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Hi, Ok, I thought the update was the solution, never mind then, I don't want to rush you, I was just curious. When I mean the ARIA setup window, it's the dialog window you get when you start up ARIA via the 'Structure- ARIA structure calculation' menu option in CcpNmr Analysis. At the bottom of this window you have the blue button to specify the CcpNmr-project location, next to this button you have some space where the directory location is specified. This location is now filled in once you select a .XML-file, this was not the case before the update. On the ARIA front (so the stand-alone GUI, not the one you launch via CcpNmr Analysis): I now see how to import a CcpNmr-project file, thanks ! Dieter Op 25-jun.-2012, om 17:45 heeft Wayne Boucher het volgende geschreven: > Hello, > > I haven't changed that code yet with the question. The problem is that there is some weird bug in the Tk (so not our) code and it's not clear how to work around this. (I found a really simple test program which involves just Tk code, so no CCPN code, and it has this bug in it.) > > I am assuming the .XML file does exist which is why the question is being asked. So if you do want the file overwritten then the best option is to remove it beforehand in the ordinary Unix shell so that the question is not asked, because, as you have noticed, the answer to the question is basically always No as far as Tk is concerned. If you don't want the file overridden (which seems a bit odd to me but perhaps there are circumstances when this makes sense) then just answer No and you will be fine. > > On the ARIA front, when you say SETUP-window you mean the ARIA GUI? So there is a tree at the left (once you have an ARIA project)?? If so, there is a line for the "CCPN data model" and in that panel you just select the CCPN project folder. Is this what you mean?? > > Wayne > > On Mon, 25 Jun 2012, Dieter Buyst wrote: > >> Hello, >> I saw last friday there was an update released which concerned Aria, so I installed it >> and restarted CcpNmr Analysis. Yet me and my co-worker are still faced with the same >> problem we had earlier: when you setup an Aria run via the menu 'Structure - >> ARIA:Structure Calculation' (setup new run, import peak lists and restraint list etc.) >> and choose the ARIA project file in the ARIA SETUP-window, it still asks for a >> specific .XML file instead of the complete project directory. When you then select a >> specific .XML-file and try to launch the ARIA GUI, the program still asks wether you >> want to override it or not. Which ever option you choose the project doesn't import in >> the ARIA GUI. >> Basically this is the same problem as I described earlier. The only thing we noticed >> did change is the fact when you specify a .XML-file in the ARIA SETUP window, a >> location is now specified next to the 'ARIA Project File' button. >> A second question I have is when you want to import the CCPN project, without using >> the Analysis dialog option and make the selections completely inside the ARIA GUI, >> which .XML-file do you have to choose ? Because there are multiple choices (e.g. in >> the ccp, ccpnmr and memos directories) and it's not completely clear to me which is >> the right one. >> Regards, >> Dieter >> Op 21-jun.-2012, om 19:10 heeft Wayne Boucher het volgende geschreven: >> >> OK, I think I might have tracked down what the problem is. The first time >> you click the Launch ARIA GUI button and it asks the question about >> whether you want to overwrite the existing ARIA project file, I think it >> pays attention to whether you say Yes or No. But the second (third, etc.) >> times it doesn't seem to pay attention to what you say but always assumes >> the answer is No. Well, this is at least what seems to happen on one of >> our Linux boxes, and it seems to be to be a bug in the Tk function we are >> using, so not in our code. One workaround is to always choose a new ARIA >> project file everytime you want to launch the GUI, so it doesn't ask the >> question. (Or delete the existing one on disk first, if you want to use >> the same filename each time.) >> >> By the way, I got one thing wrong in my earlier email. So Analysis does >> write out the ARIA project file. But ARIA can further refine that when >> you launch the ARIA GUI (etc.). >> >> Wayune >> >> On Thu, 21 Jun 2012, Dieter Buyst wrote: >> >> Hi, >> >> Yes, that's more or less what I did: select a new run, >> imported 1 peak list and no >> >> restraint list (It's a completely new project where only the >> assignment is finished at >> >> this stage). Setting the ARIA project file is the first thing >> that's giving me >> >> trouble. The difference is, that when I don't specify a >> XML-file, the ARIA GUI doesn't >> >> launch but keeps on asking to specify one. When I do specify a >> XML-file it asks me >> >> wether I want to keep or override this XML-file. No matter >> what I choose, (override or >> >> keep) the GUI then launches but doesn't display any peak or >> restraint list, just the >> >> error message I've included earlier. >> >> Dieter >> >> Op 21-jun.