Re: [Jmol-users] Detecting and gunzipping files
>>All of the styles *should* be antialiased. Perhaps Quickdraw just looks >> better than the others. >> >>What platform are you running on? > > This from Henry: MacOS X and Quartz rendering. David, Unfortunately, there are lots of bugs in the OSX Java implementation. Most that I have found are in the graphics package. Therefore, when Jmol detects the Apple platform it disables antialiasing. This avoids many of the bugs and improves performance a bit. Miguel > -- > > Henry Rzepa. Imperial College, Chemistry Dept. > +44 0778 626 8220 +44 020 7594 5804 (Fax) -- Miguel Howard [EMAIL PROTECTED] c/Peña Primera 11-13 esc dcha 6B 37002 Salamanca España Spain -- telefono casa 923 27 10 82 movil 650 52 54 58 -- To call from the US dial9:00 am Pacific US = home 011 34 923 27 10 82 12:00 noon Eastern US = cell 011 34 650 52 54 586:00 pm Spain -- --- This SF.Net email sponsored by: Free pre-built ASP.NET sites including Data Reports, E-commerce, Portals, and Forums are available now. Download today and enter to win an XBOX or Visual Studio .NET. http://aspnet.click-url.com/go/psa0013ave/direct;at.aspnet_072303_01/01 ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Detecting and gunzipping files
David, >>The command 'reset' will restore the molecule to its original scaling >> and position. >> >>But it does *not* reset the color ... nor reset to the default atom >> size. >> > I need a command that can reset the colour and the atom size, but not > the position and zoom etc. Maybe it could be along the lines of: > > reset colour; reset size; I looked at the existing "reset" command and it is behavior seems to be the same as RasMol ... restore scaling & position but don't change atom size or color. One problem is that the default atom and bond sizes can be changed by the end user. That is, they default to the values specified in the Jmol application preferences. If you want to have specific control, then I suggest that you set the sizes & colors specifically. Try the following: select all; color atoms cpk; color bonds none; spacefill -20; wireframe .1 I know that it is a little verbose. You can stick it in a script file and use the "script" command to run it. Try it out and let me know if you can live with it. >> So, frankly, there is a >> good chance that the other atom styles are going to go away in the >> future. >>So, now is your chance to give me a reason to keep them. > > They look nice!! Quickdraw mode is anti-aliased whereas I don't think > shaded is. I think from the aesthetic point of view it's nice to have a > choice of styles. Well, now that we got them looking nice I plan to throw the code away :) We'll see ... maybe we can keep them around. All of the styles *should* be antialiased. Perhaps Quickdraw just looks better than the others. What platform are you running on? Are you running the application, the web browser applet, or both? > One last request: > > Would it be possible to display a message stating that the current > molecule is in the process of loading, and also one that stated that the > molecule cannot be found? Good idea. Adios, Miguel > > Thanks, > > David > -- > > Henry Rzepa. > +44 (0870) 132 3747 (eFax) > http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, > SW7 2AZ, UK. --- This SF.Net email sponsored by: Free pre-built ASP.NET sites including Data Reports, E-commerce, Portals, and Forums are available now. Download today and enter to win an XBOX or Visual Studio .NET. http://aspnet.click-url.com/go/psa0013ave/direct;at.aspnet_072303_01/01 ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Detecting and gunzipping files
