From: Egon W. <ego...@gm...> - 2007-12-19 10:20:50
|
Mike Miller wrote: ---------- Forwarded message ---------- From: Mike Miller Date: Dec 19, 2007 11:04 AM Subject: Re: access > The question was, I have downloaded jmol, opened the appropriate file, jmol-jar, have the programme running but do not > know where or how to view any molecule what so ever. Any help would be appreciated as I am desparate to use this > system after seeing it at the ECIS conference in Madrid, ---------- End Forwarded message ---------- Egon -- ---- http://chem-bla-ics.blogspot.com/ |
From: Angel H. <ang...@ua...> - 2007-12-19 11:44:04
|
Mike, Once you open Jmol.jar, use the menu at the top of the window: File > Open and search for the molecular file in your local disk. Sorry if this sounds too obvious; please, be more specific if you have any trouble. We'll be happy to help. > From: Mike Miller > Date: Dec 19, 2007 11:04 AM > Subject: Re: access > > > The question was, I have downloaded jmol, opened the appropriate file, jmol-jar, have the programme running but do not > > know where or how to view any molecule what so ever. Any help would be appreciated as I am desparate to use this > > system after seeing it at the ECIS conference in Madrid, |
From: Bob H. <ha...@st...> - 2007-12-19 12:00:25
|
Mike, if you are interested in viewing a file from the PDB, you don't have to have that file on your computer. Just do File > Script... and then in the console type "load =" followed by the 4-digit PDB number: load =1crn That's all there is to it! We should probably make that an Open option. Angel Herraez wrote: >Mike, > >Once you open Jmol.jar, use the menu at the top of the window: >File > Open >and search for the molecular file in your local disk. >Sorry if this sounds too obvious; please, be more specific if you >have any trouble. We'll be happy to help. > > > >>From: Mike Miller >>Date: Dec 19, 2007 11:04 AM >>Subject: Re: access >> >> >> >>>The question was, I have downloaded jmol, opened the appropriate file, jmol-jar, have the programme running but do not >>>know where or how to view any molecule what so ever. Any help would be appreciated as I am desparate to use this >>>system after seeing it at the ECIS conference in Madrid, >>> >>> > > > >------------------------------------------------------------------------- >SF.Net email is sponsored by: >Check out the new SourceForge.net Marketplace. >It's the best place to buy or sell services >for just about anything Open Source. >http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >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 |
From: Mike M. <mi...@as...> - 2007-12-20 12:13:40
|
Hi Angel, I have tried typing in the code you said, but to no avail. I was under the impression that there was a "bank" of models to choose from. Or is it that I have to download a molecule from the internet and run it through jmol, Sorry for bothering you again, Mike -----Original Message----- From: Bob Hanson <ha...@st...> To: jmo...@li... Date: Wed, 19 Dec 2007 06:00:15 -0600 Subject: Re: [Jmol-users] Fwd: cannot view molecules Mike, if you are interested in viewing a file from the PDB, you don't have to have that file on your computer. Just do File > Script... and then in the console type "load =" followed by the 4-digit PDB number: load =1crn That's all there is to it! We should probably make that an Open option. Angel Herraez wrote: >Mike, > >Once you open Jmol.jar, use the menu at the top of the window: >File > Open >and search for the molecular file in your local disk. >Sorry if this sounds too obvious; please, be more specific if you >have any trouble. We'll be happy to help. > > > >>From: Mike Miller >>Date: Dec 19, 2007 11:04 AM >>Subject: Re: access >> >> >> >>>The question was, I have downloaded jmol, opened the appropriate file, jmol-jar, have the programme running but do not >>>know where or how to view any molecule what so ever. Any help would be appreciated as I am desparate to use this >>>system after seeing it at the ECIS conference in Madrid, >>> >>> > > > >------------------------------------------------------------------------- >SF.Net email is sponsored by: >Check out the new SourceForge.net Marketplace. >It's the best place to buy or sell services >for just about anything Open Source. >http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >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 ------------------------------------------------------------------------- SF.Net email is sponsored by: Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace _______________________________________________ Jmol-users mailing list Jmo...@li... https://lists.sourceforge.net/lists/listinfo/jmol-users |
From: Bob H. <ha...@st...> - 2007-12-20 12:26:12
|
