From owner-chemistry@ccl.net Thu Jan 17 00:48:00 2008 From: "Richard L. Wood woodx278-#-umn.edu" To: CCL Subject: CCL: Viewing question Message-Id: <-36043-080117004718-30953-l7JbWj9EZhG5U+EyJp+mmw[a]server.ccl.net> X-Original-From: "Richard L. Wood" Date: Thu, 17 Jan 2008 00:47:14 -0500 Sent to CCL by: "Richard L. Wood" [woodx278#,#umn.edu] Hi all, I have a series of ligands that I have docked to a protein. Each one is a pdb file and I would like software (hopefully free) that can do the following: I'd like to be able to: 1) hide all or part of the protein and 2) show the ligand as a ball and stick CPK model and 3) the the heme group of the protein as a stick CPK model. In addition (4), I would like to show the iron of the heme in ball and stick and (5) to be able to select and show all protein residues within a certain distance of the iron and to label them. I know that I can do most of this in RasMol/RasWin, but I haven't figured out if I can only show selected parts of the protein. I really only want to show the ligand and the residues around the binding site as well as the heme and the iron, which I can do in RasWin, but I don't think I can hide the residues I don't want to show. I would like this program to work under Windows if possible and to be able to save and or print the pictures I make. Thanks in advance, Richard -- Richard L. Wood, Ph. D. University of Minnesota Dept. of Medicinal Chemistry, College of Pharmacy 717 Delaware St. SE Minneapolis, MN 55414-2959 woodx278:+:umn.edu From owner-chemistry@ccl.net Thu Jan 17 02:46:00 2008 From: "Prashant Kumar prashantkbio^gmail.com" To: CCL Subject: CCL: Viewing question Message-Id: <-36044-080117022521-25926-5AAl8DuOMU70RvwHYiu19g(-)server.ccl.net> X-Original-From: "Prashant Kumar" Content-Type: multipart/alternative; boundary="----=_Part_23628_25734283.1200554708918" Date: Thu, 17 Jan 2008 12:55:08 +0530 MIME-Version: 1.0 Sent to CCL by: "Prashant Kumar" [prashantkbio/./gmail.com] ------=_Part_23628_25734283.1200554708918 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Mr. Richard L. Wood I suggest to use chimera from UCSF. Prashant On Jan 17, 2008 11:17 AM, Richard L. Wood woodx278-#-umn.edu < owner-chemistry-#-ccl.net> wrote: > > Sent to CCL by: "Richard L. Wood" [woodx278#,#umn.edu] > Hi all, > > I have a series of ligands that I have docked to a protein. > > Each one is a pdb file and I would like software (hopefully free) that can > do the following: > > I'd like to be able to: 1) hide all or part of the protein and 2) show the > ligand as a ball and stick CPK model and 3) the the heme group of the > protein as a stick CPK model. In addition (4), I would like to show the > iron of the heme in ball and stick and (5) to be able to select and show all > protein residues within a certain distance of the iron and to label them. > > I know that I can do most of this in RasMol/RasWin, but I haven't figured > out if I can only show selected parts of the protein. I really only want to > show the ligand and the residues around the binding site as well as the heme > and the iron, which I can do in RasWin, but I don't think I can hide the > residues I don't want to show. > > I would like this program to work under Windows if possible and to be able > to save and or print the pictures I make. > > Thanks in advance, > Richard > > -- > Richard L. Wood, Ph. D. > University of Minnesota > Dept. of Medicinal Chemistry, > College of Pharmacy > 717 Delaware St. SE > Minneapolis, MN 55414-2959 > woodx278^^^umn.edu> > > ------=_Part_23628_25734283.1200554708918 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Mr. Richard L. Wood
                        I suggest to use chimera from UCSF.
Prashant

On Jan 17, 2008 11:17 AM, Richard L. Wood woodx278-#-umn.edu < owner-chemistry-#-ccl.net> wrote:

Sent to CCL by: "Richard L. Wood" [woodx278#,#umn.edu]
Hi all,

I have a series of ligands that I have docked to a protein.

Each one is a pdb file and I would like software (hopefully free) that can do the following:

I'd like to be able to: 1) hide all or part of the protein and 2) show the ligand as a ball and stick CPK model and 3) the the heme group of the protein as a stick CPK model.  In addition (4), I would like to show the iron of the heme in ball and stick and (5) to be able to select and show all protein residues within a certain distance of the iron and to label them.

I know that I can do most of this in RasMol/RasWin, but I haven't figured out if I can only show selected parts of the protein.  I really only want to show the ligand and the residues around the binding site as well as the heme and the iron, which I can do in RasWin, but I don't think I can hide the residues I don't want to show.

I would like this program to work under Windows if possible and to be able to save and or print the pictures I make.