> This is David replying! Good to hear from you :) > I have found a few features that could be improved/implemented: Great! I need some feedback & suggestions on the scripting stuff. > A command to reset the molecule to its original status e.g original > atoms colours, and sizes. I have currently been using the load command > to reset the molecule however this isn't the most elegant solution, and > can't be used in all situations. The command 'reset' will restore the molecule to its original scaling and position. But it does *not* reset the color ... nor reset to the default atom size. It probably should. I need to investigate a bit and see what it does in RasMol. I'll let you know. > Turning on cpk or spacefill currently resets the style to 'shaded'. > This can be changed back to the previous setting with javascript > however it isn't always easy to know what the previous setting was. Hmmm ... yes that is true. Let's talk about these other atom styles for a minute. I am interested in knowing which atom/bond styles you are using and what your motivation is for using them. Why? Because the development version has much faster rendering. And the shaded rendering is just as fast as the others. So, frankly, there is a good chance that the other atom styles are going to go away in the future. So, now is your chance to give me a reason to keep them. > A command to turn on atom numbering within a script, possibly with a > toggle feature to make my job easier! Check out the 'label' command label %i --> turns on numbers label %a --> turns on atom type label off --> turns off atom labels As with other commands, this affects the currently selected set of atoms. > Also it might be nice to be able > to add or subtract from the zoom value instead of setting it to a > specific value. Hmmm ... I can probably make that work. A leading + sign would go up by a percentage and a leading - sign would make it go down by a percentage. (I will have to look at the parser and see how happy it will be with a leading plus sign.) So, presumably the following sequences would be exactly the same zoom 250 zoom 100; zoom +150 zoom 100; zoom +100; zoom +50 zoom 300; zoom -50 > It seems that some .pdb's refuse to load ( one attached ). I'll check it out. But probably Egon will have to look at it. He is the "file" guy. > Sending scripts to applets that are currently running a loop e.g. > rotating molecules, cancels the loop. The answer I am supposed to give at this point is ... that is a feature, not a bug :-) The loop command is an implementation of the same command in Chime. I don't have any idea what happens in Chime. But I decided that I could only handle one script running at a time. If it is not doing what you need, then talk to me about what you are trying to accomplish. I'm sure we can work something out. Excellent suggestions and feedback. Keep it coming :-) Gracias y Adios, Miguel --- This SF.Net email sponsored by: Free pre-built ASP.NET sites including Data Reports, E-commerce, Portals, and Forums are available now. Download today and enter to win an XBOX or Visual Studio .NET. http://aspnet.click-url.com/go/psa0013ave/direct;at.aspnet_072303_01/01 ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Detecting and gunzipping files
Henry, I just checked in the code to auto-detect/uncompress files which have been compressed with gzip. File extension is unimportant. Gzip is designed to compress a single file. Therefore, it is pretty straightforward. An associate from the University of Salamanca told me that he thought Chime only supports .gz files. hemoglobin.pdb442.017 bytes hemoglobin.pdb.gz 106.371 bytes It is less clear to me whether/how we should support something like .zip (.jar) files. This file format is for a set of files (a directory tree) rather than for a single file. Therefore, to support it we need to either: 1. always take the first file inside the .zip file or 2. provide some mechanism for the user to specify which file inside the .zip archive they want to select. I didn't feel like working on this right now, so I did *not* add any support for .zip compression. Developers: I checked this into both the B6 branch and HEAD. Miguel > Henry, > > Good idea! > > Should be easy for us to put this in. And will help a lot with larger > .pdb files. > > Miguel > >> In the olden days of modem bandwidths, it became common to gzip >> molecule coordinate files (compression ratios of 10:1 made this very >> worth while, particularly for medium sized molecules). Software such >> as Chime would auto-detect this (even though the file name extension >> retained the uncompressed value, ie .mol, .pdb etc). >> >> Can I put in a request for such autodetection and decompression to be >> added to JMol and the Applet/ >> -- >> >> Henry Rzepa. >> +44 (0870) 132 3747 (eFax) >> http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College >> London, >> SW7 2AZ, UK. >> >> >> >> >> --- >> This