Re: [Jmol-users] electrostatic potential surface coloring
Thank you again, Bob, for your help. The trick is to use Jmol's
calculated values for surface MEP as the defining points for the
coloring scale, and not the partial charges values in the coordinate
file. (Maybe not so much of a trick if I knew what I was doing to
start with!) These values appear in the console when you set
debugscript on, which is very handy Bob!
I have posted a page with a grid for comparing the results of
"... color range all ... " with "... color range [defined] ..."
and
calculating the MEP over the side chain only vs. calculating for the
whole amino acid., i.e., the option including "select {*}" that Bob
outlines below.
http://moleculesinmotion.com/patterson_aas2/aminoacids/index.htm
The isosurface command used is listed above each column, and the data
calculated by Jmol are listed in a table below the applets. I hope
this may be useful to others pondering some of the options for MEP
display.
To me, for teaching about polar and non-polar side chains, calculating
over the side chain alone looks like the way to go, and restricting
the color range creates a very non-polar looking surface for valine,
contrasting with a nice charge level for asp. I am not sure I can
figure out what is going on with valine with 'color range all' and
calculating only over the side chain. (Top row, third column).
I'll be using this to make a page that will enable students to compare
the MEP of any two amino acid side chains and hopefully also
nucleotide bases and a few other small molecules. When it's finished I
will post the URL to the list, hope it may be of interest to some for
teaching purposes.
Best,
Frieda
On Aug 6, 2008, at 2:25 AM, Bob Hanson wrote:
> I think you want
>
> isosurface select {} molecular map select {*} mep
>
> That is, when you run the mep, you want to indicate that for THAT part
> of the calculation, you want all atoms selected. I hadn't realized
> myself that two selects work here -- I suppose it could be useful.
> Or not.
//
Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
413-253-2405
//
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Re: [Jmol-users] bug in "select"
this is corrected for 11.4.7 Sérgio Ceroni da Silva wrote: > Just noticed that 11.4.6 has the old bug where H1, H2 and H3 from DNA > bases are selected as backbone. > Did it resurface or the fix was applied only to 11.5.x ? > >-- >Dr. Sérgio Ceroni da Silva >Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul >Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005 >Porto Alegre, RS - Brasil - 91501-970 >== >Tel.: +55 (51) 3316-6091 | Fax: +55 (51) 3316-7309 >http://www6.ufrgs.br/bioquimica > > > > >- >This SF.Net email is sponsored by the Moblin Your Move Developer's challenge >Build the coolest Linux based applications with Moblin SDK & win great prizes >Grand prize is a trip for two to an Open Source event anywhere in the world >http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > > >___ >Jmol-users mailing list >Jmol-users@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] command echo in console
Could be due to changes I implemented, Karl. If you want to see the commands reflected in the output part (applet, right?) then issue set debugscript Bob Karl Oberholser wrote: > Hi All, > > When I enter a command in the console, it is no longer echoed in the > output section of the console. This started occurring about two days > ago. Any ideas as to what caused this effect? > > Karl > > > > >- >This SF.Net email is sponsored by the Moblin Your Move Developer's challenge >Build the coolest Linux based applications with Moblin SDK & win great prizes >Grand prize is a trip for two to an Open Source event anywhere in the world >http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > > >___ >Jmol-users mailing list >Jmol-users@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Load command and NMR structures
Angel Herraez wrote: >Chris Weichenberger escribió: > > > >> It also seems to be >>inconsistent since the 'load' command asks for consecutive integers >>starting with 1 whereas the 'frame'/'model' command requires the PDB model >>number. >> >> > > >I've checked the doc and it's correct, "frame" and "model" will use >the PDB MODEL number if available. >"In the case of the loading of a single PDB file containing MODEL >records, the integer used here corresponds to the number in that >record." >I guess that for sequential numbers we now have the n.m syntax, that >is, "frame 1.0" will display the first model, irrespective of its >internally-assigned number --or won't it? >No! It's "frame 1.1" > >The key issue is that only pdb files have model numbers, so Jmol is >taking a general solution for "load". > > > Jmol 11.6.RC1 will have a change in the LOAD command such that for PDB files, the number designated is the model number in the MODEL record. Bob > > > >>May I ask the Jmol developers to extend the 'load' command such that it >>can cope with model numbers contained in the PDB file? To assist you, I >>have included pathologic cases I found when scanning our database for this >>problem. >> >> > >That should be some kind of switch or new parameter, maybe? >How about "load model " ? >for backward-compatibility > > > >- >This SF.Net email is sponsored by the Moblin Your Move Developer's challenge >Build the coolest Linux based applications with Moblin SDK & win great prizes >Grand prize is a trip for two to an Open Source event anywhere in the world >http://moblin-contest.org/redirect.php?banner_id=100&url=/ >___ >Jmol-users mailing list >Jmol-users@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] RFC - new look for toolbar
Angel, I think the Jmol icon could be tuned up a bit. (The one with the J and three balls. It looks clunky to me. The rest look great! Nice to have a new look for 11.6. Bob Angel Herráez wrote: >Hi all >After Bob's recent message about implementation of functions for some >toolbar buttons in the Jmol application, today I decided to try a new icon for >the "rotate" function in the toolbar. So, I am renewing some of the toolbar >icons. Before they are updated for good, I will welcome any comments. >A preview is online at http://biomodel.uah.es/Jmol/toolbar/ > > > > > >- >This SF.Net email is sponsored by the Moblin Your Move Developer's challenge >Build the coolest Linux based applications with Moblin SDK & win great prizes >Grand prize is a trip for two to an Open Source event anywhere in the world >http://moblin-contest.org/redirect.php?banner_id=100&url=/ >___ >Jmol-users mailing list >Jmol-users@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
