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. > > -- 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 ------------------------------------------------------------------------- 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