Thanks in advance,
Richard

--
Richard L. Wood, Ph. D.
University of Minnesota
Dept. of Medicinal Chemistry,
College of Pharmacy
717 Delaware St. SE
Minneapolis, MN 55414-2959
woodx278^^^umn.edu



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------=_Part_23628_25734283.1200554708918-- From owner-chemistry@ccl.net Thu Jan 17 03:20:01 2008 From: "Jerome Kieffer jerome.Kieffer{:}terre-adelie.org" To: CCL Subject: CCL: Software for Electron Spin Density Message-Id: <-36045-080117022055-25502-wYq5jktgwGHwmwMKPgY+MA:_:server.ccl.net> X-Original-From: Jerome Kieffer Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-15 Date: Thu, 17 Jan 2008 08:21:33 +0100 Mime-Version: 1.0 Sent to CCL by: Jerome Kieffer [jerome.Kieffer|,|terre-adelie.org] On Wed, 16 Jan 2008 21:13:03 -0500 "Sina T reli sinatureli,gmail.com" wrote: >=20 > Sent to CCL by: "Sina T reli" [sinatureli*|*gmail.com] > Hello, >=20 > Do you know of any FREE and good tool for calculation of electron spin de= nsities and visualization of molecular orbitals.. Have you tried Gabedit ? --=20 J=E9r=F4me KIEFFER : http://www.terre-adelie.org =C0 v=E9lo, prendre une rue =E0 contre-sens est moins dangeureux que prendre un boulevard dans le sens l=E9gal. =C0 qui la faute ? From owner-chemistry@ccl.net Thu Jan 17 03:56:00 2008 From: "Bjoern Windshuegel bjorn.windshugel,,uku.fi" To: CCL Subject: CCL: Viewing question Message-Id: <-36046-080117025325-30952-Rr4o5aWi4ZjsqLT0dVNTgw##server.ccl.net> X-Original-From: Bjoern Windshuegel Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-15" Date: Thu, 17 Jan 2008 09:14:45 +0200 MIME-Version: 1.0 Sent to CCL by: Bjoern Windshuegel [bjorn.windshugel%uku.fi] Hi, I recommend to use VMD instead of rasmol if you don't have experience with = it.=20 It also works under windows and doesn't take long to get used to it. Also y= ou=20 can get fancy pictures using internal or external renderers. Your set of representations in "graphical"-> "representations" for the prot= ein=20 would be something like that: =09 resname HEM name FE within 5 of name FE Using the drawing method you can choose between several representations (CP= C,=20 vdW, et.). Best regards, Bj=F6rn > Sent to CCL by: "Richard L. Wood" [woodx278#,#umn.edu] > Hi all, > > I have a series of ligands that I have docked to a protein. > > Each one is a pdb file and I would like software (hopefully free) that can > do the following: > > I'd like to be able to: 1) hide all or part of the protein and 2) show the > ligand as a ball and stick CPK model and 3) the the heme group of the > protein as a stick CPK model. In addition (4), I would like to show the > iron of the heme in ball and stick and (5) to be able to select and show > all protein residues within a certain distance of the iron and to label > them. > > I know that I can do most of this in RasMol/RasWin, but I haven't figured > out if I can only show selected parts of the protein. I really only want > to show the ligand and the residues around the binding site as well as the > heme and the iron, which I can do in RasWin, but I don't think I can hide > the residues I don't want to show. > > I would like this program to work under Windows if possible and to be able > to save and or print the pictures I make. > > Thanks in advance, > Richard =2D-=20 Dr. Bj=F6rn Windsh=FCgel Department of Pharmaceutical Chemistry University of Kuopio P.O. Box 1627 70211 Kuopio, FINLAND Email: bjorn.windshugel]~[uku.fi Phone: (+358) 17 162463 =46ax: (+358) 17 162456 Web: www.uku.fi/farmasia/fake/modelling/index.shtml From owner-chemistry@ccl.net Thu Jan 17 04:31:01 2008 From: "Frank Neese neese=thch.uni-bonn.de" To: CCL Subject: CCL: Software for Electron Spin Density Message-Id: <-36047-080117031819-10588-6Wpnn7KDp2rpt6LSU0DJ8A|server.ccl.net> X-Original-From: Frank Neese Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Thu, 17 Jan 2008 08:17:58 +0100 MIME-Version: 1.0 Sent to CCL by: Frank Neese [neese- -thch.uni-bonn.de] Sina T reli sinatureli,gmail.com schrieb: > Hello, > > Do you know of any FREE and good tool for calculation of electron spin densities and visualization of molecular orbitals.. > > Thanks > > The orca program is specialized in spin dependent properties and is completely free. Download is at http://www.thch.uni-bonn.de/tc/orca/ the next version is closely ahead. best regards, Frank From owner-chemistry@ccl.net Thu Jan 17 05:39:00 2008 From: "Andrew Turner andrew.turner,ed.ac.uk" To: CCL Subject: CCL: Viewing question Message-Id: <-36048-080117045411-15056-oDhtiHHFVFS5E4ehgFog5Q#,#server.ccl.net> X-Original-From: Andrew Turner Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 17 Jan 2008 09:13:46 +0000 MIME-Version: 1.0 Sent to CCL by: Andrew Turner [andrew.turner(_)ed.ac.uk] Hi Richard, In my opinion the best program for this type of problem is VMD. You can easily select the parts of the system you want in the Representations dialog and set how they are displayed. I have used it for many different systems from small molecules all the way up to proteins and DNA simulations. Any view can then be rendered using POV-Ray to produce really nice images. Good luck Andy Richard L. Wood woodx278-#-umn.edu wrote: > Sent to CCL by: "Richard L. Wood" [woodx278#,#umn.edu] > Hi all, > > I have a series of ligands that I have docked to a protein. > > Each