Dear Helen and Andrew, Thank you very much for your suggestions and help. It is working now and able to run the aimless successfully.
Your help is much appreciated Mike On Thu, Jul 11, 2019 at 7:53 PM Helen Ginn <heleng...@hginn.co.uk> wrote: > Dear Mike and Andrew, > > I've since updated to a later version of ccp4 (7.0.076) and now have the > XMLOUT tags specified automatically. Woops! > > Thanks for that error log Andrew - I had a look at the aimless.script file > to see how that filename was generated, and looked up the command on the > CCP4 developer's guide for programmers. > > Image hosted remotely to avoid mailbox indigestion: > https://www.hginn.co.uk/ccp4bb/aimless_script.png > > Here, the variable `root` is set to [SetOutputFileRoot], defined in the > bottom half of the image online, and is used to generate the Pointless XML > file path. It is also used later and may cause similar problems for > AIMLESS's output of .scales, graphs and other logs, so there is an > underlying problem that ought to be solved for Mike. > > It seems that in order to have a filepath in the root of the filesystem > itself (which is reassuringly non-writeable), judging from the definition, > the project directory would have to be an empty string. None of the > pointless GUI scripts rely on [SetOutputFileRoot], which would be > consistent with the fact they work for Mike. > > So it might be worth Mike checking this: in the main window of the ccp4i > interface, click Change Project and then Add/Edit Project. Find the project > you are working on and confirm the directory path for your current project > is a subdirectory in your home directory. > > Best wishes > Helen > > On Thu, 11 Jul 2019 13:54:20 +0100 > Andrew Leslie <and...@mrc-lmb.cam.ac.uk> wrote: > > > Dear Mike and Helen, > > > > As I understand it, the XML is only written when POINTLESS/AIMLESS are > run through the CCP4 GUI and the command comes from the GUI script, so > there is no way you can turn this off from POINTLESS itself. > > > > However, if you use the “Run&View com file” option from CCP4i GUI, you > will see the XMLOUT command there (see attached figure). If you delete this > (for both POINTLESS and AIMLESS and CTRUNCATE) then the jobs will run and > produce an MTZ file, but it did give a "job failed" message: > > > > #CCP4I TERMINATION STATUS 0 Error from script > /Applications/ccp4-7.0/share/ccp4i/scripts/aimless.script: couldn't open > "/Users/andrew/g4/MOSFLM/camillo/camillo_1_pointless.xml": no such file or > directory > > > > However the MTZ file was there. > > > > Did your job produce a final MTZ file in spite of the warning? > > > > I’m afraid I don’t understand why the XML file was not written in your > case, are you sure the path shown in the “Command Line” output from the GUI > is OK for writing to? > > > > Best wishes, > > > > Andrew > > > > > > > > > On 11 Jul 2019, at 13:34, Helen Ginn <ccp...@hginn.co.uk> wrote: > > > > > > Dear Mike, > > > > > > No problem! Happy to provide suggestions, though I'd prefer to be > addressed directly on here. > > > > > > Here's another suggestion, no promises. If you can provide more detail > on the GUI input and the output log files, it would be easier to know why > this is happening in the first place. However, you can also click and hold > "Run" in ccp4i and select "Run&View Com File". Then you will receive each > program's command line input and you can edit them before you run them. I > suggest removing or correcting any instances of `XMLOUT <filename>`. > > > > > > Thanks Andrew for confirming with Phil on the behaviour of pointless. > I have looked at the ccp4i interface and cannot find any option for > enabling XML output for pointless in the Symmetry/scale/merge pipeline. The > option to output to XML in the standalone pointless does not seem to > transfer this to the command line options, but Mike is probably using the > former GUI input window anyway. As such I'm not sure where the XMLOUT > command is coming from. > > > > > > Best wishes > > > Helen > > > > > >> Dear Andrew, > > >> > > >> Thanks for your suggestion. Yes, you are right that the error is > because .xml file is not being written. but not able to find the > reasons...I checked...Disk space is free and have permission to write also. > I could able to run Pointless, but not Aimless. > > >> > > >> Any other reason?? > > >> > > >> Thanks > > >> > > >> Mike > > >> > > >> On Wed, Jul 10, 2019 at 5:37 PM Andrew Leslie <[log in to unmask]> > wrote: > > >> > > >> I think Helen’s answer is absolutely right. I asked Phil Evans > about this when I saw him yesterday, and he said that error usually arises > when it is not possible to write the xml file, either because a disk is > full, or because you do not have permission to write to that area. > > >> > > >> Andrew > > >> > > >>> On 3 Jul 2019, at 15:09, Mike Xishan <[log in to unmask]> wrote: > > >>> > > >>> Dear all, > > >>> > > >>> Sorry for asking for a very naive question that might be asked > before. > > >>> > > >>> After integration, I am trying to do "data reduction" through > Aimless, but task fails with an error message as > > >>> > > >>> #CCP4I TERMINATION STATUS 0 "FILEIO: cannot open file > /Processing1_8_pointless.xml > > >>> > > >>> I really appreciate for your opinion and help to fix this problem. > > >>> > > >>> Thanks, > > >>> > > >>> Mike > > >>> > > >>> > > >>> To unsubscribe from the CCP4BB list, click the following link: > > >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > >> > > >> > > >> To unsubscribe from the CCP4BB list, click the following link: > > >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > >> > > > > > -- > Helen Ginn <heleng...@hginn.co.uk> > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
