Re: [COOT] Proxy server setting
> Is it possible to tell coot to use a proxy server? Hi Arnaud, Under linux, normally, setting up the variable proxy_http or http_proxy should be enough. For example if you're using bash : export proxy_http=http://proxy.toto.fr:1234 export http_proxy=http://proxy.toto.fr:1234 should do the job. Hope it help, Yves, -- Watier Yves PhD Student, European Synchrotron Radiation Facility (ESRF) Experiments Division / Materials Science Group ID31 high resolution powder diffraction beamline. 6 Rue Jules Horowitz, BP 220, 38043 Grenoble, Cedex 9, France. Office: 10.01.06 Tel. (+)33(0)4.76.88.29.67 Fax. (+)33(0)4.76.88.27.07 http://www.esrf.fr/UsersAndScience/Experiments/MaterialsScience/ID31/
Re: [COOT] Problem displaying R3 spacegroup maps in coot
> This is TERRIBLY complicated - there must be an easier way.. Paul?? The Sftools part (4) is complicated ? Or playing with powder patterns of proteins ? Because 1) 2) 3) are the normal steps with powder ... Regards, -- Watier Yves PhD Student, European Synchrotron Radiation Facility (ESRF) Experiments Division / Materials Science Group ID31 high resolution powder diffraction beamline. 6 Rue Jules Horowitz, BP 220, 38043 Grenoble, Cedex 9, France. Office: 10.01.06 Tel. (+)33(0)4.76.88.29.67 Fax. (+)33(0)4.76.88.27.07 http://www.esrf.fr/UsersAndScience/Experiments/MaterialsScience/ID31/
Re: [COOT] Problem displaying R3 spacegroup maps in coot
Hi, Problem resolved ! Thanks to Jon Wright ! Here is the tip if someone google here (me probably). 1) The GSAS file should be as it should be for a R3 spacegroup, with : CRS1 SG SYM R3 1146 2) Then compute the map with fourrier. 3) Then export it with Gsas2map ( need to set the SG as 1146 the first time) to CCP4 format. At this moment the ccp4 map is not openable by coot. 4) Use sftools, with MAPIN exportMap.ccp4 , MAPOUT thisMapWillWork.ccp4 then play (or work) with coot ... Thanks everybody ! -- Watier Yves PhD Student, European Synchrotron Radiation Facility (ESRF) Experiments Division / Materials Science Group ID31 high resolution powder diffraction beamline. 6 Rue Jules Horowitz, BP 220, 38043 Grenoble, Cedex 9, France. Office: 10.01.06 Tel. (+)33(0)4.76.88.29.67 Fax. (+)33(0)4.76.88.27.07 http://www.esrf.fr/UsersAndScience/Experiments/MaterialsScience/ID31/
Re: [COOT] Problem displaying R3 spacegroup maps in coot
>> Try to change the SG to H3. Worked for me > or "R3 :H" or "R3: R" depending on indexing convention. Thanks for the tips, If I try to change the ccp4 spacegroup number to H3 into my GSAS (1146 => 146) EXP file, coot refuse to open it "Bad ASU (inconsistant gridding?)" . Any idea from where it can come ? -- CCP4 map filename: FCLF.ccp4 INFO:: map file type was determined to be CCP4 type allocating space in read_ccp4_map attempting to read CCP4 map: FCLF.ccp4 Xmap: Internal map ASU error - R 3 Nuvw = ( 160, 160, 76) WARNING:: failed to read FCLF.ccp4 Bad ASU (inconsistant gridding?). closing CCP4 map: FCLF.ccp4 DEBUG:: Erasing the back molecule 2 which says that it has molecule number 2 Read map FCLF.ccp4 failed ------ -- -- Watier Yves PhD Student, European Synchrotron Radiation Facility (ESRF) Experiments Division / Materials Science Group ID31 high resolution powder diffraction beamline. 6 Rue Jules Horowitz, BP 220, 38043 Grenoble, Cedex 9, France. Office: 10.01.06 Tel. (+)33(0)4.76.88.29.67 Fax. (+)33(0)4.76.88.27.07 http://www.esrf.fr/UsersAndScience/Experiments/MaterialsScience/ID31/
[COOT] Problem displaying R3 spacegroup maps in coot
Dear coot users, I've got a strange map while trying to load an R3 map. I've got no problem when I try within pymol. No errors messages appears in the coot console. The map is compute via the fourrier option of GSAS, and export with Gsas2map. The ccp4 number for R3 is 1146 (according to the symop.lib) for the iucr it's 146. For illustration I attach a screen capture with a Fcalc map + the model, coot vs pymol, same map, same molecule same orientation... not easy to spot the problem... Did someone experience similar problems with trigonal maps ? Any idea how to fix it ? last coot version tested is the nightly coot-0.5-pre-1-revision-1254-binary-Linux-i386-redhat-8.0-python.tar.gz 11-Jul-2008 12:53 96M. Best regards, -- Watier Yves PhD Student, European Synchrotron Radiation Facility (ESRF) Experiments Division / Materials Science Group ID31 high resolution powder diffraction beamline. 6 Rue Jules Horowitz, BP 220, 38043 Grenoble, Cedex 9, France. Office: 10.01.06 Tel. (+)33(0)4.76.88.29.67 Fax. (+)33(0)4.76.88.27.07 http://www.esrf.fr/UsersAndScience/Experiments/MaterialsScience/ID31/
