Re: [phenixbb] Error in running Autosol....
Hi Karthikeyan, I'm sorry for the trouble! I see that you are running the very latest phenix from last night. This version passed our automated tests and it appears fine in general. Somehow the solve scaling step is not working in your run. I haven't seen this happen before, but my guesses are: 1. I have been making small changes in the autosol printout and it is possible that there is a place where solve is printing something out and the format does not match the variable type, and I didn't catch it in our tests. If this is the case you should be able to find it by running from the command-line and adding the keyword debug=true and it should print out a clearer error message for you that you can send me. You can run from the command line in the same place you ran from the GUI by saying phenix.autosol autosol.eff debug=True because the GUI writes out autosol.eff when it runs, saving your inputs. Then you can override those values by putting debug=True on the command line. Other less-likely possibilities: 2. your input datafiles are of a type that was unexpected (normally .sca, .mtz are fine, but perhaps the columns in an mtz are unusual). 3. Your structure is very large or high-resolution. 4. Something is unusual in your setup so that not much memory is available. If none of these helps, you are welcome to send me the files and I'll check it out. All the best, Tom T
Dear All,
I am using phenix-1.4-138 in RHEL5 Xeon-64 bit workstation.
I am trying to solve a structure of Se-Met through phenix.autosol_gui. Once the programs starts it goes to several stages including converting from mtz to sca, xtriage and so on. Finally it gives an error message as follows:
******************************************************************************** Failed to carry out AutoSol_scale_and_analyze_mad:
None of the solve versions worked See overall log file and also solve log file (in AutoSol_run_2_/LAST.LOG) ******************************************************************************** I found the LAST.LOG file is empty.
I am trying to find out what could be problem? Any suggestions or help is much appreciated!
Thanking you
S.Karthikeyan
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On Aug 15, 2009, at 7:51 AM, Thomas C. Terwilliger wrote:
You can run from the command line in the same place you ran from the GUI by saying
phenix.autosol autosol.eff debug=True
because the GUI writes out autosol.eff when it runs, saving your inputs. Then you can override those values by putting debug=True on the command line.
One small correction to this: the .eff file gets written to a different location now (not the current directory). It will be in the directory phenix/project_data/ in whatever the project directory is, and it will have a name like "autosol_0.eff". I only use these internally in the GUI; to re-run the project, you should use the file autosol.eff in whatever the output directory was, e.g.: % phenix.autosol AutoSol_run_1_/autosol.eff debug=True This has the final parameters that AutoSol actually used once it started (it figures out some things automatically that the GUI doesn't bother with). If it works this way, there may be something wrong with the GUI; I'll check and make sure nothing has broken, but it hasn't changed recently (although the next build will have some unrelated fixes). -Nat -------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]
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Nathaniel Echols -
Thomas C. Terwilliger