one is a pdb file and I would like software (hopefully free) that can do the following: > > I'd like to be able to: 1) hide all or part of the protein and 2) show the ligand as a ball and stick CPK model and 3) the the heme group of the protein as a stick CPK model. In addition (4), I would like to show the iron of the heme in ball and stick and (5) to be able to select and show all protein residues within a certain distance of the iron and to label them. > > I know that I can do most of this in RasMol/RasWin, but I haven't figured out if I can only show selected parts of the protein. I really only want to show the ligand and the residues around the binding site as well as the heme and the iron, which I can do in RasWin, but I don't think I can hide the residues I don't want to show. > > I would like this program to work under Windows if possible and to be able to save and or print the pictures I make. > > Thanks in advance, > Richard > -- ================================== Dr Andrew R. Turner Research Computing Officer e: andrew.turner*_*ed.ac.uk t: +44 (0)131 650 7748 w: http://www.eastchem.ac.uk/rcf icq: 370-899-715 p: School of Chemistry University of Edinburgh EH9 3JJ ================================== From owner-chemistry@ccl.net Thu Jan 17 07:11:00 2008 From: "Rene Thomsen rt[A]molegro.com" To: CCL Subject: CCL: Viewing question Message-Id: <-36049-080117070259-31415-c2sqHY18CXdcLDgThnYs2w]_[server.ccl.net> X-Original-From: "Rene Thomsen" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 17 Jan 2008 12:07:17 +0100 MIME-Version: 1.0 Sent to CCL by: "Rene Thomsen" [rt^molegro.com] Hi Richard, You can also try out Molegro Molecular Viewer (MMV), which is a free cross-platform application for visualization of molecules and docking results. Using MMV you can do the following: - Hide residues outside a user-defined sphere (e.g. centered on the iron) using the 'Hide Residues' dialog. - Select different visualization/rendering settings for proteins, ligands, cofactors, etc. - Create labels (e.g. for residues shown). - Take a screenshot using the built-in screen capture dialog. You can download MMV from http://www.molegro.com/mmv-product.php. Kind regards, Rene 2008/1/17 Richard L. Wood woodx278-#-umn.edu : > > Sent to CCL by: "Richard L. Wood" [woodx278#,#umn.edu] > Hi all, > > I have a series of ligands that I have docked to a protein. > > Each one is a pdb file and I would like software (hopefully free) that can do the following: > > I'd like to be able to: 1) hide all or part of the protein and 2) show the ligand as a ball and stick CPK model and 3) the the heme group of the protein as a stick CPK model. In addition (4), I would like to show the iron of the heme in ball and stick and (5) to be able to select and show all protein residues within a certain distance of the iron and to label them. > > I know that I can do most of this in RasMol/RasWin, but I haven't figured out if I can only show selected parts of the protein. I really only want to show the ligand and the residues around the binding site as well as the heme and the iron, which I can do in RasWin, but I don't think I can hide the residues I don't want to show. > > I would like this program to work under Windows if possible and to be able to save and or print the pictures I make. > > Thanks in advance, > Richard Rene Thomsen --- Molegro Hoegh-Guldbergs Gade 10, Bldg. 1090 DK-8000 Aarhus C Denmark www.molegro.com From owner-chemistry@ccl.net Thu Jan 17 07:46:01 2008 From: "=?ISO-8859-1?Q?Sina_T=FCreli?= sinatureli^gmail.com" To: CCL Subject: CCL: Software for Electron Spin Density Message-Id: <-36050-080117061114-17620-uLwSx55in7VRJyj0eg7BSA ~ server.ccl.net> X-Original-From: "=?ISO-8859-1?Q?Sina_T=FCreli?=" Content-Type: multipart/alternative; boundary="----=_Part_191_18123160.1200564663372" Date: Thu, 17 Jan 2008 12:11:03 +0200 MIME-Version: 1.0 Sent to CCL by: "=?ISO-8859-1?Q?Sina_T=FCreli?=" [sinatureli###gmail.com] ------=_Part_191_18123160.1200564663372 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline I will try, though I am using mopac which is not on the list of programs that gabedit can read. I will also try some other programs listed in mopac website but I dont if they can calculate spin density.. On Jan 17, 2008 9:21 AM, Jerome Kieffer jerome.Kieffer{:}terre-adelie.org < owner-chemistry{=}ccl.net> wrote: > > Sent to CCL by: Jerome Kieffer [jerome.Kieffer|,|terre-adelie.org] > On Wed, 16 Jan 2008 21:13:03 -0500 > "Sina T reli sinatureli,gmail.com" wrote: > > > > > Sent to CCL by: "Sina T reli" [sinatureli*|*gmail.com] > > Hello, > > > > Do you know of any FREE and good tool for calculation of electron spin > densities and visualization of molecular orbitals.. > > > Have you tried Gabedit ? > > -- > J=E9r=F4me KIEFFER : http://www.terre-adelie.org > =C0 v=E9lo, prendre une rue =E0 contre-sens est moins dangeureux > que prendre un boulevard dans le sens l=E9gal. =C0 qui la faute ? > > > > - This is automatically added to each message by the mailing script -> > > ------=_Part_191_18123160.1200564663372 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline I will try, though I am using mopac which is not on the list of programs th= at gabedit can read. I will also try some other programs listed in mopac we= bsite but I dont if they can calculate spin density..