Mike, what happens when you type the following command within Jmol within the Jmol scripting console? load =1crn Ah, also, make sure you download the very latest version from sourceForge, 11.3.62: http://sourceforge.net/project/showfiles.php?group_id=23629 If you are interested in just PDB files, there is no need to have any data files on your computer. Bob Mike Miller wrote: > Hi Angel, > I have tried typing in the code you said, but to no avail. I was > under the impression that there was a "bank" of models to choose > from. Or is it that I have to download a molecule from the internet > and run it through jmol, > Sorry for bothering you again, > Mike > > > -----Original Message----- > From: Bob Hanson <ha...@st...> > To: jmo...@li... > Date: Wed, 19 Dec 2007 06:00:15 -0600 > Subject: Re: [Jmol-users] Fwd: cannot view molecules > > Mike, if you are interested in viewing a file from the PDB, you don't > have to have that file on your computer. Just do > > > File > Script... > > and then in the console type "load =" followed by the 4-digit PDB > number: > > load =1crn > > That's all there is to it! > > We should probably make that an Open option. > > > Angel Herraez wrote: > > >Mike, > > > >Once you open Jmol.jar, use the menu at the top of the window: > >File > Open > >and search for the molecular file in your local disk. > >Sorry if this sounds too obvious; please, be more specific if you > >have any trouble. We'll be happy to help. > > > > > > > >>From: Mike Miller > >>Date: Dec 19, 2007 11:04 AM > >>Subject: Re: access > >> > >> > >> > >>>The question was, I have downloaded jmol, opened the > appropriate file, jmol-jar, have the programme running but do not > >>>know where or how to view any molecule what so ever. Any help > would be appreciated as I am desparate to use this > >>>system after seeing it at the ECIS conference in Madrid, > >>> > >>> > > > > > > > >------------------------------------------------------------------------- > >SF.Net email is sponsored by: > >Check out the new SourceForge.net Marketplace. > >It's the best place to buy or sell services > >for just about anything Open Source. > > > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace > > >_______________________________________________ > >Jmol-users mailing list > >Jmo...@li... > > 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 > > > > ------------------------------------------------------------------------- > SF.Net email is sponsored by: > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services > for just about anything Open Source. > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace > > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >SF.Net email is sponsored by: >Check out the new SourceForge.net Marketplace. >It's the best place to buy or sell services >for just about anything Open Source. >http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace > >------------------------------------------------------------------------ > >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >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 |
From: Bob H. <ha...@st...> - 2007-12-20 12:32:31
|
sorry, 11.3.62 is broken. Mike Miller wrote: > Hi Angel, > I have tried typing in the code you said, but to no avail. I was > under the impression that there was a "bank" of models to choose > from. Or is it that I have to download a molecule from the internet > and run it through jmol, > Sorry for bothering you again, > Mike > > > -----Original Message----- > From: Bob Hanson <ha...@st...> > To: jmo...@li... > Date: Wed, 19 Dec 2007 06:00:15 -0600 > Subject: Re: [Jmol-users] Fwd: cannot view molecules > > Mike, if you are interested in viewing a file from the PDB, you don't > have to have that file on your computer. Just do > > > File > Script... > > and then in the console type "load =" followed by the 4-digit PDB > number: > > load =1crn > > That's all there is to it! > > We should probably make that an Open option. > > > Angel Herraez wrote: > > >Mike, > > > >Once you open Jmol.jar, use the menu at the top of the window: > >File > Open > >and search for the molecular file in your local disk. > >Sorry if this sounds too obvious; please, be more specific if you > >have any trouble. We'll be happy to help. > > > > > > > >>From: Mike Miller > >>Date: Dec 19, 2007 11:04 AM > >>Subject: Re: access > >> > >> > >> > >>>The question was, I have downloaded jmol, opened the > appropriate file, jmol-jar, have the programme running but do not > >>>know where or how to view any molecule what so ever. Any help > would be appreciated as I am desparate to use this > >>>system after seeing it at the ECIS conference in Madrid, > >>> > >>> > > > > > > > >------------------------------------------------------------------------- > >SF.Net email is sponsored by: > >Check out the new SourceForge.net Marketplace. > >It's the best place to buy or sell services > >for just about anything Open Source. > > > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace > > >_______________________________________________ > >Jmol-users mailing list > >Jmo...@li... > > 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 > > > > ------------------------------------------------------------------------- > SF.Net email is sponsored by: > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services > for just about anything Open Source. > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace > > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >SF.Net email is sponsored by: >Check out the new SourceForge.net Marketplace. >It's the best place to buy or sell services >for just about anything Open Source. >http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace > >------------------------------------------------------------------------ > >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >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 |
From: Bob H. <ha...@st...> - 2007-12-20 12:46:48
|
