From owner-chemistry@ccl.net Sat Jun 2 02:02:00 2007 From: "John Stone johns|*|ks.uiuc.edu" To: CCL Subject: CCL: show ruler in VMD Message-Id: <-34400-070601233706-12345-mftR0zm+Dd9NSA32QrLp7Q]-[server.ccl.net> X-Original-From: John Stone Content-Disposition: inline Content-Type: multipart/mixed; boundary="gKMricLos+KVdGMg" Date: Fri, 1 Jun 2007 14:11:07 -0500 Mime-Version: 1.0 Sent to CCL by: John Stone [johns%x%ks.uiuc.edu] --gKMricLos+KVdGMg Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Hi, My coworker Jordi wrote up a useful VMD script for displaying a "ruler" grid that automatically rescales along with the molecule. This script could be modified slightly to draw various other scale bars if you prefer something different, but it should be a good starting point as it handles the trickiest parts such as automatically updating when the user zooms in and out etc. I've attached the script to this email. Cheers, John Stone vmd[A]ks.uiuc.edu On Wed, May 30, 2007 at 09:33:09AM +0300, Liisa laakkonen llaakkon::cc.helsinki.fi wrote: > > Sent to CCL by: Liisa laakkonen [llaakkon===cc.helsinki.fi] > Hello Yubo, > > I've done the angstrom ruler simply by building a dummy pdb with > enough points to measure the desired distance, and displaying it side > by side with my molecule. Works equally well for a compass. > > Greetings, > Liisa > > liisa.laakkonen ~ helsinki.fi > > On Tue, May 29, 2007 at 09:29:44AM -0400, Chelsey Crosse cmcrosse*_*mtu.edu wrote: > > Yubo, > > > > The only way that I know of to put a ruler in VMD by opening the Tcl > > console and drawing it in yourself. However, I'm not positive about > > how accurate you can make it. > > > > Chelsey > > > > On 25 May 2007, at 10:17, Yubo Fan yubofan(0)mail.chem.tamu.edu wrote: > > > > > Hello, > > > > > > A quick question about VMD. Is there any way to show ruler (ie > > > angstroms in unit) in VMD window? > > > > > > Thanks, > > > > > > Yubo > > > ============================================================ > > > Dr. Yubo Fan Email: yubofan^^^mail.chem.tamu.edu > > > Department of Chemistry Tel: 1-979-845-5237 > > > Texas A&M University > > > College Station, TX 77843 > > > ============================================================ > > > > > > > -- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns[A]ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 --gKMricLos+KVdGMg Content-Type: text/plain Content-Disposition: attachment; filename="ruler.tcl" Content-Transfer-Encoding: quoted-printable # Overlays=0A# Author: Jordi Cohen=0A#=0A# For now, implements a grid overl= ay=0A=0A=0Anamespace eval ::Overlays:: {=0A set grid_on 0=0A set grid_dir= ty 1 ;# ruler needs a refresh=0A set grid_scale 0=0A set grid_scale_grap= hics_id -1=0A set grid_mol -1=0A}=0A=0A=0Aproc ::Overlays::setup_grid {} {= =0A variable grid_mol=0A variable grid_on=0A variable grid_dirty=0A = =0A set top [molinfo top]=0A set grid_mol [mol new]=0A mol rename $grid_= mol "Grid"=0A if {$top >=3D 0} {=0A mol top $top=0A molinfo $grid_mo= l set scale_matrix [molinfo $top get scale_matrix] =0A }=0A redraw_grid= =0A =0A trace add variable ::vmd_logfile write ::Overlays::logfile_cb=0A = =0A set grid_on 1=0A set grid_dirty 1=0A}=0A=0A=0Aproc ::Overlays::rem= ove_grid {} {=0A variable grid_mol=0A variable grid_on=0A =0A trace rem= ove variable ::vmd_logfile write ::Overlays::logfile_cb=0A=0A mol delete $= grid_mol=0A set grid_on 0=0A}=0A=0A=0Aproc ::Overlays::redraw_grid {} {=0A= variable grid_mol=0A variable grid_on=0A variable grid_scale=0A variab= le grid_dirty=0A variable grid_scale_graphics_id=0A =0A molinfo $grid_mo= l set center_matrix [list [transidentity]]=0A molinfo $grid_mol set rotate= _matrix [list [transidentity]]=0A molinfo $grid_mol set global_matrix [lis= t [transidentity]]=0A =0A set realscale [lindex [molinfo $grid_mol get sc= ale_matrix] 0 0 0]=0A set scale [expr round(-log10($realscale))-1]=0A if = {$scale !