On Jan 17, 2008 9:21 AM, Jerome Kieffer jerome.Kieffer{:}terre-adelie.org &= lt;owner-chemistry{=}ccl.net&g= t; wrote:

Sent to CCL by: Jerome Kieffer [jerome.Kieffer|,|terre-adelie.org]
On Wed, 16 Jan 2008 21:1= 3:03 -0500
"Sina T reli sinatureli, gmail.com" <owner-chemistry/a\ccl.net> wrote:

>> Sent to CCL by: "Sina  T  reli" [sinatureli*|*gmail.com]
> Hello,>
> Do you know of any FREE and good tool for calculation of electron spin= densities and visualization of molecular orbitals..


Have you tr= ied Gabedit ?

--
J=E9r=F4me KIEFFER  : http://www.terre-adelie.org
=C0 v=E9lo, prendre une rue =E0 contre-s= ens est moins dangeureux
que prendre un boulevard dans le sens l=E9gal. = =C0 qui la faute ?



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------=_Part_191_18123160.1200564663372-- From owner-chemistry@ccl.net Thu Jan 17 08:21:00 2008 From: "Praveen Depa praveen_depa : yahoo.com" To: CCL Subject: CCL: Viewing question Message-Id: <-36051-080117070649-31664-0JmAIz969NwWaNOyo3GRzw#,#server.ccl.net> X-Original-From: Praveen Depa Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 17 Jan 2008 03:06:33 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Praveen Depa [praveen_depa=-=yahoo.com] Dear Richard, I guess you can use VMD, which is quite flexible and has number of options for visualization purposes. And, it satisfies your requirements: Windows version and Free!! -Praveen. --- "Richard L. Wood woodx278-#-umn.edu" wrote: > > Sent to CCL by: "Richard L. Wood" > [woodx278#,#umn.edu] > Hi all, > > I have a series of ligands that I have docked to a > protein. > > Each one is a pdb file and I would like software > (hopefully free) that can do the following: > > I'd like to be able to: 1) hide all or part of the > protein and 2) show the ligand as a ball and stick > CPK model and 3) the the heme group of the protein > as a stick CPK model. In addition (4), I would like > to show the iron of the heme in ball and stick and > (5) to be able to select and show all protein > residues within a certain distance of the iron and > to label them. > > I know that I can do most of this in RasMol/RasWin, > but I haven't figured out if I can only show > selected parts of the protein. I really only want > to show the ligand and the residues around the > binding site as well as the heme and the iron, which > I can do in RasWin, but I don't think I can hide the > residues I don't want to show. > > I would like this program to work under Windows if > possible and to be able to save and or print the > pictures I make. > > Thanks in advance, > Richard > > -- > Richard L. Wood, Ph. D. > University of Minnesota > Dept. of Medicinal Chemistry, > College of Pharmacy > 717 Delaware St. SE > Minneapolis, MN 55414-2959 > woodx278^^^umn.edu > > > > -= 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.> > E-mail to administrators: CHEMISTRY-REQUEST[]ccl.net > or use> > Before posting, check wait time at: > http://www.ccl.net> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: > ccl, Password: search) > > If your mail bounces from CCL with 5.7.1 error, > check:> > RTFI: > http://www.ccl.net/chemistry/aboutccl/instructions/ > > > ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ From owner-chemistry@ccl.net Thu Jan 17 08:59:01 2008 From: "Acharya, Priyamvada (NIH/VRC) F acharyap-.-mail.nih.gov" To: CCL Subject: CCL: Viewing question Message-Id: <-36052-080117020627-24321-1R4IqcLSQ7t8nU1vHTpwLA*|*server.ccl.net> X-Original-From: "Acharya, Priyamvada (NIH/VRC) [F]" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Thu, 17 Jan 2008 01:33:58 -0500 MIME-Version: 1.0 Sent to CCL by: "Acharya, Priyamvada (NIH/VRC) [F]" [acharyap=-=mail.nih.gov] PYMOL http://pymol.sourceforge.net/ can do all of this.=20 Best, Priyamvada Priyamvada Acharya, Ph.D. Visiting Fellow Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4609B 40 Convent Drive, MSC3027 Bethesda, MD 20892 -----Original Message----- > From: Richard L. Wood woodx278-#-umn.edu [mailto:owner-chemistry.:.ccl.net]=20 Sent: Thursday, January 17, 2008 12:47 AM To: Acharya, Priyamvada (NIH/VRC) [F] Subject: CCL: Viewing question Sent to CCL by: "Richard L. Wood" [woodx278#,#umn.edu] Hi all, I have a series of ligands that I have docked to a protein. Each one is a pdb file and I would like software (hopefully free) that can do the following: I'd like to be able to: 1) hide all or part of the protein and 2) show the ligand as a ball and stick CPK model and 3) the the heme group of the protein as a stick CPK model. In addition (4), I would like to show the iron of the heme in ball and stick and (5) to be able to select and show all protein residues within a certain distance of the iron and to label them. I know that I can do most of this in