From: Robert H. <ha...@st...> - 2011-02-09 14:11:24
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I'll need that file. ha...@st... On Mon, Feb 7, 2011 at 3:54 PM, Oliver Stueker < rev...@us...> wrote: > Hi Bob, Nico, > > Thanks for the fast response but unfortunately that doesn't fix it for me. > (No need to rush this - it's early enough to fix it after you have > returned back to home. I still can use 12.0.28 in the mean time) > > I'm using Jmol to inspect PDB files that were produced by Gromacs > which unfortunately are missing the element in Col 77-78 and Jmol just > can't guess the element for certain atoms from the name (and thus > assigns Xx). > > That's why I want to correct the element for hundreds or thousands of > atoms batch-wise with a script by their atom-name. e.g.: > > {*.?H??}.element=1 ; # fails > {*.?H??}.element="H" ; # fails > > What 12.0.31 (and 12.1.34) does different to 12.0.30 is that now at > least the element of the first atom is assigned, but the others still > remain Dummies (Xx). > > One more thing: > I have a PDB file with an embedded Jmol-script; say: > ... > REMARK jmolscript: select *.?H?? ; cpk on ; > ... > > If I load that PDB file from within the Application via the GUI or by > script: ' load "test.pdb"; ', > this embedded script is executed. > > But if I fire up jmol from the console and load up the PDB at the same > time: > > stuekero@ubuntu:~ $ jmol test.pdb # jmol being > the the "jmol" shell script from the *-binary.tar.gz distribution > > the PDB file gets loaded but the script is not executed. Instead I see > the attached output. > (note that the script is printed as a comment in the line after "The > Resolver thinks Pdb" > > Is this behaviour intended? (If yes: why?) > > I was able to track this back to jmol-12.0.11 (which is the oldest > version I still have on this machine > > Thanks, > > Oliver > > > ------------------------------8><--------------------snipp--------------------><8------------------------------ > stuekero@ubuntu:~ $ jmol test.pdb > > splash_image=jar:file:/home/stuekero/local/jmol/jmol-12.0.31/Jmol.jar!/org/openscience/jmol/app/images/Jmol_splash.jpg > history file is /home/stuekero/.jmol/history > 1714 script command tokens > (C) 2009 Jmol Development > Jmol Version: 12.0.31 2011-02-04 14:47 > java.vendor: Sun Microsystems Inc. > java.version: 1.6.0_22 > os.name: Linux > memory: 45.7/514.5 > processors available: 16 > useCommandThread: false > JmolConsole is initializing > User macros dir: /home/stuekero/.jmol/macros > exists: true > isDirectory: true > > FileManager.getAtomSetCollectionFromFile(test.pdb) > FileManager opening /home/stuekero/test.pdb > The Resolver thinks Pdb > #jmolScript: select *.?H?? ; cpk on ; > Setting space group name to P 1 > openFile(test.pdb): 135 ms > reading 14378 atoms > ModelSet: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false > 1 model in this collection. Use getProperty "modelInfo" or getProperty > "auxiliaryInfo" to inspect them. > Default Van der Waals type for model set to Babel > Time to autoBond: 117 ms > ModelSet: autobonding; use autobond=false to not generate bonds > automatically > > ------------------------------8><--------------------snipp--------------------><8------------------------------ > > > On Mon, Feb 7, 2011 at 07:21, Robert Hanson <ha...@st...> wrote: > > Great, thanks. > > > > On Mon, Feb 7, 2011 at 7:12 AM, Nicolas Vervelle <nve...@gm...> > > wrote: > >> > >> I should be able to do the release, hotel internet access seems correct. > >> Nico > >> > >> On Mon, Feb 7, 2011 at 2:10 PM, Robert Hanson <ha...@st...> > wrote: > >>> > >>> thanks -- that's fixed. Not sure how that got lost. It's fixed in > 12.1.34 > >>> and 12.0.31, which I hope Nico can release later today. > >>> > >>> On Fri, Feb 4, 2011 at 4:51 PM, Oliver Stueker > >>> <rev...@us...> wrote: > >>>> > >>>> Hi, > >>>> > >>>> I just noticed that the element assignment via atom properties is > >>>> broken in Jmol 12.0.30: > >>>> > >>>> {*.?H??}.element=1 ; # fails > >>>> {*.?H??}.element="H" ; # fails > >>>> > >>>> while it still works for individual atoms: > >>>> > >>>> {atomno=2734}.element=1 ; # works > >>>> > >>>> In Jmol 12.0.28 it still worked. > >>>> > >>>> > >>>> Oliver > >>>> > >>>> > >>>> > ------------------------------------------------------------------------------ > >>>> The modern datacenter depends on network connectivity to access > >>>> resources > >>>> and provide services. The best practices for maximizing a physical > >>>> server's > >>>> connectivity to a physical network are well understood - see how these > >>>> rules translate into the virtual world? > >>>> http://p.sf.net/sfu/oracle-sfdevnlfb > >>>> _______________________________________________ > >>>> Jmol-users mailing list > >>>> Jmo...@li... > >>>> https://lists.sourceforge.net/lists/listinfo/jmol-users > >>> > >>> > >>> > >>> -- > >>> Robert M. Hanson > >>> Professor of Chemistry > >>> St. Olaf College > >>> 1520 St. Olaf Ave. > >>> Northfield, MN 55057 > >>> http://www.stolaf.edu/people/hansonr > >>> phone: 507-786-3107 > >>> > >>> > >>> If nature does not answer first what we want, > >>> it is better to take what answer we get. > >>> > >>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > >>> > >>> > >>> > ------------------------------------------------------------------------------ > >>> The modern datacenter depends on network connectivity to access > resources > >>> and provide services. The best practices for maximizing a physical > >>> server's > >>> connectivity to a physical network are well understood - see how these > >>> rules translate into the virtual world? > >>> http://p.sf.net/sfu/oracle-sfdevnlfb > >>> _______________________________________________ > >>> Jmol-users mailing list > >>> Jmo...@li... > >>> https://lists.sourceforge.net/lists/listinfo/jmol-users > >>> > >> > >> > >> > >> > ------------------------------------------------------------------------------ > >> The modern datacenter depends on network connectivity to access > resources > >> and provide services. The best practices for maximizing a physical > >> server's > >> connectivity to a physical network are well understood - see how these > >> rules translate into the virtual world? > >> http://p.sf.net/sfu/oracle-sfdevnlfb > >> _______________________________________________ > >> Jmol-users mailing list > >> Jmo...@li... > >> https://lists.sourceforge.net/lists/listinfo/jmol-users > >> > > > > > > > > -- > > Robert M. Hanson > > Professor of Chemistry > > St. Olaf College > > 1520 St. Olaf Ave. > > Northfield, MN 55057 > > http://www.stolaf.edu/people/hansonr > > phone: 507-786-3107 > > > > > > If nature does not answer first what we want, > > it is better to take what answer we get. > > > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > > > ------------------------------------------------------------------------------ > > The modern datacenter depends on network connectivity to access resources > > and provide services. The best practices for maximizing a physical > server's > > connectivity to a physical network are well understood - see how these > > rules translate into the virtual world? > > http://p.sf.net/sfu/oracle-sfdevnlfb > > _______________________________________________ > > Jmol-users mailing list > > Jmo...@li... > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > > > ------------------------------------------------------------------------------ > The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: > Pinpoint memory and threading errors before they happen. > Find and fix more than 250 security defects in the development cycle. > Locate bottlenecks in serial and parallel code that limit performance. > http://p.sf.net/sfu/intel-dev2devfeb > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |