Re: [Jmol-users] 10.2.0 application
Brian Salter-Duke wrote: On Mon, Apr 17, 2006 at 02:43:49PM -0400, Jules Moskowitz wrote: I have been able to use jmol-10.00.45 as both and applet with a browser and as an application to look at some molecules from terminal (imacg5, OS 10.4). I have been able to use jmol-10.2.0 with the browser but not as an application. When I go from the terminal to the jmol-10.2.0 folder and attempt to use the command jmol, I get: tcsh: jmol: Command not found. I had a similar problem on linux. dos2unix < jmol > ttt mv ttt jmol fixed it. Brian. Thanks for the explanation. Miguel is usually making the release on Unix system, I made it on Windows. Nico --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Google map fun: where are those Jmol users/developers?
On Mon, Apr 17, 2006 at 07:51:47PM +0200, Egon Willighagen wrote: > > Hi all, > > I learned this weekend that setting up a Google map is very easy, so set up > one for Jmol too: > > http://jmol.sourceforge.net/maps/people/ > > If you would like to be added to this map, please send your name, URL (e.g. > you page in the Jmol wiki [1]) and longtitude and latitude, with four digits, > like 50.0563, to this mailing list. > > Developers will have a red marker, users a yellow marker. Great fun. I'm a user, -37.8283, 144.8811 (I think I have the sign convention right) Melbourne Australia. Jmol wiki [[User:Bduke]] Cheers, Brian. > Egon > > -- > [EMAIL PROTECTED] > Cologne University Bioinformatics Center (CUBIC) > Blog: http://chem-bla-ics.blogspot.com/ > GPG: 1024D/D6336BA6 > > > --- > This SF.Net email is sponsored by xPML, a groundbreaking scripting language > that extends applications into web and mobile media. Attend the live webcast > and join the prime developer group breaking into this new coding territory! > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Brian Salter-Duke (Brian Duke) [EMAIL PROTECTED] Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ. --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Google map fun: where are those Jmol users/developers?
I am a jmol user. Lat and long is 33.7037,-117.7950http://www.medicalcomputing.net/endocrine.htmlAlex Amies On 4/17/06, Egon Willighagen <[EMAIL PROTECTED]> wrote: Hi all,I learned this weekend that setting up a Google map is very easy, so set upone for Jmol too: http://jmol.sourceforge.net/maps/people/ If you would like to be added to this map, please send your name, URL (e.g.you page in the Jmol wiki [1]) and longtitude and latitude, with four digits,like 50.0563, to this mailing list.Developers will have a red marker, users a yellow marker. Egon--[EMAIL PROTECTED]Cologne University Bioinformatics Center (CUBIC)Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6---This SF.Net email is sponsored by xPML, a groundbreaking scripting languagethat extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory!http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 ___Jmol-users mailing listJmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] 10.2.0 application
On Mon, Apr 17, 2006 at 02:43:49PM -0400, Jules Moskowitz wrote: > I have been able to use jmol-10.00.45 as both and applet with a > browser and as an application to look at some molecules from terminal > (imacg5, OS 10.4). > I have been able to use jmol-10.2.0 with the browser but not as an > application. > > When I go from the terminal to the jmol-10.2.0 folder and attempt > to use the command jmol, I get: > tcsh: jmol: Command not found. I had a similar problem on linux. dos2unix < jmol > ttt mv ttt jmol fixed it. Brian. > Both jmol and jmol.sh are executables as in 10.00.45. > > Anybody know what I am doing wrong or is there a bug in jmol? > > Professor Jules W. Moskowitz > Chemistry Department > New York University > 100 Washington Square East > New York, NY 10003-6688 > Phone: (212)998-8437 > Fax: (212) 260-7905 > Email: [EMAIL PROTECTED] > -- Brian Salter-Duke (Brian Duke) [EMAIL PROTECTED] Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ. --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] 10.2.0 application
Egon Willighagen wrote: On Monday 17 April 2006 20:43, Jules Moskowitz wrote: Both jmol and jmol.sh are executables as in 10.00.45. Anybody know what I am doing wrong or is there a bug in jmol? Haven't checked wether the files are missing or not. But you can always do this: java -jar Jmol.jar from the command line in the dir where the Jmol.jar is located. This is what the shell script does too. If they are missing, please file a bug report, so that we don't forgot to include them again in the bin distribs for the next release. Files are in the release, so it's not the problem. If you go in the jmol 10.2.0 folder, and execute the command "./jmol", is there something different ? What happens if you execute the command "which jmol" Nico --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] 10.2.0 application
On Monday 17 April 2006 20:43, Jules Moskowitz wrote: > Both jmol and jmol.sh are executables as in 10.00.45. > > Anybody know what I am doing wrong or is there a bug in jmol? Haven't checked wether the files are missing or not. But you can always do this: java -jar Jmol.jar from the command line in the dir where the Jmol.jar is located. This is what the shell script does too. If they are missing, please file a bug report, so that we don't forgot to include them again in the bin distribs for the next release. Egon -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] 10.2.0 application
I have been able to use jmol-10.00.45 as both and applet with a browser and as an application to look at some molecules from terminal (imacg5, OS 10.4).I have been able to use jmol-10.2.0 with the browser but not as an application. When I go from the terminal to the jmol-10.2.0 folder and attempt to use the command jmol, I get:tcsh: jmol: Command not found.Both jmol and jmol.sh are executables as in 10.00.45.Anybody know what I am doing wrong or is there a bug in jmol? Professor Jules W. Moskowitz Chemistry Department New York University 100 Washington Square East New York, NY 10003-6688 Phone: (212)998-8437 Fax: (212) 260-7905 Email: [EMAIL PROTECTED]
[Jmol-users] Google map fun: where are those Jmol users/developers?
