 2011 05:31:24 -0500 Sent to CCL by: "Giovanni Allegretta" [g.allegretta~!~inwind.it] Hi all. I would like to study the behavior of molecules when they are mixed with fullerene for application in bulk heterojunction solar cells. The main interactions that may occur are: pi-pi configuration, or T-type configuration. My biggest problem is to calculate the binding energy of these two possible "complex" but I have no idea on how to do it. Can you guide me step by step for realize this study? Just for example in the following link (Figure S8) you can get an idea of the study I want to do. http://www.rsc.org/suppdata/cc/c0/c0cc01229g/c0cc01229g.pdf Best Regards. Dr Giovanni Allegretta PhD ISUFI National Nanotechnology Laboratory Organic Division University of Lecce Via Arnesano - 73100 Lecce - Italy Tel +39 0832 298205 fax +39 0832 298238 From owner-chemistry@ccl.net Wed Dec 21 08:44:01 2011 From: "Iain Moal Iain.Moal:+:cancer.org.uk" To: CCL Subject: CCL: superposition of pdb files from discontiguous selection Message-Id: <-46068-111221033043-32663-lS/MqfskGzDDDzuUgUWZjw],[server.ccl.net> X-Original-From: Iain Moal Content-Language: en-GB Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 21 Dec 2011 08:29:13 +0000 MIME-Version: 1.0 Sent to CCL by: Iain Moal [Iain.Moal+/-cancer.org.uk] ProFit should be able to do that for you: http://www.bioinf.org.uk/software/profit/index.html Iain ________________________________________ > From: owner-chemistry+iain.moal==cancer.org.uk##ccl.net [owner-chemistry+iain.moal==cancer.org.uk##ccl.net] On Behalf Of Arnout RD Voet arnout.voet~~riken.jp [owner-chemistry##ccl.net] Sent: 21 December 2011 00:35 To: Iain Moal Subject: CCL: superposition of pdb files from discontiguous selection Sent to CCL by: "Arnout RD Voet" [arnout.voet(~)riken.jp] Dear all, I am trying to find a program that allows me the superposition of pdb files according to a discontiguous selection: I would like to superpose like this: residues x1 x2 x3 ... onto residues a1 a2 a3 ... respectively and y1 y2 y3 ... onto residues b1 b2 b3 ... respectively and z1 z2 z3 ... onto residues c1 c2 c3 ... respectively and .... in which x y z are part of the first pdb file and a b c of the second the amino acid sequences also are not conserved within these files Can somebody please direct me to a tool that allows this? kindest regards Arnout Voet Riken, jphttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtNOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). 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From owner-chemistry@ccl.net Wed Dec 21 09:19:00 2011 From: "Djordje Francuski djordjef_-_imgge.bg.ac.rs" To: CCL Subject: CCL: superposition of pdb files from discontiguous selection Message-Id: <-46069-111221085036-3839-CZNnVtlkZD1Nqvt/rGGAqQ- -server.ccl.net> X-Original-From: "Djordje Francuski" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=utf-8 Date: Wed, 21 Dec 2011 14:50:14 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: "Djordje Francuski" [djordjef/./imgge.bg.ac.rs] You can use the tools from the ccp4 program package. Under the "->Coordinate utilities-> Superpose molecules" task you can find what your looking for. The programs Lsqkab, superpose and topp are actually hiding underneath this task. There you can do a number of things among which is also what you need. The GUI is intuitive so you should find your way. That is the simplest method I know but there should be also some internet version you can use (without the need to install the whole package). Djordje Francuski Laboratory of Theoretical Physics and Condensed Matter Physics Vinca Institute > > Sent to CCL by: "Arnout RD Voet" [arnout.voet(~)riken.jp] > Dear all, > > I am trying to find a program that allows me the superposition of pdb > files according to a discontiguous selection: > I would like to superpose like this: > residues x1 x2 x3 ... onto residues a1 a2 a3 ... respectively > and y1 y2 y3 ... onto residues b1 b2 b3 ... respectively > and z1 z2 z3 ... onto residues c1 c2 c3 ... respectively > and .... > in which x y z are part of the first pdb file and a b c of the second > the amino acid sequences also are not conserved within these files > > Can somebody please direct me to a tool that allows this? > > kindest regards > Arnout Voet > Riken, jp> From owner-chemistry@ccl.net Wed Dec 21 09:53:00 2011 From: "Lev Gorenstein lev+/-ledorub.poxod.com" To: CCL Subject: CCL: superposition of pdb files from discontiguous selection Message-Id: <-46070-111221030454-19517-omq1S9lBvWE7CUbkuSiEKA###server.ccl.net> X-Original-From: Lev Gorenstein Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Wed, 21 Dec 2011 03:04:48 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: Lev Gorenstein [lev]~[ledorub.poxod.com] On Tue, 20 Dec 2011, Arnout RD Voet arnout.voet~~riken.jp wrote: ARVa> Sent to CCL by: "Arnout RD Voet" [arnout.voet(~)riken.jp] ARVa> Dear all, ARVa> ARVa> I am trying to find a program that allows me the superposition of pdb files according to a discontiguous selection: ARVa> I would like to superpose like this: ARVa> residues x1 x2 x3 ... onto residues a1 a2 a3 ... respectively ARVa> and y1 y2 y3 ... onto residues b1 b2 b3 ... respectively ARVa> and z1 z2 z3 ... onto residues c1 c2 c3 ... respectively ARVa> and .... ARVa> in which x y z are part of the first pdb file and a b c of the second ARVa> the amino acid sequences also are not conserved within these files ARVa> ARVa> Can somebody please direct me to a tool that allows this? MMTSB toolkit (http://blue11.bch.msu.edu/mmtsb/Main_Page) has a nice utility 'lsqfit.pl' that does exactly that. Regards, Lev -- Have you ever imagined a world with no hypothetical situations? From owner-chemistry@ccl.net Wed Dec 21 19:24:00 2011 From: "Elaine Meng meng:-:cgl.ucsf.edu" To: CCL Subject: CCL: superposition of pdb files from discontiguous selection Message-Id: <-46071-111221185058-29727-F5J5nz2XhaVy5a71LFwYFQ]*[server.ccl.net> X-Original-From: "Elaine Meng" Date: Wed, 21 Dec 2011 18:50:56 -0500 Sent to CCL by: "Elaine Meng" [meng::cgl.ucsf.edu] Hi Arnout, You could do it with the "match" command in Chimera. Description and examples: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/images.html#matching Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco