I just thought that there wasn't much discussion on molecular modelling of biological compounds. This seemed kind of strange to me; but since I'm a novice in this arena, I was just sitting around watching for a while. I have now subscribe to the JMOL uses list to hopefully learn a bit more about this field and what is going on with molecular modelling. --- molvis-list-request at bioinformatics.org wrote: > Send Molvis-list mailing list submissions to > molvis-list at bioinformatics.org > > To subscribe or unsubscribe via the World Wide Web, > visit > > https://bioinformatics.org/mailman/listinfo/molvis-list > or, via email, send a message with subject or body > 'help' to > molvis-list-request at bioinformatics.org > > You can reach the person managing the list at > molvis-list-owner at bioinformatics.org > > When replying, please edit your Subject line so it > is more specific > than "Re: Contents of Molvis-list digest..." > > > Today's Topics: > > 1. Recent MolVis articles in BAMBEd (Eric Martz) > 2. Drop in use of this list (Eric Martz) > 3. Re: Drop in use of this list (Dan Bolser) > 4. Re: Drop in use of this list (Timothy > Driscoll) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 06 Sep 2006 17:34:20 -0400 > From: Eric Martz <emartz at microbio.umass.edu> > Subject: [Molvis-list] Recent MolVis articles in > BAMBEd > To: molvis-list at bioinformatics.org > Cc: jvoet1 at swarthmore.edu, hardy at chem.umass.edu, > voet at sas.upenn.edu, > garman at biochem.umass.edu, theis at biochem.umass.edu > Message-ID: > <5.2.0.9.2.20060906170131.02ee5ec0 at marlin.bio.umass.edu> > Content-Type: text/plain; charset="us-ascii"; > format=flowed > > The journal "Biochemical and Molecular Biology > Education" (BAMBEd, > http://www.bambed.org/ www required) continues to > grow and thrive under the > editorship of Don and Judy Voet. > > The May/June issue includes "A new three-dimensional > educational model kit > for building DNA and RNA molecules: development and > evaluation", which > describes injection-molded plastic models with > attention to pedagogically > important detail. The authors are in Brazil and I > found no mention of > whether their models are available for purchase. > > The July/August issue contains three articles > relevant to MolVis. > > Tim Herman and others contribute "Tactile teaching, > exploring protein > structure/function using physical models". They make > a compelling case for > the impact of physical models in learning. They have > led exciting model > designing collaborations between educators/students > and researchers > reporting cutting edge molecular structures. They > have initiated impressive > model-building challenges for the Science Olympiad > competition. A cut-away > spacefilled model of the active site of > acetylcholinesterase combats the > mis-impression (from ball and stick models) that > "proteins are made mostly > of air". Models can be borrowed by educators from > their lending library > (http://www.rpc.msoe.edu/cbm/lib/). > > Angel Herraez contributes "Biomolecules in the > computer: Jmol to the > rescue", introducing Jmol and arguing effectively > for the ability of the > Jmol java applet to replace Chime, avoiding many of > the problematic issues > with Chime. This is a meaty and scholarly article, > amply illustrated, and > including a short glossary. > > Finally, I personally enjoyed Howard Dintzis' "The > wandering pathway to > determining N to C synthesis of proteins - Some > recollections concerning > protein structure and biosynthesis". As a student, > he was taught that the > function of DNA is to maintain osmotic balance in > the nucleus. His > descriptions of rubbing elbows with Max Perutz, John > Kendrew, and Francis > Crick are fascinating, including early searches for > mutant human proteins > (culminating in sickle cell hemoglobin). In 1954, > they were calculating a > Patterson maps for heavy metal derivitives of > myoglobin and hemoglobin on > the vacuum-tube (valve) EDSAC 1, the most powerful > digital computer of the > day. Its 1 kilobyte dynamic memory utilized an iron > pipe filled with > mercury, in which sound waves traveling between a > speaker and a microphone > encoded the data! > > -Eric > > ---- > Eric Martz, Professor Emeritus, Dept Microbiology > University of Massachusetts, Amherst MA US > http://www.umass.edu/molvis/martz > > > > ------------------------------ > > Message: 2 > Date: Wed, 06 Sep 2006 20:21:13 -0400 > From: Eric Martz <emartz at microbio.umass.edu> > Subject: [Molvis-list] Drop in use of this list > To: molvis-list at bioinformatics.org > Cc: jeff at bioinformatics.org > Message-ID: > <5.2.0.9.2.20060906200024.02488010 at marlin.bio.umass.edu> > Content-Type: text/plain; charset="us-ascii"; > format=flowed > > Dear MolVis-List Subscribers, > > During 1996-2004, this