=3D $grid_scale} {set grid_dirty 1}=0A set display_ratio [expr 1.= *[lindex [display get size] 0]/[lindex [display get size] 1]]=0A set div [= expr pow(10,$scale)]=0A =0A if {$grid_dirty} {=0A set grid_scale $sc= ale=0A =0A set minx [expr -200*$div]=0A set maxx [expr 200*$div]= =0A set miny [expr -50*$div]=0A set maxy [expr 50*$div]=0A =0A = graphics $grid_mol delete all=0A =0A graphics $grid_mol color gray=0A = # draw material Transparent=0A for {set tick $minx} {$tick <=3D $maxx}= {set tick [expr $tick + $div]} {=0A graphics $grid_mol line [list $t= ick $miny 0] [list $tick $maxy 0] width 1 style dashed=0A }=0A for {s= et tick $miny} {$tick <=3D $maxy} {set tick [expr $tick + $div]} {=0A = graphics $grid_mol line [list $minx $tick 0] [list $maxx $tick 0] width 1 = style dashed=0A }=0A =0A draw color gray=0A# draw material Opaque= =0A for {set tick $minx} {$tick <=3D $maxx} {set tick [expr $tick + 10.*= $div]} {=0A graphics $grid_mol line [list [expr $tick] $miny 0] [list = [expr $tick] $maxy 0] width 2=0A }=0A for {set tick $miny} {$tick <= =3D $maxy} {set tick [expr $tick + 10.*$div]} {=0A graphics $grid_mol = line [list $minx $tick 0] [list $maxx $tick 0] width 2=0A }=0A=0A = =0A set grid_scale_graphics_id [graphics $grid_mol text [list [expr 1.2*= $display_ratio/$realscale] [expr -1.4/$realscale] 0] "[format "%g" $div]A" = size 0.8]=0A =0A set grid_dirty 0=0A } else {=0A graphics $gr= id_mol delete $grid_scale_graphics_id=0A set grid_scale_graphics_id [gra= phics $grid_mol text [list [expr 1.2*$display_ratio/$realscale] [expr -1.4/= $realscale] 0] "[format "%g" $div]A" size 0.8]=0A }=0A}=0A=0A=0Aproc ::Ove= rlays::logfile_cb { args } {=0A variable grid_mol=0A =0A # Check for dis= play transforms=0A if { [string match "rotate*" $::vmd_logfile] || [string= match "translate*" $::vmd_logfile] || \=0A [string match "scale= *" $::vmd_logfile] || [string match "display*" $::vmd_logfile]} { =0A = redraw_grid=0A } =0A}=0A=0A=0A=0Aproc ::Overlays::overlay {args} {=0A v= ariable grid_mol=0A variable grid_on=0A =0A set overlay [lindex $args 0]= =0A set state [string is true [lindex $args 1]]=0A =0A if {"$overlay" = =3D=3D "grid"} {=0A if {$state} {=0A if {$grid_on} {remove_grid}=0A= setup_grid=0A } else {=0A if {$grid_on} {remove_grid}=0A }= =0A } else {=0A puts "overlay: Unknown overlay"=0A }=0A}=0A=0A=0Aproc = overlay {args} {=0A eval ::Overlays::overlay $args=0A}=0A=0A=0A=0Aoverlay = grid on=0A --gKMricLos+KVdGMg-- From owner-chemistry@ccl.net Sat Jun 2 09:55:00 2007 From: "Grigoriy Zhurko reg_zhurko(!)chemcraftprog.com" To: CCL Subject: CCL: Gaussian/PCM/chemical shifts Message-Id: <-34401-070602092128-23467-vb35gPsDzJ+Zl+OEsVKPVg .. server.ccl.net> X-Original-From: Grigoriy Zhurko Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Sat, 2 Jun 2007 17:20:46 -0700 MIME-Version: 1.0 Sent to CCL by: Grigoriy Zhurko [reg_zhurko]*[chemcraftprog.com] This problem is interesting for me too. I have found that computed gas-phase 13C chemical shifts (GIAO B3LYP/6-311G(D,P)) correlate very well with the experiment (in CCl4), but the computed values of chemical shifts are significantly overestimated. Maybe the problem is in the reference value for converting isotropic shielding into chemical shifts (e.g. with TMS). What value of the TMS shielding on carbon should be used? > Sent to CCL by: "David Santos Carballal" [spectrum_dav]![operamail.com] > Dear CCL'rs: > I want to estimate the solvent effect on shielding constants. > I calculated shielding constants with DFT/PCM using optimized > structures with DFT/PCM. However, the calculated shielding constants > don't agree to experimental chemical shifts. > I repeated the calculation of shielding constants (without PCM) using > the