Hi all, I learned this weekend that setting up a Google map is very easy, so set up one for Jmol too: http://jmol.sourceforge.net/maps/people/ If you would like to be added to this map, please send your name, URL (e.g. you page in the Jmol wiki [1]) and longtitude and latitude, with four digits, like 50.0563, to this mailing list. Developers will have a red marker, users a yellow marker. Egon -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol and mmCIF
On Mon, April 17, 2006 5:40 am, Egon Willighagen said: > As long as the informat is split up > over several data substructures, and one has to get those bits of > information > together, it does not really matter wether it is PDB, mmCIF or XML syntax. This is true. CIF is an information exchange format and it is the reading program's responsibility to fill its own data structures as needed from the information in the CIF. This is why it is necessary to parse a complete CIF and not make any assumptions (other than those inherent in the (mm)CIF definitions) about where the data lie. Rich --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] hbond display in 10.2
I find that the "connect hbonds auto (*) (*)" script that enabled the hbond statements in Jmol 10.00.60, no longer has an effect in Jmol 10.2.0. How can one modify existing pages to display hydrogen bonds in 10.2.0 ? Bill --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol and mmCIF
On Monday 17 April 2006 11:20, Jaime Prilusky wrote: > According to Eric Martz: > > Several errors in PDB files were reported to RCSB recently. Often their > > response is "it is fixed in the mmCIF". CIF is a burning issue for now > > (for FirstGlance), but it is GREAT that Jmol will be able to read mmCIF > > in future. Are you reporting the errors you found in mmCIF files to RCSB? > > ([EMAIL PROTECTED]) > > There's more than one way of writing a valid mmCIF file, and RCSB is > intermixing them. Probably the parsing problem you report is due to > alternative mmCIF 'flavors'. > > What about parsing PDB's XML? These files (should) reflect all fixes and > improvements from mmCIF files in an easy to parse XML format. Structures > in PDBML format are available from RCSB PDB website or ftp, and from OCA's > mirrors http://bip.weizmann.ac.il/oca-bin/send-xml?1d66 I have looked at them earlier, and noted that while the syntax is 'easier' (i.e. XML based), it is really the data structure that is the problem. I have not checked the files from the URL you gave, but the XMLs from pdb.org itself are really not easier to parse. As long as the informat is split up over several data substructures, and one has to get those bits of information together, it does not really matter wether it is PDB, mmCIF or XML syntax. > The XML Schema for Exchange Data dictionary is available from > http://pdbml.rcsb.org/schema/pdbx.xsd Egon -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol and mmCIF
According to Eric Martz: > Several errors in PDB files were reported to RCSB recently. Often their > response is "it is fixed in the mmCIF". CIF is a burning issue for now (for > FirstGlance), but it is GREAT that Jmol will be able to read mmCIF in future. > Are you reporting the errors you found in mmCIF files to RCSB? ([EMAIL > PROTECTED]) There's more than one way of writing a valid mmCIF file, and RCSB is intermixing them. Probably the parsing problem you report is due to alternative mmCIF 'flavors'. What about parsing PDB's XML? These files (should) reflect all fixes and improvements from mmCIF files in an easy to parse XML format. Structures in PDBML format are available from RCSB PDB website or ftp, and from OCA's mirrors http://bip.weizmann.ac.il/oca-bin/send-xml?1d66 The XML Schema for Exchange Data dictionary is available from http://pdbml.rcsb.org/schema/pdbx.xsd Jaim -- Dr Jaime Prilusky | [EMAIL PROTECTED] Head of Bioinformatics ISPC| R&D Bioinformatics and Data Management | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 info URL http://bip.weizmann.ac.il/staff/jaime_prilusky.html OCA is at http://bip.weizmann.ac.il/oca/ --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