SF.Net email sponsored by: Free pre-built ASP.NET sites including >> Data Reports, E-commerce, Portals, and Forums are available now. >> Download today and enter to win an XBOX or Visual Studio .NET. >> http://aspnet.click-url.com/go/psa0013ave/direct;at.aspnet_072303_01/01 >> ___ >> Jmol-users mailing list >> [EMAIL PROTECTED] >> https://lists.sourceforge.net/lists/listinfo/jmol-users > > > -- > Miguel Howard [EMAIL PROTECTED] > c/Peña Primera 11-13 esc dcha 6B > 37002 Salamanca > España Spain > -- > telefono casa 923 27 10 82 movil 650 52 54 58 > -- > To call from the US dial9:00 am Pacific US = > home 011 34 923 27 10 82 12:00 noon Eastern US = > cell 011 34 650 52 54 586:00 pm Spain > -- > > > > > --- > This SF.Net email sponsored by: Free pre-built ASP.NET sites including > Data Reports, E-commerce, Portals, and Forums are available now. > Download today and enter to win an XBOX or Visual Studio .NET. > http://aspnet.click-url.com/go/psa0013ave/direct;at.aspnet_072303_01/01 > ___ > Jmol-users mailing list > [EMAIL PROTECTED] > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Miguel Howard [EMAIL PROTECTED] c/Peña Primera 11-13 esc dcha 6B 37002 Salamanca España Spain -- telefono casa 923 27 10 82 movil 650 52 54 58 -- To call from the US dial9:00 am Pacific US = home 011 34 923 27 10 82 12:00 noon Eastern US = cell 011 34 650 52 54 586:00 pm Spain -- --- This SF.Net email sponsored by: Free pre-built ASP.NET sites including Data Reports, E-commerce, Portals, and Forums are available now. Download today and enter to win an XBOX or Visual Studio .NET. http://aspnet.click-url.com/go/psa0013ave/direct;at.aspnet_072303_01/01 ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Detecting and gunzipping files
Henry, Good idea! Should be easy for us to put this in. And will help a lot with larger .pdb files. Miguel > In the olden days of modem bandwidths, it became common to gzip > molecule coordinate files (compression ratios of 10:1 made this very > worth while, particularly for medium sized molecules). Software > such as Chime would auto-detect this (even though the file name > extension retained the uncompressed value, ie .mol, .pdb etc). > > Can I put in a request for such autodetection and decompression to be > added to JMol and the Applet/ > -- > > Henry Rzepa. > +44 (0870) 132 3747 (eFax) > http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, > SW7 2AZ, UK. > > > > > --- > This SF.Net email sponsored by: Free pre-built ASP.NET sites including > Data Reports, E-commerce, Portals, and Forums are available now. > Download today and enter to win an XBOX or Visual Studio .NET. > http://aspnet.click-url.com/go/psa0013ave/direct;at.aspnet_072303_01/01 > ___ > Jmol-users mailing list > [EMAIL PROTECTED] > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Miguel Howard [EMAIL PROTECTED] c/Peña Primera 11-13 esc dcha 6B 37002 Salamanca España Spain -- telefono casa 923 27 10 82 movil 650 52 54 58 -- To call from the US dial9:00 am Pacific US = home 011 34 923 27 10 82 12:00 noon Eastern US = cell 011 34 650 52 54 586:00 pm Spain -- --- This SF.Net email sponsored by: Free pre-built ASP.NET sites including Data Reports, E-commerce, Portals, and Forums are available now. Download today and enter to win an XBOX or Visual Studio .NET. http://aspnet.click-url.com/go/psa0013ave/direct;at.aspnet_072303_01/01 ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Detecting and gunzipping files
In the olden days of modem bandwidths, it became common to gzip molecule coordinate files (compression ratios of 10:1 made this very worth while, particularly for medium sized molecules). Software such as Chime would auto-detect this (even though the file name extension retained the uncompressed value, ie .mol, .pdb etc). Can I put in a request for such autodetection and decompression to be added to JMol and the Applet/ -- Henry Rzepa. +44 (0870) 132 3747 (eFax) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. --- This SF.Net email sponsored by: Free pre-built ASP.NET sites including Data Reports, E-commerce, Portals, and Forums are available now. Download today and enter to win an XBOX or Visual Studio .NET. http://aspnet.click-url.com/go/psa0013ave/direct;at.aspnet_072303_01/01 ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