I take that back -- it's 11.3.61 that was broken -- 11.3.62 is good. Mike Miller wrote: > Hi Angel, > I have tried typing in the code you said, but to no avail. I was > under the impression that there was a "bank" of models to choose > from. Or is it that I have to download a molecule from the internet > and run it through jmol, > Sorry for bothering you again, > Mike > > > -----Original Message----- > From: Bob Hanson <ha...@st...> > To: jmo...@li... > Date: Wed, 19 Dec 2007 06:00:15 -0600 > Subject: Re: [Jmol-users] Fwd: cannot view molecules > > Mike, if you are interested in viewing a file from the PDB, you don't > have to have that file on your computer. Just do > > > File > Script... > > and then in the console type "load =" followed by the 4-digit PDB > number: > > load =1crn > > That's all there is to it! > > We should probably make that an Open option. > > > Angel Herraez wrote: > > >Mike, > > > >Once you open Jmol.jar, use the menu at the top of the window: > >File > Open > >and search for the molecular file in your local disk. > >Sorry if this sounds too obvious; please, be more specific if you > >have any trouble. We'll be happy to help. > > > > > > > >>From: Mike Miller > >>Date: Dec 19, 2007 11:04 AM > >>Subject: Re: access > >> > >> > >> > >>>The question was, I have downloaded jmol, opened the > appropriate file, jmol-jar, have the programme running but do not > >>>know where or how to view any molecule what so ever. Any help > would be appreciated as I am desparate to use this > >>>system after seeing it at the ECIS conference in Madrid, > >>> > >>> > > > > > > > >------------------------------------------------------------------------- > >SF.Net email is sponsored by: > >Check out the new SourceForge.net Marketplace. > >It's the best place to buy or sell services > >for just about anything Open Source. > > > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace > > >_______________________________________________ > >Jmol-users mailing list > >Jmo...@li... > > 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 > > > > ------------------------------------------------------------------------- > SF.Net email is sponsored by: > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services > for just about anything Open Source. > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace > > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >SF.Net email is sponsored by: >Check out the new SourceForge.net Marketplace. >It's the best place to buy or sell services >for just about anything Open Source. >http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace > >------------------------------------------------------------------------ > >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >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 |
From: Angel H. <ang...@ua...> - 2007-12-20 12:46:21
|
On 20 Dec 2007 at 13:23, Mike Miller wrote: > Hi Angel, > Ihave tried typing in the code you said, but to no avail. Hi Mike So clearly we haven't understood each other; I was not aware of your current state of Jmol proficiency. I understood that you are using the application, so I was not talking about any code, but just using the application top menu, which is the easiest way to start using Jmol. You have several choices: > I was under the impression that there > was a "bank" of models to choose from. There is not, except the PDB database which, as Bob pointed out, can be accessed directly by Jmol -provided there is an internet connection, of course. For that, if you know the 4-character PDB ID, you can type in Jmol console (opened with "File > Script" in the top menu or with "Console" in the pop-up menu): load =yourPDBID (the "=" is singular in the sense that it diirects Jmol to the internet instead of to the hard disk) You can also download the pdb file from the internet (http://pdb.org) and then open from your hard disk as below. > Or is it that I have to download a molecule from the > internet and run it through jmol, That's the usual way. You get the molecule from any database or web page, download to your hard disk, then open it in Jmol using either: Jmol top menu, File > Open or Jmol console (see above), then type load PathnameForYourFile (this is more cumbersome than using the menu) or even drag and drop the file to the Jmol window. > Sorry for bothering you again, Not at all! Please, keep us posted of your progress |
From: Eric M. <em...@mi...> - 2007-12-20 21:25:16
|
Dear Mike: Perhaps you will find it useful to start with FirstGlance in Jmol (http://firstglance.jmol.org ) as a simpler alternative to the Jmol application. FirstGlance in Jmol used the Jmol applet, which has capabilities identical to those of the application, but works within a web browser (nothing to install). At FirstGlance in Jmol you will find a Gallery of molecules (PDB id codes with descriptions) ready to view. FirstGlance in Jmol has been adopted by a number of journals including Nature. Another resource that may be of interest is the Atlas of Macromolecules (http://atlas.proteinexplorer.org ) which has some interesting molecules, with brief descriptions, and links for viewing each in FirstGlance in Jmol. As to "what is the Protein Data Bank", please see http://proteinexplorer.org/igloss.htm#pdb Please don't hesitate to ask if I can be of any help. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Top Five 3D MolVis Technologies http://Top5.MolviZ.Org 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - */ |