Dear Appu, in addition to the option via Coot, you can convert SHELX map files directly to CCP4 format with shelx2map, suitable for Pymol. Shelx2map is distributed as part of CCP4 and converts both phs/pha maps and fcf maps to CCP4 format. It was designed to facilitate the use of these map in Pymol.
Unlike fcf-files, pha/phs files do not contain symmetry or unit cell information and this has to be provided via a PDB file with the -s switch. Shelx2map also has some additional command line options e.g. for making the map appear smoother (-r) or downweight weak data (-w), or not weight data at all. Best regards, Tim On Tuesday, February 28, 2017 8:37:35 PM CET Appu kumar wrote: > Hi Paul and Clement, > As suggested by the Paul, Export the map fragment from the COOT, did the > trick. It worked perfectly fine. > > Thank for valuable suggestions, indeed helpful. > > Appu > > On 28 February 2017 at 19:55, Appu kumar <[email protected]> wrote: > > Hi, > > Yes I tried renaming the file to .map, .ccp4, .map.xplor. Nothing seems > > to be making mesh in pymol around the corresponding atom. > > > > Thank you for help and time > > Appu > > > > On 28 February 2017 at 19:38, Clement Angkawidjaja <[email protected]> > > > > wrote: > >> Have you tried changing the file extension to .ccp4 instead of .map? > >> > >> Cheers, > >> Clement > >> > >> *From:* Appu kumar <[email protected]> > >> *Sent:* Wednesday, March 01, 2017 7:54 AM > >> *To:* [email protected] > >> *Subject:* Re: [ccp4bb] ANODE anomalous map in pymol > >> > >> Hi, > >> I Already did that in COOT, but PYMOL does not read it in map format. > >> Pymol fail to show mesh in isomesh command. > >> Thank you > >> > >> Appu > >> > >> On 28 February 2017 at 16:31, Paul Emsley <[email protected]> > >> > >> wrote: > >>> On 28/02/2017 20:44, Appu kumar wrote: > >>>> Dear CCP4 Users, > >>>> I ran anode to calculate the anomalous map for heavy atoms in protein. > >>>> ANODE output the > >>>> anomalous map in .pha file, which can be viewed in COOT. However, I > >>>> want to get the > >>>> anomalous map from .pha file to .map or .xplor file, which can be feed > >>>> into PYMOL to make > >>>> maps. Is there a way to extract the anomalous map information from .pha > >>>> file to .map or > >>>> .xplor file. > >>> > >>> In Coot: > >>> > >>> File -> Export Map -- -- Paul Scherrer Institut Tim Gruene - persoenlich - OFLC/104 CH-5232 Villigen PSI phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A
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