Bob - just wanted to confirm that the bug fix works for me as well. Thank you for the quick turnaround!
-Al Bob Hanson wrote: > OK, it's a bug -- assigning a property to the very last atom in a > model using "set propertyAtomNumberField = 1" fails for Jmol 11.5.9 > and Jmol 11.4.RC7 and all previous versions. That is fixed now. > > You can find the updated jar files in > > http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11_5.zip > > > Bob > > > Al Ramsey wrote: > >> Bob, >> >> I wanted to follow up again regarding my data loading issue. I >> believe the true issue was either the fact that there are multiple >> chains in my structure or simple the size of the overall structure >> itself. In my second iteration I used the PDB file you used (1CRN) >> and I got the script to work. However, the structure I was >> originally using was 1RUZ. The PDB file is linked here for convenience: >> >> http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1RUZ >> >> >> >> 1RUZ has more than one chain and it is about 20 times bigger. I >> believe it might be due to the presence of multiple chains but not >> sure how to prove this. The only verification I could do was to >> change the script from using "select *" to "select *:i" to pick a >> specific chain, which then fixed my loading issue. (Also to answer >> your earlier question - I am able to open and close the console, but >> the 3D screen simply doesn't refresh). >> >> Is there anything I can do to verify if the problem is due to the >> presence of multiple chains? >> >> Thanks, >> Al >> >> >> >> Al Ramsey wrote: >> >>> Bob - thanks for the help. I was running 11.2.14 and was >>> encountering the issue I described, but when I used 11.5.9, it >>> finally worked. I may have a corrupt copy or there was an issue >>> with version 11.2.14. >>> >>> Thanks! >>> -Al >>> >>> >>> If we wanted to use the most recent "stable" version, >>> >>> Bob Hanson wrote: >>> >>>> Al, what you are doing looks right to me. Hmm, I don't know. The >>>> following script worked for me in Jmol 11.5.9: >>>> >>>> load data/1crn.pdb >>>> set propertyAtomNumberField 1 >>>> set propertyDataField 2 >>>> x=load("atomData.dat") >>>> select * >>>> display * >>>> data "property_score @x" >>>> propertyColorScheme = "bwr" >>>> color property_score >>>> >>>> >>>> where atomData.dat is >>>> >>>> 19 -1.038 >>>> 20 -1.038 >>>> 21 -1.038 >>>> 22 0.5235 >>>> 23 0.5235 >>>> >>>> When I instead select only atomno>20, then only three atoms are >>>> assigned the property. So that is working OK. >>>> >>>> When you say "hangs" I have to ask more. Can you call up a Java >>>> console? Is it giving an error report of some sort by chance? >>>> >>>> So I might need to see the files so I can try to reproduce that. >>>> You can send those directly to [EMAIL PROTECTED] >>>> >>>> >>>> Al Ramsey wrote: >>>> >>>> >>>> >>>>> Greetings - I'm hoping to get a suggestion on how I can >>>>> troubleshoot a problem I'm facing regarding the loading of user >>>>> data. There are computed scores that were generated for each atom >>>>> and I'd like to display as a color gradient. >>>>> >>>>> Below is the script I am using. I'm using the applet and it seems >>>>> to hang at the last line... the console just says "pending" and >>>>> just stays there: >>>>> >>>>> ##### >>>>> load "protein.pdb" >>>>> set propertyAtomNumberField 1 >>>>> set propertyDataField 2 >>>>> >>>>> # The file "atomData.dat" is a two-column data file >>>>> # with the first column being the atom number and the >>>>> # second column being the data value, for example: >>>>> # 2519 -1.038 >>>>> # 2520 -1.038 >>>>> # 2521 -1.038 >>>>> # 2522 0.5235 >>>>> # 2523 0.5235 >>>>> x=load("atomData.dat") >>>>> select :i # data is for chain I >>>>> display :i # display only chain I >>>>> data "property_score @x" >>>>> propertyColorScheme = "bwr" >>>>> >>>>> # Jmol applet hangs at this line >>>>> color property_score >>>>> >>>>> ##### >>>>> >>>>> Any advice on how I should troubleshoot would be greatly appreciated. >>>>> >>>>> Thanks, >>>>> Al >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>>> >>>> >>> >>> -- >>> Alvin Ramsey, PhD. >>> Senior Researcher/Senior Systems Architect >>> [EMAIL PROTECTED] >>> 703.998.5333 >>> http://www.vecna.com >>> >>> Vecna Technologies, Inc. >>> 5205 Leesburg Pike, Suite 210 >>> Falls Church, VA 22041 >>> t: 703.998.5333 >>> f: 703.998.5816 >>> >>> >>> Better Technology, Better World (TM) >>> >>> The contents of this message may be privileged and confidential. >>> Therefore, if this message has been received in error, please delete >>> it without reading it. Your receipt of this message is not intended >>> to waive any applicable privilege. Please do not disseminate this >>> message without the permission of the author. >>> >>> >> >> -- >> Alvin Ramsey, PhD. >> Senior Researcher/Senior Systems Architect >> [EMAIL PROTECTED] >> 703.998.5333 >> http://www.vecna.com >> >> Vecna Technologies, Inc. >> 5205 Leesburg Pike, Suite 210 >> Falls Church, VA 22041 >> t: 703.998.5333 >> f: 703.998.5816 >> >> >> Better Technology, Better World (TM) >> >> The contents of this message may be privileged and confidential. >> Therefore, if this message has been received in error, please delete >> it without reading it. Your receipt of this message is not intended >> to waive any applicable privilege. Please do not disseminate this >> message without the permission of the author. >> >> > > -- Alvin Ramsey, PhD. Senior Researcher/Senior Systems Architect [EMAIL PROTECTED] 703.998.5333 http://www.vecna.com Vecna Technologies, Inc. 5205 Leesburg Pike, Suite 210 Falls Church, VA 22041 t: 703.998.5333 f: 703.998.5816 Better Technology, Better World (TM) The contents of this message may be privileged and confidential. Therefore, if this message has been received in error, please delete it without reading it. Your receipt of this message is not intended to waive any applicable privilege. Please do not disseminate this message without the permission of the author. ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
