From owner-chemistry@ccl.net Fri Sep 22 05:51:02 2006 From: "Irilenia Nobeli irilenia.nobeli[*]kcl.ac.uk" To: CCL Subject: CCL: Contour Plot Program for Intel Macs Message-Id: <-32595-060922054843-24936-Q0/ba8ktyANAsLcovOkC6g . server.ccl.net> X-Original-From: Irilenia Nobeli Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Fri, 22 Sep 2006 09:45:30 +0100 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Irilenia Nobeli [irilenia.nobeli=kcl.ac.uk] Dear Ben, R should do the job. Does all sorts of complex plots and it's great for statistics. It's free and there is a version for Mac OSX. If you want a quick solution for a single plot, it may not be ideal as there is a learning curve, but once you start using it, you 'll never look back! See: http://www.apple.com/downloads/macosx/math_science/rformacosx.html and http://www.r-project.org/ Regards, Irilenia On 21 Sep 2006, at 23:10, Ben Shepler bcshepl]-[emory.edu wrote: > Sent to CCL by: "Ben Shepler" [bcshepl#emory.edu] > I am looking for a program to make contour plots that is compatible > with Mac OSX. In the past we > have used Transform, but it is a classic application and classic is > not supported by the new Intel > machines. > > I've experimented with gnuplot, but the options for customizing the > colors seem pretty limited, as is > the ability to label contours. Perhaps there are some more > advanced gnuplot options that I am not > aware of? > > I've also downloaded a trial version of the commercial program Igor > Pro, and it seems to do okay. Any > Igor users have any opinions. It is quite expensive at ~400 for an > academic license. > > Anyone aware of any other options? > > 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> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > ----------------------------- Irilenia (Irene) Nobeli Randall Division of Cell and Molecular Biophysics New Hunt's House (room 3.14) King's College London, Guy's Campus London, SE1 1UL U.K. irilenia.nobeli,,kcl.ac.uk +44(0)207-8486329 From owner-chemistry@ccl.net Fri Sep 22 07:01:00 2006 From: "Sebastian Rohrer sebastian.rohrer^^mail.uni-wuerzburg.de" To: CCL Subject: CCL: Electrostatic surface OpenEye Vida2 Message-Id: <-32596-060922065807-6737-j9VzQDQ0EKdLnWp51kBV4w###server.ccl.net> X-Original-From: Sebastian Rohrer Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 22 Sep 2006 12:01:16 +0200 MIME-Version: 1.0 Sent to CCL by: Sebastian Rohrer [sebastian.rohrer+/-mail.uni-wuerzburg.de] Hi all, does anyone know what OpenEye Vida2 actually computes, when you click the "Color surface by electrostatics"? Does it calculate Gasteiger partial charges? Thanks a lot, Sebastian From owner-chemistry@ccl.net Fri Sep 22 10:10:01 2006 From: "John Daily john.daily:+:colorado.edu" To: CCL Subject: CCL: Contour Plot Program for Intel Macs Message-Id: <-32597-060921232655-14255-gZJoBjGIGD4icAwnUznqHQ..server.ccl.net> X-Original-From: John Daily Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Thu, 21 Sep 2006 20:41:40 -0600 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: John Daily [john.daily~~colorado.edu] Ben, FYI I use Igor Pro for general purpose plotting. It has a bit of steep learning curve, but is very flexible. John On Sep 21, 2006, at 4:10 PM, Ben Shepler bcshepl]-[emory.edu wrote: > Sent to CCL by: "Ben Shepler" [bcshepl#emory.edu] > I am looking for a program to make contour plots that is compatible > with Mac OSX. In the past we > have used Transform, but it is a classic application and classic is > not supported by the new Intel > machines. > > I've experimented with gnuplot, but the options for customizing the > colors seem pretty limited, as is > the ability to label contours. Perhaps there are some more > advanced gnuplot options that I am not > aware of? > > I've also downloaded a trial version of the commercial program Igor > Pro, and it seems to do okay. Any > Igor users have any opinions. It is quite expensive at ~400 for an > academic license. > > Anyone aware of any other options? > > 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> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > From owner-chemistry@ccl.net Fri Sep 22 10:54:00 2006 From: "Joe Corkery jcorkery|eyesopen.com" To: CCL Subject: CCL: Electrostatic surface OpenEye Vida2 Message-Id: <-32598-060922103026-16793-n27gLqdisGfbGe+aPpAM5Q .. server.ccl.net> X-Original-From: Joe Corkery Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 22 Sep 2006 09:42:22 -0400 MIME-Version: 1.0 Sent to CCL by: Joe Corkery [jcorkery[A]eyesopen.com] Hi Sebastian, VIDA2 does not use Gasteiger charges. When you "Color surface by electrostatics", VIDA first checks to see if the molecule already has partial charges assigned (specified in input file) and if present, it uses those to generate the coloring. If charges are not already assigned, VIDA checks to see if the molecule is a protein. If the molecule is a protein, it assigns specific partial charges to the charged atoms in charged residues. If the molecule is not a protein, VIDA calculates MMFF charges and uses those. I hope that this helps. Joe Corkery OpenEye Scientific Software Sebastian Rohrer sebastian.rohrer^^mail.uni-wuerzburg.de wrote: > Sent to CCL by: Sebastian Rohrer [sebastian.rohrer+/-mail.uni-wuerzburg.de] > Hi all, > > does anyone know what OpenEye Vida2 actually computes, when you click > the "Color surface by electrostatics"? Does it