RasMol/RasWin, but I haven't figured out if I can only show selected parts of the protein. I really only want to show the ligand and the residues around the binding site as well as the heme and the iron, which I can do in RasWin, but I don't think I can hide the residues I don't want to show. I would like this program to work under Windows if possible and to be able to save and or print the pictures I make. Thanks in advance, Richard --=20 Richard L. Wood, Ph. D. University of Minnesota Dept. of Medicinal Chemistry, College of Pharmacy 717 Delaware St. SE Minneapolis, MN 55414-2959 woodx278^^^umn.edu -=3D This is automatically added to each message by the mailing script = =3D-http://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 Thu Jan 17 09:31:00 2008 From: "PANKAJ SAGDEO phankus%x%yahoo.com" To: CCL Subject: CCL: Crystal field splitting calculation for 3d and 4f Message-Id: <-36053-080117061503-19204-CG8zR3PVOngQlLBthqM11w(a)server.ccl.net> X-Original-From: "PANKAJ SAGDEO" Date: Thu, 17 Jan 2008 06:14:59 -0500 Sent to CCL by: "PANKAJ SAGDEO" [phankus ~ yahoo.com] Dear All, I am looking for a computer program or a softward which can calculate the splitting in the energy level due to neighbouring atoms. As an example in LaFeO3 Fe is sorrounded by six oxygen atoms in that case is it possible to calculate the effect of oxygen on the 3d level of Fe atoms using some computer program? Kindly suggest me some computer program, Thanks With Regards Pankaj Sagdeo phankus++yahoo.com From owner-chemistry@ccl.net Thu Jan 17 10:06:01 2008 From: "Ioana Sovago isovago(-)chem.ubbcluj.ro" To: CCL Subject: CCL:G: question Message-Id: <-36054-080117070010-31165-0X5ofbA/di9P722Br2ihdw{:}server.ccl.net> X-Original-From: "Ioana Sovago" Date: Thu, 17 Jan 2008 07:00:07 -0500 Sent to CCL by: "Ioana Sovago" [isovago[a]chem.ubbcluj.ro] Here is my question: when I try to optimise the calculation of a metal transition cluster compound with Gaussian '03 with B3LYP/6-31G(d) method "single point" the converge wave function is working fine. When the converged wave function is used with "B3LYP/6-31G(d) opt" I get this message " Convergence failure -- run terminated.". If somebody can help I would be grateful. Thanks From owner-chemistry@ccl.net Thu Jan 17 11:13:01 2008 From: "Ramachandran chelat rcchelat ~ rediffmail.com" To: CCL Subject: CCL: non adiabatic interaction energy from coupling matrix elements Message-Id: <-36055-080117110920-21434-YEkwq8kAyWsiojjstlR87A() server.ccl.net> X-Original-From: "Ramachandran chelat" Date: Thu, 17 Jan 2008 11:09:17 -0500 Sent to CCL by: "Ramachandran chelat" [rcchelat[*]rediffmail.com] Dear CCL users, I calculated the nonadiabatic coupling elements for the LiF system and got the following results at different scanning distances. How can I get the non adiabatic corrections to the energy from this? Non-adiabatic couplings for LiF R NACME1P NACME1M NACMEAV NACME2 10.0 -0.22821455 -0.22388857 -0.22605156 -0.22605156 10.5 -0.51692057 -0.50826346 -0.51259201 -0.51259201 11.0 0.76241141 0.76487272 0.76364206 0.76364206 11.5 0.42254569 0.42988512 0.42621540 0.42621540 12.0 0.19031583 0.19369470 0.19200526 0.19200526 CI MULTI CI MULTI CI MULTI CI MULTI -106.84478016 -106.84478016 -106.84464924 -106.84464924 -106.84471470 -106.84471470 -106.84802840 -106.84802840 ********************************************************************************************************************************** Variable memory released what are these Multi and CI values means....? of course it can't be the corrected energies for differen distances (as only 4 values are given whereas 5 distances are there) Thanks in advance From owner-chemistry@ccl.net Thu Jan 17 12:07:01 2008 From: "maxim totrov max^molsoft.com" To: CCL Subject: CCL: Viewing question Message-Id: <-36056-080117050448-19642-J+nfq/vOWC9qpbSXXB8DZA^server.ccl.net> X-Original-From: maxim totrov Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Thu, 17 Jan 2008 01:04:28 -0800 Mime-Version: 1.0 (Apple Message framework v753) Sent to CCL by: maxim totrov [max(-)molsoft.com] Hi Richard, try free Molsoft Browser, it can do all that you describe, both through GUI or scripting : http://www.molsoft.com/icm_browser.html Max Totrov > > Sent to CCL by: "Richard L. Wood" [woodx278#,#umn.edu] > Hi all, > > I have a series of ligands that I have docked to a protein. > > Each one is a pdb file and I would like software (hopefully free) > that can do the following: > > I'd like to be able to: 1) hide all or part of the protein and 2) > show the ligand as a ball and stick CPK model and 3) the the heme > group of the protein as a stick CPK model. In addition (4), I > would like to show the iron of the heme in ball and stick and (5) > to be able to select and