Re: [COOT] auto open MTZ problem

[Paul Emsley]

On 31/01/17 13:26, mesters wrote:


Hi,

I currently run ccp4 version 7.0.028 on a Mac Air with OS X 10.11.6 
and experience no problems if start Coot from within qtRView (model 
and maps are displayed correctly)


If a start Coot by itself and load a PDB model and then use "auto open 
MTZ" and select the model in order to calculate the maps, it comes up 
with the following:


/In /Applications/ccp4-7.0/share/guile/gtk-2.0/gtk.scm://
// 147:  0* [apply # ()]//
//In unknown file://
//   ?:  1  [#]//
//In /Applications/ccp4-7.0/share/coot/scheme/coot-gui.scm://
// 750:  2* (let* ((active-mol-no #)) (if (not #) (begin #) (begin #)))//
// 754:  3  (if (not #) (begin #) (begin #))//
//In /Applications/ccp4-7.0/share/coot/scheme/refmac.scm://
//...//
// 514:  4  (let* (# # # ...) (write-pdb-file imol pdb-in) ...)//
// 525:  5* [run-refmac-by-filename 
"coot-refmac/refmac-for-phases.pdb" ...]//

//In unknown file://
//   ?:  6  (letrec # # # ...)//
//In /Applications/ccp4-7.0/share/coot/scheme/refmac.scm://
//...//
// 241:  7  (let* (#) (local-format #t "INFO:: test-refmac-status: 
~s~%" ...) ...)//

// 241:  8* [goosh-command "refmac5" () ...]//
//In /Applications/ccp4-7.0/share/coot/scheme/coot-utils.scm://
// 676:  9  (if (not #) (begin # 255) (let* # # #))//
//In unknown file://
//...//
//   ?: 10  [call-with-output-file 
"refmac-from-coot-refmac-for-phases-0.log" ...]//

//   ?: 11  (let* ((file #) (ans #)) (close-output-port file) ans)//
//   ?: 12* [open-output-file 
"refmac-from-coot-refmac-for-phases-0.log"]//

//   ?: 13  [open-file "refmac-from-coot-refmac-for-phases-0.log" "w"]//
/


/
I think that this is the pertinent text:

/


///: In procedure open-file in expression (open-file str 
OPEN_WRITE)://
//: Permission denied: 
"refmac-from-coot-refmac-for-phases-0.log"/





You can't write to the directory in which you are running coot.

Coot could handle this problem more elegantly - thanks for letting me know.

Paul.

[COOT] auto open MTZ problem

[mesters]

Hi,

I currently run ccp4 version 7.0.028 on a Mac Air with OS X 10.11.6 and 
experience no problems if start Coot from within qtRView (model and maps 
are displayed correctly)


If a start Coot by itself and load a PDB model and then use "auto open 
MTZ" and select the model in order to calculate the maps, it comes up 
with the following:


/In /Applications/ccp4-7.0/share/guile/gtk-2.0/gtk.scm://
// 147:  0* [apply # ()]//
//In unknown file://
//   ?:  1  [#]//
//In /Applications/ccp4-7.0/share/coot/scheme/coot-gui.scm://
// 750:  2* (let* ((active-mol-no #)) (if (not #) (begin #) (begin #)))//
// 754:  3  (if (not #) (begin #) (begin #))//
//In /Applications/ccp4-7.0/share/coot/scheme/refmac.scm://
//...//
// 514:  4  (let* (# # # ...) (write-pdb-file imol pdb-in) ...)//
// 525:  5* [run-refmac-by-filename "coot-refmac/refmac-for-phases.pdb" 
...]//

//In unknown file://
//   ?:  6  (letrec # # # ...)//
//In /Applications/ccp4-7.0/share/coot/scheme/refmac.scm://
//...//
// 241:  7  (let* (#) (local-format #t "INFO:: test-refmac-status: ~s~%" 
...) ...)//

// 241:  8* [goosh-command "refmac5" () ...]//
//In /Applications/ccp4-7.0/share/coot/scheme/coot-utils.scm://
// 676:  9  (if (not #) (begin # 255) (let* # # #))//
//In unknown file://
//...//
//   ?: 10  [call-with-output-file 
"refmac-from-coot-refmac-for-phases-0.log" ...]//

//   ?: 11  (let* ((file #) (ans #)) (close-output-port file) ans)//
//   ?: 12* [open-output-file "refmac-from-coot-refmac-for-phases-0.log"]//
//   ?: 13  [open-file "refmac-from-coot-refmac-for-phases-0.log" "w"]//
//: In procedure open-file in expression (open-file str 
OPEN_WRITE)://
//: Permission denied: 
"refmac-from-coot-refmac-for-phases-0.log"/


Actually, I updated Quartz very recently and today, reinstalled both 
Quartz and CCP4 in an attempt to solve this problem.


Any ideas?

Regards

Jeroen

--
Dr.math. et dis. nat. Jeroen R. Mesters
Deputy, Senior Researcher & Lecturer
Program Coordinator /Infection Biology/ 



Institute of Biochemistry, University of Lübeck
Ratzeburger Allee 160, 23538 Lübeck, Germany
phone: +49-451-31013105 (secretariate -31013101)
fax: +49-451-31013104

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http://www.eine-stadt-sieht-gelb.de 
http://www.uni-luebeck.de/studium/studiengaenge/infection-biology
http://www.iobcr.org 

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