calculate Gasteiger > partial charges? > > Thanks a lot, > > Sebastian> > > From owner-chemistry@ccl.net Fri Sep 22 13:35:00 2006 From: "Vasileios Tatsis btatsis^^^gmail.com" To: CCL Subject: CCL: QM/MD (TINKER + GAMESS) Message-Id: <-32599-060922132535-29316-K8TqRzRDkxFz0ZdCcmUZDw-*-server.ccl.net> X-Original-From: "Vasileios Tatsis" Date: Fri, 22 Sep 2006 13:25:34 -0400 Sent to CCL by: "Vasileios Tatsis" [btatsis_._gmail.com] Greetings to all CCL subscribers I am looking for a way to do a classical Molecular Dynamics simulation of a hexapeptide (using TINKER) combined with AM1 (GAMESS). I know that there is the GAMESS-TINKER combination, but it seems that it does not allow to compute trajectories (also the version of Tinker used seems to be a bit old). Anyone knows a (short???) path to accomplish this? Additional programming accepted. Thank in advance Vasilis From owner-chemistry@ccl.net Fri Sep 22 14:42:00 2006 From: "Matthew Sundling sundlm###rpi.edu" To: CCL Subject: CCL: Contour Plot Program for Intel Macs Message-Id: <-32600-060922124744-21833-ilYqxCjbMssYN98V+gFv8w-$-server.ccl.net> X-Original-From: Matthew Sundling Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Fri, 22 Sep 2006 11:40:33 -0400 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Matthew Sundling [sundlm#%#rpi.edu] I've been using R (http://www.r-project.org/) to make high quality contour plots for a while. And it's free! Using the script below, and starting with a datafile "data_file.txt", which should be a comma separated file with three columns (x, y, z), it will generate a pdf file with your contour plot. R offers a variety of data reformatting procedures, as well as density estimation routines, which can take your raw x,y data, and formulate the contours to reveal the distribution of your x,y data. Look at the command 'kde2d' for contour estimation from raw data. Hope this helps, Matt S. --SNIP-- # load libraries require("MASS"); require("lattice"); require("grid"); # read data file V <- read.table("data_file.txt", colClasses="numeric", sep=",", header=TRUE); x <- V[,1]; y <- V[,2]; z <- V[,3]; # generate dd dd <- list(); dd\$x <- unique(x); x_len = length(dd\$x); dd\$y <- unique(y); y_len = length(dd\$y); dd\$z <- matrix(nrow=x_len, ncol=y_len); for (i in 0:x_len-1) dd\$z[i+1,] <- z[(i*y_len+1):((i+1)*y_len)]; # open pdf 'device' to accept plot commands pdf(file="file.pdf", w=8.5, h=8.5); # inches # configure plot region par(bg="white", fg="black", col="black", col.axis="black", col.lab="black", col.main="black", col.sub="black", lwd=3, cex.main=2.5, cex.axis=2, cex.lab=2.5, plt=c(0.16, 0.95, 0.1, 0.9)); # plot axis, labels, titles plot(x=0:1, y=0:1, type="n", main="TITLE", xlab="X", ylab="Y"); # add contour contour(dd, add=T, nlevels=10, drawlabels = TRUE, lwd="3", col="red"); # Close pdf dev.off() --SNIP-- >> Sent to CCL by: "Ben Shepler" [bcshepl#emory.edu] >> I am looking for a program to make contour plots that is compatible >> with Mac OSX. In the past we >> have used Transform, but it is a classic application and classic is >> not supported by the new Intel >> machines. >> >> I've experimented with gnuplot, but the options for customizing the >> colors seem pretty limited, as is >> the ability to label contours. Perhaps there are some more >> advanced gnuplot options that I am not >> aware of? >> >> I've also downloaded a trial version of the commercial program Igor >> Pro, and it seems to do okay. Any >> Igor users have any opinions. It is quite expensive at ~400 for an >> academic license. >> >> Anyone aware of any other options? >> >> Thank you in advance. From owner-chemistry@ccl.net Fri Sep 22 15:24:01 2006 From: "MARY O CONNOR MOCONNOR{=}mail2.wlsc.edu" To: CCL Subject: CCL: Silica (alpha quartz) configuration Message-Id: <-32601-060922140204-17414-Ysv47WrohPHMPL/DABJRsg]|[server.ccl.net> X-Original-From: "MARY O'CONNOR" Content-Type: text/plain; charset=us-ascii Date: Fri, 22 Sep 2006 13:03:39 -0400 Mime-Version: 1.0 Sent to CCL by: "MARY O'CONNOR" [MOCONNOR-.-mail2.wlsc.edu] Materials Studio is a software package designed for crystal modelling. I believe the package contains already generated structures of quartzes.In Reviews in Mineralogy and Geochemistry Vol 42 Molecular modeling Theory:Applications in the Geosciences, there is a chapter on various studies on glasses.(Published by the Mineralogical Society of America). I hope this was useful. Regards, Mary M.V. O'Connor, Ph.D. West Liberty State College 139 Campus Service Center West Liberty, WV 26074 Office : (304) 336 - 8394 ---------- Original Message ---------------------------------- > From: "Parveen Sachdeva pksiit]![gmail.com" Reply-To: "CCL Subscribers" Date: Thu, 21 Sep 2006 21:52:53 -0400 >Sent to CCL by: "Parveen Sachdeva" [pksiit+*+gmail.com] >Hi Everybody, > >I want to generate various configurations of SiO2 (alpha quartz) for molecular dynamics study. I was trying to find some literature online but did not manage much. If anyone can help me suggest some method of generating lattice structures or some software that does that it would be great help. > >I want to generates coordinates of SiO2 as nx,ny,nz number of unit cells in each direction. I hope I'm able to explain what I am trying to do here. > >thanks for the help in advance. >Parveen> > > > ________________________________________________________________ Sent via the WebMail system at mail2.wlsc.edu