show all protein residues within a certain > distance of the iron and to label them. > > I know that I can do most of this in RasMol/RasWin, but I haven't > figured out if I can only show selected parts of the protein. I > really only want to show the ligand and the residues around the > binding site as well as the heme and the iron, which I can do in > RasWin, but I don't think I can hide the residues I don't want to > show. > > I would like this program to work under Windows if possible and to > be able to save and or print the pictures I make. > > Thanks in advance, > Richard > > -- > Richard L. Wood, Ph. D. > University of Minnesota > Dept. of Medicinal Chemistry, > College of Pharmacy > 717 Delaware St. SE > Minneapolis, MN 55414-2959 > woodx278^^^umn.edu > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> From owner-chemistry@ccl.net Thu Jan 17 12:41:01 2008 From: "Jeff Nauss jnauss*|*accelrys.com" To: CCL Subject: CCL: Viewing question Message-Id: <-36057-080117120609-26514-6zc0y7WygBR78CT8N6bbCQ()server.ccl.net> X-Original-From: Jeff Nauss Content-Type: text/plain; charset="US-ASCII" Date: Thu, 17 Jan 2008 08:54:49 -0800 MIME-Version: 1.0 Sent to CCL by: Jeff Nauss [jnauss%accelrys.com] > Sent to CCL by: "Richard L. Wood" [woodx278#,#umn.edu] > > I would like this program to work under Windows if possible and to > be able to save and or print the pictures I make. You may also want to look at the new release of Discovery Studio Visualizer 2.0 and the ActiveX control. Both are free (after a registration process) from http://www.accelrys.com/products/downloads/ds_visualizer/index.html. The Hierarchy View will easily provide tremendous flexibility to select specific parts of your molecule and display them as you indicated. Jeff -- Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys 10188 Telesis Court, Suite 100 San Diego, CA 92121-4779 Phone: +1-858-799-5555 Fax: +1-858-799-5100 http://www.accelrys.com/services/training/ From owner-chemistry@ccl.net Thu Jan 17 13:16:00 2008 From: "Miklos Vargyas mvargyas(~)chemaxon.com" To: CCL Subject: CCL: Viewing question Message-Id: <-36058-080117115049-20449-7O3wSFnkpEl1TK1t9Bau2A~!~server.ccl.net> X-Original-From: Miklos Vargyas Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Thu, 17 Jan 2008 16:44:43 +0100 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Miklos Vargyas [mvargyas(!)chemaxon.com] Hi Richard, MarvinSpace by ChemAxon can do all 5 for you. It's cross-platform (Java), works well under Windows, you can print (and save) arbitrarily large pictures. And it's free :-) You may wish to - take a quick tour: http://www.chemaxon.com/product/mspace.html - try it online: http://www.chemaxon.com/marvinspace/html/webstart.html Btw, you are entitled to use all ChemAxon products for free, just apply for an Academic License: http://www.chemaxon.com/ acpack_conditions.html Hope this help and that you will like MarvinSpace. Regards, Miklos -- Miklos Vargyas, PhD CTO ChemAxon Ltd. Maramaros koz 3/A, Budapest, 1037 Hungary http://www.chemaxon.com Cell: +3670 3813205 Tel: +361 4532661 Skype: miklos.vargyas Fax: +361 4532659 e-mail: mvargyas###chemaxon.com On Jan 17, 2008, at 6:47 AM, Richard L. Wood woodx278-#-umn.edu wrote: > > Sent to CCL by: "Richard L. Wood" [woodx278#,#umn.edu] > Hi all, > > I have a series of ligands that I have docked to a protein. > > Each one is a pdb file and I would like software (hopefully free) > that can do the following: > > I'd like to be able to: 1) hide all or part of the protein and 2) > show the ligand as a ball and stick CPK model and 3) the the heme > group of the protein as a stick CPK model. In addition (4), I > would like to show the iron of the heme in ball and stick and (5) > to be able to select and show all protein residues within a certain > distance of the iron and to label them. > > I know that I can do most of this in RasMol/RasWin, but I haven't > figured out if I can only show selected parts of the protein. I > really only want to show the ligand and the residues around the > binding site as well as the heme and the iron, which I can do in > RasWin, but I don't think I can hide the residues I don't want to > show. > > I would like this program to work under Windows if possible and to > be able to save and or print the pictures I make. > > Thanks in advance, > Richard > > -- > Richard L. Wood, Ph. D. > University of Minnesota > Dept. of Medicinal Chemistry, > College of Pharmacy > 717 Delaware St. SE > Minneapolis, MN 55414-2959 > woodx278^^^umn.edu > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > From owner-chemistry@ccl.net Thu Jan 17 13:51:01 2008 From: "Pierre Archirel pierre.archirel*_*lcp.u-psud.fr" To: CCL Subject: CCL:G: convergence threshold Message-Id: <-36059-080117122754-5235-GgQGGE73fv3xAgOALoDHjA|server.ccl.net> X-Original-From: Pierre Archirel Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 17 Jan 2008 17:47:28 +0100 MIME-Version: 1.0 Sent to CCL by: Pierre Archirel [pierre.archirel-#-lcp.u-psud.fr] Here is my question: when I try to optimise the calculation of a metal transition cluster compound with Gaussian '03 with B3LYP/6-31G(d) method "single point" the converge wave function is working fine. When the converged wave function is used with "B3LYP/6-31G(d) opt" I get this message " Convergence failure -- run terminated.". Dear collegue, This is due to different convergence thresholds of the dft calculation, that Gaussian uses for single point and opt calculations. This is explained in the Gaussian manual, page 202 (keyword singlepoint). You can help DFT convergence in an opt calculation with the keyword: scf=(conv=4, or 5), but accuracy can be partly lost. __________________________________________________________ Pierre Archirel Groupe de Chimie Théorique Laboratoire de Chimie Physique Tel: 01 69 15 63 86 Bat 349 Fax: 01 69 15 61 88 91405 Orsay Cedex France pierre.archirel_._lcp.u-psud.fr __________________________________________________________ From owner-chemistry@ccl.net Thu Jan 17 14:26:01 2008 From: "Elaine Meng meng~~cgl.ucsf.edu" To: CCL Subject: CCL: Viewing question Message-Id: <-36060-080117130654-14366-klFS503TC2zzpfYVLbewHQ|a|server.ccl.net> X-Original-From: "Elaine Meng" Date: Thu, 17 Jan 2008 13:06:50 -0500 Sent to CCL by: "Elaine Meng" [meng|cgl.ucsf.edu] Hi Richard, As you can tell from the responses, many graphics programs can do this. However, here is how to do it with commands in Chimera. This could also be done with the menu, but that would take me longer to type! (Chimera is free for noncommercial use and available for Windows) Start Chimera, open files (File... Open). For this example, I opened the protein first to make it model 0, the ligand second to make it model 1. Show Command Line (Favorites... Command Line), then enter something like: rep stick #0 rep bs #1 show #0 & Fe z<6 rlabel #0 rep sphere Fe The "z" specifies all residues within the zone. You could use "za" instead to get atoms rather than whole residues, but the whole residues approach usually looks better. You could use a different distance than 6 angstroms to define the zone. The default Fe radius is pretty small in Chimera, so the example above shows its full VDW radius (rep sphere) instead of "ball" radius (rep bs). You could also change the radius. Use File... Save Image to save TIFF, PNG, etc. You can raytrace (there is a POV-Ray option) or not, as preferred. You'd probably want to do other things such as color atoms by element, change background color, etc. before saving the image. For a publication image, I'd use "2D Labels" rather than the standard Chimera labels, which are mainly for interactive viewing purposes: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html Image creation info: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/print.html I'd be happy to help if you would like any further specifics. Elaine ----- Elaine C. Meng, Ph.D. meng:+:cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From owner-chemistry@ccl.net Thu Jan 17 17:40:00 2008 From: "Hans Himmler contact.openchemsoft],[openchemsoft.eu" To: CCL Subject: CCL: InChI webservices/search Message-Id: <-36061-080117101158-10363-YmmI2mdmh04vSPfK74ridw*o*server.ccl.net> X-Original-From: "Hans Himmler" Date: Thu, 17 Jan 2008 10:11:54 -0500 Sent to CCL by: "Hans Himmler" [contact.openchemsoft_._openchemsoft.eu] HI, I look for internet URLs that offer InChI code (name/key) related webservices (like e.g. ChemSpider). I am also interested in internet sites that allow to search for InChI codes (name/key). In addition I am interested in recent publications regarding usage of InChI to locate molecules in internet databases. Any feedback regarding the topic is appreciated. Regards HansH From owner-chemistry@ccl.net Thu Jan 17 18:40:01 2008 From: "Rajarshi Guha rguha^indiana.edu" To: CCL Subject: CCL: InChI webservices/search Message-Id: <-36062-080117183859-31591-Wj2ykyNMMpuF02CQVNH1yA,server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Thu, 17 Jan 2008 18:38:34 -0500 Mime-Version: 1.0 (Apple Message framework v753) Sent to CCL by: Rajarshi Guha [rguha,indiana.edu] On Jan 17, 2008, at 10:11 AM, Hans Himmler contact.openchemsoft], [openchemsoft.eu wrote: > > Sent to CCL by: "Hans > Himmler" [contact.openchemsoft_._openchemsoft.eu] > HI, > > I look for internet URLs that offer InChI code (name/key) related > webservices (like e.g. ChemSpider). > I am also interested in internet sites that allow to search for > InChI codes (name/key). It's possible to access the