same optimized structures (with DFT/PCM). This time, the > calculated chemical shifts agree to experimental data. > Is the correct methodology to estimate the solvent effect on > shielding constants: > -to optimize geometry and to calculate shielding constants using > DFT/PCM on both, or > -to optimize geometry using DFT/PCM and to calculate shielding > constants using DFT (without PCM)? > Any suggest about the correct procedure to estimate the solvent > effect on shielding constants will be appreciated. > David Santos Grigoriy Zhurko. From owner-chemistry@ccl.net Sat Jun 2 12:08:00 2007 From: "Marc Baaden baaden{=}smplinux.de" To: CCL Subject: CCL: Gaussian/PCM/chemical shifts Message-Id: <-34402-070602115931-25552-pLqRcnHTSUQpYoTFrPWzfg:+:server.ccl.net> X-Original-From: Marc Baaden Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Sat, 02 Jun 2007 17:08:09 +0200 Mime-Version: 1.0 Sent to CCL by: Marc Baaden [baaden[]smplinux.de] Dear Grigoriy Zhurko, in [1] we discuss the importance of the TMS 13C reference values. Please find a paragraph which might be relevant to your message cited below: [..] Particular attention should be paid to the case of TMS. For this reference compound in proton and carbon-13 NMR, two structures of Td symmetry exist, as illustrated in ¨gure 1. The one in ¨gure 1 (a) is the global minimum, and the structure of ¨gure 1 (b) is a fourth-order saddle point. The energy of the global minimum (¨gure 1 (a)) , taken from the B3LYP calcula- tion, is 27. 3 kJ molÁ1 lower than the one for structure (b). The corresponding absolute shielding value for 13 C is 200.3 ppm. We chose this value as the reference chemi- cal shift as it corresponds to a true minimum structure. Cheeseman et al. [49] report a 13 C chemical shielding of 195.1 ppm for TMS, whereas our calculation for the non-minimum structure of ¨gure 1 (b) reproduced a value of 195.4 ppm. [..] There is a little more discussion in the paper. Regards, Marc Baaden [1] M. Baaden, P. Granger and A. Strich; "Dependence of isotropic shift averages and nuclear shielding tensors on the internal rotation of the functional group X about the C-X bond in seven simple vinylic derivatives H2C=CH-X.", Mol. Phys., 98, 2000, 329-342. >>> "Grigoriy Zhurko reg_zhurko(!)chemcraftprog.com" said: >> >> Sent to CCL by: Grigoriy Zhurko [reg_zhurko]*[chemcraftprog.com] >> This problem is interesting for me too. I have found that computed gas-ph ase 13C chemical shifts (GIAO B3LYP/6-311G(D,P)) correlate very well with the experiment (in CCl4), but the computed values of chemical shifts are s ignificantly overestimated. Maybe the problem is in the reference value fo r converting isotropic shielding into chemical shifts (e.g. with TMS). Wha t value of the TMS shielding on carbon should be used? -- 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 From owner-chemistry@ccl.net Sat Jun 2 13:28:00 2007 From: "Tanja van Mourik tanja.vanmourik[a]st-andrews.ac.uk" To: CCL Subject: CCL: Gaussian/PCM/chemical shifts Message-Id: <-34403-070602132314-23646-om6U+3TMoL0jyI7yPy4jfg(a)server.ccl.net> X-Original-From: Tanja van Mourik Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 2 Jun 2007 17:53:04 +0100 MIME-Version: 1.0 Sent to CCL by: Tanja van Mourik [tanja.vanmourik^st-andrews.ac.uk] Hi All, I would like to reconfirm Chris' remark that specific interactions with water molecules (not included in continuum solvation models) can be important in certain cases. We found recently that explicit waters are needed to obtain good agreement with experiment for the amino 1H chemical shift in guanine. Interaction with just one or two water molecules increased the chemical shift > from 3.3 to 6.1/7.3 ppm, whereas PCM increased the value to only 4.1 ppm, see J. Chem. Phys. (Communication), 125, 191101 (2006). Tanja -- ================================================================= Tanja van Mourik Royal Society University Research Fellow School of Chemistry, University of St. Andrews North Haugh, St. Andrews Fife KY16 9ST, Scotland (UK) email: tanja.vanmourik _ st-andrews.ac.uk web: http://chemistry.st-and.ac.uk/staffmember.php?id=tvm ================================================================= > In Wiitala et al., JCTC 2 (2006) 1085, for a test set of 43 molecules > with 141 and 255 unique 13C and 1H chemical shifts, it was found that > mean unsigned errors for 13C shifts were 3.3, 3.2, and 3.1 ppm for > gas//gas, solvated//gas, and solvated//solvated calculations with a > good functional/basis set (where "gas" or "solvated" before the > double solidus refers to the density, and after refers to the > geometry optimization). For 1H the corresponding MUEs were 0.14, > 0.14, and 0.10 ppm. Thus, continuum chloroform solvation (the method > used here) had relatively little impact. > > However, the test set molecules were relatively rigid. It is possible > that a molecule having one or more very floppy degrees of freedom > might have a sufficiently different solvated structured compared to > the gas phase that larger effects might be seen. In addition, > specific interactions with first-shell solvent molecules (not present > by default in a continuum treatment) can be important (see, for > instance, Klein et al. JPC A 108 (2004) 5851). > > The observation that gas-phase chemical shifts computed at solvated > geometries seem to agree better than solvated shifts at solvated > geometries would seem to me a random manifestation of the many > possible errors in the model (one-particle basis set size, > functional, continuum approximation, etc.) and by no means > representative of a preferred protocol. > > Chris > > On Jun 1, 2007, at 10:05 AM, David Santos Carballal spectrum_dav_- > _operamail.com wrote: > > > > > Sent to CCL by: "David Santos Carballal" [spectrum_dav]! > > [operamail.com] > > Dear CCL'rs: > > I want to estimate the solvent effect on shielding constants. > > I calculated shielding constants with DFT/PCM using optimized > > structures with DFT/PCM. However, the calculated shielding constants > > don't agree to experimental chemical shifts. > > > > I repeated the calculation of shielding constants (without PCM) using > > the same optimized structures (with DFT/PCM). This time, the > > calculated chemical shifts agree to experimental data. > > > > Is the correct methodology to estimate the solvent effect on > > shielding constants: > > -to optimize geometry and to calculate shielding constants using > > DFT/PCM on both, or > > -to optimize geometry using DFT/PCM and to calculate shielding > > constants using DFT (without PCM)? > > > > Any suggest about the correct procedure to estimate the solvent > > effect on shielding constants will be appreciated. > > David Santos > > > > -- > > _______________________________________________ > > Surf the Web in a faster, safer and easier way: > > Download Opera 9 at http://www.opera.com > > > > Powered by Outblaze > > > > > > > > -= 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)> > > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > > +-+-+ > > > > > > > > -- > > Christopher J. Cramer > University of Minnesota > Department of Chemistry > 207 Pleasant St. SE > Minneapolis, MN 55455-0431 > -------------------------- > Phone: (612) 624-0859 || FAX: (612) 626-2006 > Mobile: (952) 297-2575 > cramer!^!pollux.chem.umn.edu > http://pollux.chem.umn.edu/~cramer > (website includes information about the textbook "Essentials > of Computational Chemistry: Theories and Models, 2nd Edition") > > ------------------------------------------------------------------ University of St Andrews Webmail: https://webmail.st-andrews.ac.uk