-2012, om 17:03 heeft Wayne Boucher het volgende >> geschreven: >> >> Hello, >> >> OK, that helps me understand a bit more! >> >> Let me tell you what I've done to try and figure out what >> is going on, so >> >> to see if it is similar to what you've done. >> >> In that Analysis ARIA dialog I selected New Run and then >> I added a couple >> >> of NOESY peak lists and some restraint lists. Setting >> the ARIA Project >> >> File didn't seem to work properly for me so I'll look >> into that as well. >> >> That might be part of the problem. >> >> Then I hit "Launch ARIA GUI" and in that I can see the >> peak lists (under >> >> Spectra) and the various restraint lists (under Dihedral >> angles, Hydrogen >> >> bonds, etc., dependent on the restraint type). So are >> you not seeing any >> >> of those?? >> >> Wayne >> >> On Thu, 21 Jun 2012, Dieter Buyst wrote: >> >> Hi, >> >> indeed, this error pops up when I try to launch >> Aria via the >> >> 'CcpNmr Analysis - Structure - Aria Structure >> Calculation' >> >> dialog. Then I get the ARIA setup window to specify >> the peak >> >> list etc. It's just when everything is set up and >> you have to >> >> specify the ARIA project file and then click >> 'Launch ARIA >> >> GUI', the GUI starts up but doesn't seem to be able >> to read >> >> the information from the CcpNmr project. I can >> launch the Aria >> >> GUI on it's own without any problems, just the >> import process >> >> from CcpNmr to ARIA doesn't seem to work properly, >> at least >> >> with CcpNmr 2.2. >> >> Dieter >> >> Op 21-jun.-2012, om 15:48 heeft Wayne Boucher het >> volgende >> >> geschreven: >> >> Hello, >> >> We're not 100% sure of how you are doing >> this. So >> >> are you using the CcpNmr Analysis Structure >> --> >> >> ARIA dialog? If so, then Analysis does not >> import >> >> the information from the ARIA Project file >> into >> >> Analysis but instead that file is only >> written to, >> >> and by ARIA not Analysis. The "Setup >> Project" >> >> button in effect is like running "aria -s >> ****" >> >> and the "Launch ARIA GUI" is in effect like >> >> running "aria -gui ****", where **** is that >> >> specfied file name. The main point of that >> >> Analysis dialog is to let you set up details >> like >> >> peak list selection (etc.) there rather than >> in >> >> the ARIA GUI. So the alternative is to >> completely >> >> ignore this dialog and instead just to save >> the >> >> CCPN project and then import the CCPN project >> and >> >> make the selections completely inside the >> ARIA >> >> GUI. >> >> But are you saying instead that you are >> having a >> >> problem working completely inside the ARIA >> GUI?? >> >> Wayne >> >> On Thu, 21 Jun 2012, Dieter Buyst wrote: >> >> Hello, >> >> I'm working on Mac OS X 10.7 (lion) >> >> with CCPNMR 2.2.2 (fully updated) and >> >> have the problem that I can't import >> >> the data from a ccpnmr-project into >> >> ARIA 2.3.1 to launch a structure >> >> calculation. When everything is set >> >> up, the only thing left to do is to >> >> import an ARIA project file, in which >> >> you need to specify the location of >> >> the ccpnmr project. When you select >> >> it, it doesn't seem to be able to >> >> import the data, only when you >> >> specifically select an XML-file does >> >> it launch the ARIA GUI. First it ask >> >> if you want to override the current >> >> XML-project file, but then it doesn't >> >> matter what you choose, it refuses to >> >> import the data or gives the following >> >> error message: >> >> MESSAGE [GUI]: Could not load project: >> >> USER ERROR >> >> <aria.AriaXML.AriaXMLPickler> File >> >> "/Users/Dieter/Documents/aria2.3/src/py/aria/AriaXML.py", >> >> line 256 in load_relaxed >> /Users/Dieter/Documents/Doctoraat/Projectenccpnmr/Projecten/Wild_Type/ >> ccpnmr/Analysis/Wild_Type+Wild_Type_dieter_2012-05-04-16-22-29-989 >> >> _00001.xml: USER ERROR >> >> <aria.AriaXML.AriaXMLPickler> File >> >> "/Users/Dieter/Documents/aria2.3/src/py/aria/AriaXML.py", >> >> line 222 in parse_doc_type Unknown >> >> DOCTYPE: "None". Check your XML file. >> >> A co-worker is experiencing the exact >> >> same problem and she is working on >> >> Ubuntu also with CCPNMR 2.2.2. The >> >> thing is, when she tries to do the >> >> same thing with CCPNMR 2.1.5, >> >> everything works just fine. Could this >> >> be a bug specific for the 2.2 version >> >> ? >> >> In the command line the traceback is >> >> the following: >> >> Traceback (most recent call last): >> >> File >> >> "/Users/Dieter/Documents/aria2.3/src/py/aria/gui/gui.py", >> >> line 655, in load_project >> >> project = >> >> pickler.load_relaxed(filename) >> >> File >> >> "/Users/Dieter/Documents/aria2.3/src/py/aria/AriaXML.py", >> >> line 256, in load_relaxed >> >> x = self.__load(filename, gzip) >> >> File >> >> "/Users/Dieter/Documents/aria2.3/src/py/aria/AriaXML.py", >> >> line 244, in __load >> >> self.error(Exception, '%s: %s' % >> >> (filename, msg)) >> >> File >> >> "/Users/Dieter/Documents/aria2.3/src/py/aria/ariabase.py", >> >> line 211, in error >> >> raise exception, msg >> >> Exception: USER ERROR >> >> <aria.AriaXML.AriaXMLPickler> File >> >> "/Users/Dieter/Documents/aria2.3/src/py/aria/AriaXML.py", >> >> line 256 in load_relaxed >> /Users/Dieter/Documents/Doctoraat/Projectenccpnmr/Projecten/Wild_Type/ >> ccpnmr/Analysis/Wild_Type+Wild_Type_dieter_2012-05-04-16-22-29-989 >> >> _00001.xml: USER ERROR >> >> <aria.AriaXML.AriaXMLPickler> File >> >> "/Users/Dieter/Documents/aria2.3/src/py/aria/AriaXML.py", >> >> line 222 in parse_doc_type >> >> Unknown DOCTYPE: "None". Check your >> >> XML file. >> >> Regards, >> >> Dieter