Pub3D database (http://rguha.ath.cx/ ~rguha/cicc/p3d/) via SOAP based web services which take CID or InChI. WSDL is at http://rguha.ath.cx:8080/pws/services/Struct3D?wsdl and docs are at http://cheminfo.informatics.indiana.edu/~rguha/ws/pws/ api/net/sf/ciccgrid/pws/Struct3D.html There is also a REST interface to this database: http://www.chembiogrid.org/rest/db/pub3d/InChI=1/C9H8O4/c1-6(10) 13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)/f/h11H will return a 3D structure of aspirin in SDF format. You can also use CID, such as http://www.chembiogrid.org/cheminfo/rest/db/pub3d/2244 See http://www.chembiogrid.org/projects/proj_rest.html for current and upcoming REST interfaces ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- Psychology is merely producing habits out of rats. From owner-chemistry@ccl.net Thu Jan 17 20:03:01 2008 From: "Gunes Bender gbender . wisc.edu" To: CCL Subject: CCL:G: Gaussian'98 Message-Id: <-36063-080117160526-23995-NBZxECVtJgh6eQ7h2GwBpQ- -server.ccl.net> X-Original-From: "Gunes Bender" Date: Thu, 17 Jan 2008 16:05:22 -0500 Sent to CCL by: "Gunes Bender" [gbender{=}wisc.edu] I am trying to do QCISD(T) level calculations on a molecule about 20 atoms big using Gaussian'98 on a linux platform. I tried creating extra scr and rwf files and specifying their sizes; so, I try to use many 240MW big files for the calculation to use. My question is: Gaussian seems to read only the first 12 files, even when I try to make it use more files than that. Does anyone know why Gaussian does this? And second of all, I am always running out of space. Does anyone know any other tricks to do QCISD(T) calculations on fairly large molecules? Any information or help would be much appreciated. Thank you, Gunes From owner-chemistry@ccl.net Thu Jan 17 21:43:00 2008 From: "Jan Labanowski janl!A!speakeasy.net" To: CCL Subject: CCL: Two papers deposited in CCL archives Message-Id: <-36064-080117213217-26477-Kn5tvvLo2yEB7J+OeKym0Q*o*server.ccl.net> X-Original-From: "Jan Labanowski" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 18 Jan 2008 02:31:51 +0000 MIME-Version: 1.0 Sent to CCL by: "Jan Labanowski" [janl#%#speakeasy.net] Dear CCL Members, There are two additions to CCL Document Archive at: http://www.ccl.net/chemistry/resources/overview Namely: # 2008.01.10 Protonate 3D: Assignment of Macromolecular Protonation State and Geometry by Paul Labute and # 2008.01.10 Ligand Scaffold Replacement using MOE Pharmacophore Tools by Alain Deschenes and Elizabeth Sourial Papers contain very good description on methodology and are well illustrated. Have a nice reading... I am grateful to Chemical Computing Group for these valuable contributions to the CCL Archives. I encourage all CCL members to contribute their materials to CCL Web Site for the common good. Your moderator Jan Labanowski From owner-chemistry@ccl.net Thu Jan 17 22:17:01 2008 From: "=?ISO-8859-1?Q?Sina_T=FCreli?= sinatureli a gmail.com" To: CCL Subject: CCL: Software for Electron Spin Density Message-Id: <-36065-080117073022-20347-Rf1BBcLvjlqmuxdxLwEUyg||server.ccl.net> X-Original-From: "=?ISO-8859-1?Q?Sina_T=FCreli?=" Content-Type: multipart/alternative; boundary="----=_Part_705_27563342.1200572637634" Date: Thu, 17 Jan 2008 14:23:57 +0200 MIME-Version: 1.0 Sent to CCL by: "=?ISO-8859-1?Q?Sina_T=FCreli?=" [sinatureli-*-gmail.com] ------=_Part_705_27563342.1200572637634 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Thanks, I will try Orca. On Jan 17, 2008 9:17 AM, Frank Neese neese=thch.uni-bonn.de < owner-chemistry{:}ccl.net> wrote: > > Sent to CCL by: Frank Neese [neese- -thch.uni-bonn.de] > Sina T reli sinatureli,gmail.com schrieb: > > Hello, > > > > Do you know of any FREE and good tool for calculation of electron spin > densities and visualization of molecular orbitals.. > > > > Thanks > > > > > The orca program is specialized in spin dependent properties and is > completely free. > Download is at http://www.thch.uni-bonn.de/tc/orca/ > the next version is closely ahead. > > best regards, > Frank> > > ------=_Part_705_27563342.1200572637634 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Thanks, I will try Orca.

On Jan 17, 2008 9:17 AM, Frank Neese neese=thch.uni-bonn.de <owner-chemistry{:}ccl.net > wrote:

Sent to CCL by: Frank Neese [neese- - thch.uni-bonn.de]
Sina T reli sinatureli,gmail.com schrieb:
> Hello,
>
> Do you know of any FREE and good tool for calculation of electron spin densities and visualization of molecular orbitals..
>
> Thanks
>
>
The orca program is specialized in spin dependent properties and is
completely free.
Download is at http://www.thch.uni-bonn.de/tc/orca/
the next version is closely ahead.

best regards,
Frank

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