list averaged 1.15 > messages/day (420/year, range > 352-526). There was no trend in traffic despite the > fact that in the first > few years, there were less than half as many > subscribers. > > Last year, the traffic dropped to 1/3 of the > previous level (132 in 2005, > 0.36/day). In the first half of 2006, there were 89 > messages (about 0.5 > messages/day). > > The number of subscribers plateaued at about 600 > from 2001 through 2004, > but has now grown to 740. > > I suspect that the dizzying level of traffic on the > jmol-users list, and > the well-justified excitement about Jmol, has > diverted some traffic from > molvis-list. I myself am working more and more with > Jmol. > > Of course, modest traffic is not necessarily bad, > especially if the quality > of, and interest in message content is high. > > As a reminder, quoting from our website > (http://bioinformatics.org/mailman/listinfo/molvis-list): > > "Molvis-list is for discussion of molecular > visualization software, > especially free software and its uses in education, > such as MDL Chime, > Protein Explorer, and RasMol, among many. Technical > questions, "How do I > ...", comparisons between software packages, or > questions about pros and > cons, are welcome. Discussions may include molvis > packages that have their > own dedicated email lists, such as Jmol or DeepView, > although technical > questions about those packages should be sent to > their dedicated lists. > Discussions may also include commercial molvis > software packages. > > Subscribers with commercial affiliations are > welcome. Advertising is > prohibited, but occasional, brief, low-key > announcements of commercial > products of interest to the subscribership are > welcome, as are > announcements of relevant meetings, positions > available or sought." > > Feel free to use this list! Ideas to increase the > usefulness of this list > are welcome! > > I'd like to extend my heartfelt appreciation to Tim > Driscoll, who has > kindly taken over the day to day maintenance of this > list on a volunteer > basis for the past couple of years. His work > consists mostly of deleting > spam, thereby sparing us from all receiving it -- so > I'm sure you > appreciate him too! > > -Eric (who founded this list in 1995) > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - > - - > Eric Martz, Professor Emeritus, Dept Microbiology > U Mass, Amherst -- http://www.umass.edu/molvis/martz > > Biochem 3D Education Resources http://MolviZ.org > See 3D Molecules, Install Nothing! - > http://firstglance.jmol.org > Protein Explorer - 3D Visualization: > http://proteinexplorer.org > Workshops: http://workshops.proteinexplorer.org > World Index of Molecular Visualization Resources: > http://molvisindex.org > ConSurf - Find Conserved Patches in Proteins: > http://consurf.tau.ac.il > Atlas of Macromolecules: > http://atlas.proteinexplorer.org > PDB Lite Macromolecule Finder: http://pdblite.org > Molecular Visualization EMail List (molvis-list): > > http://bioinformatics.org/mailman/listinfo/molvis-list > - - - - - - - - - - - - - - - - - - - - - - - - - - > - */ > > > > ------------------------------ > > Message: 3 > Date: Thu, 07 Sep 2006 15:58:58 +0100 > From: Dan Bolser <dmb at mrc-dunn.cam.ac.uk> > Subject: Re: [Molvis-list] Drop in use of this list > To: "Molecular Visualization, especially in > education with freeware" > <molvis-list at bioinformatics.org> > Message-ID: <450033B2.5000302 at mrc-dunn.cam.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1; > format=flowed > > Eric Martz wrote: > > Dear MolVis-List Subscribers, > > > > During 1996-2004, this list averaged 1.15 > messages/day (420/year, range > > 352-526). There was no trend in traffic despite > the fact that in the > > first few years, there were less than half as many > subscribers. > > > > Last year, the traffic dropped to 1/3 of the > previous level (132 in > > 2005, 0.36/day). In the first half of 2006, there > were 89 messages > > (about 0.5 messages/day). > > > > The number of subscribers plateaued at about 600 > from 2001 through 2004, > > but has now grown to 740. > > > > I suspect that the dizzying level of traffic on > the jmol-users list, and > > the well-justified excitement about Jmol, has > diverted some traffic from > > molvis-list. I myself am working more and more > with Jmol. > > > > Of course, modest traffic is not necessarily bad, > especially if the > > quality of, and interest in message content is > high. > > > > As a reminder, quoting from our website > > > (http://bioinformatics.org/mailman/listinfo/molvis-list): > > > > "Molvis-list is for discussion of molecular > visualization software, > > especially free software and its uses in > education, such as MDL Chime, > > Protein Explorer, and RasMol, among many. > Technical questions, "How do I > > ...", comparisons between software packages, or > questions about pros and > > cons, are welcome. Discussions may include molvis > packages that have > > their own dedicated email lists, such as Jmol or > DeepView, although > > technical questions about those packages should be > sent to their > > dedicated lists. Discussions may also include > commercial molvis software > > packages. > > > > Subscribers with commercial affiliations are > welcome. Advertising is > > prohibited, but occasional, brief, low-key > announcements of commercial > > products of interest to the subscribership are > welcome, as are > > announcements of relevant meetings, positions > available or sought." > > > > Feel free to use this list! Ideas to increase the > usefulness of this > > list are welcome! > > > > I'd like to extend my heartfelt appreciation to > Tim Driscoll, who has > > kindly taken over the day to day maintenance of > this list on a volunteer > > basis for the past couple of years. His work > consists mostly of deleting > > spam, thereby sparing us from all receiving it -- > so I'm sure you > > appreciate him too! > > How much spam gets through the members list? (Or is > this an 'anyone can > post' list?) > > > > I wonder if anyone can tell me how to select only > the 'aligned' residues > in pymol after running the 'align x, y' command? > > I see that atoms (and distinct residues?) are > rejected during the > alignment, but how can I 'see' them? > > Cheers, > > Dan. > > > > > -Eric (who founded this list in 1995) > > > > > > /* - - - - - - - - - - - - - - - - - - - - - - - - > - - - > > Eric Martz, Professor Emeritus, Dept Microbiology > > U Mass, Amherst -- > http://www.umass.edu/molvis/martz > > > > Biochem 3D Education Resources http://MolviZ.org > > See 3D Molecules, Install Nothing! - > http://firstglance.jmol.org > > Protein Explorer - 3D Visualization: > http://proteinexplorer.org > > Workshops: http://workshops.proteinexplorer.org > > World Index of Molecular Visualization Resources: > http://molvisindex.org > > ConSurf - Find Conserved Patches in Proteins: > http://consurf.tau.ac.il > > Atlas of Macromolecules: > http://atlas.proteinexplorer.org > > PDB Lite Macromolecule Finder: http://pdblite.org > > Molecular Visualization EMail List (molvis-list): > > > http://bioinformatics.org/mailman/listinfo/molvis-list > > - - - - - - - - - - - - - - - - - - - - - - - - - > - - */ > > > > _______________________________________________ > > Molvis-list mailing list > > Molvis-list at bioinformatics.org > > > https://bioinformatics.org/mailman/listinfo/molvis-list > > > > ------------------------------ > > Message: 4 > Date: Thu, 7 Sep 2006 11:43:07 -0400 > From: Timothy Driscoll <molvisions at mac.com> > Subject: Re: [Molvis-list] Drop in use of this list > To: "Molecular Visualization, especially in > education with freeware" > <molvis-list at bioinformatics.org> > Message-ID: > <3AFF11E7-1450-4110-B4EE-AB092174D72D at mac.com> > Content-Type: text/plain; charset=US-ASCII; > delsp=yes; format=flowed > > On Sep 7, 2006, at 10:58 AM, Dan Bolser wrote: > > > Eric Martz wrote: > >> His work consists mostly of deleting spam, > thereby sparing us > >> from all receiving it -- so I'm sure you > appreciate him too! > > > > How much spam gets through the members list? (Or > is this an 'anyone > > can post' list?) > > > > howdy, > > this list is live-moderated (which means a moderator > must approve > every message before it is broadcast, and every > subscription request > before it is activated). our policy is that only > subscribers are > allowed to post. occasionally, we will allow a > relevant post from a > non-subscriber; however, this is strongly > discouraged because it is > extra work for the moderators. especially since... > > the amount of spam sent to the list has risen > dramatically in the > past few months. fortunately, such messages are > manually identified > and discarded before they hit the list, so nobody is > the wiser > (except the moderators, who like to complain about > that sort of > thing ;-). > > > warm regards, > > tim > -- > Timothy Driscoll em: > molvis at vbi.vt.edu > Virginia Bioinformatics Institute ph: > 540-231-3007 > Bioinformatics I: M-1 im: > molvisions > Washington St., Blacksburg, VA 24061 > > "Anyone who considers arithmetical methods of > producing random digits > is, of course, in a state of sin." - J von Neumann > > > > > > ------------------------------ > > _______________________________________________ > Molvis-list mailing list > Molvis-list at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/molvis-list > > > End of Molvis-list Digest, Vol 23, Issue 1 > ****************************************** > __________________________________________________ Do You Yahoo!? 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