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 <[log in to unmask]> 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 <[log in to unmask]>
> >
> > wrote:
> >> Have you tried changing the file extension to .ccp4 instead of .map?
> >>
> >> Cheers,
> >> Clement
> >>
> >> *From:* Appu kumar <[log in to unmask]>
> >> *Sent:* Wednesday, March 01, 2017 7:54 AM
> >> *To:* [log in to unmask]
> >> *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 <[log in to unmask]>
> >>
> >> 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
--
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Paul Scherrer Institut
Tim Gruene
- persoenlich -
OFLC/104
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297
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