Hi George,
As you suggested , I generate a .phs phase file in shelxpro and load this
file to COOT, then COOT said:
.phs files additonally need cell and symmetry. We need a pdb file to assign
them.
then I gave COOT a corresponding pdb file to read, then COOT shut itself off
again!
Thanks.
deliang
----- Original Message -----
From: "George M. Sheldrick" <[EMAIL PROTECTED]>
To: <[email protected]>
Sent: Thursday, June 14, 2007 11:09 PM
Subject: Re: [ccp4bb] conversion of .fcf to 2fo-fc.map and fo-fc.map of ccp4
format
For all normal purposes please read the .fcf file into Coot directly, it
makes very nice maps automatically!
The binary map files from SHELXPRO were intended ONLY for input to O (and
Bobscript). In general binary map files are a BAD THING, there are often
unexpected incompatibilities (e.g. the big/little endian problem). These
days it is usually faster and wastes less disk space to calculate maps
on the fly.
The rest of this message should be skipped by most readers!
If you really want to modify the map, you can either (a) use the option in
SHELXPRO to generate a .phs phase file corresponding to different types of
map, this is ASCII and can be read by Coot and even f2mtz, or (b) take
advantage of the fact that the .fcf file is a CIF file and so every
number that appears in this file has a precisely defined meaning.
Unfortunately there is not a big choice of programs that can actually read
CIF and to make it worse, some of them only read MMCIF which (of course)
is not fully compatible with CIF, although the intention was that the core
CIF (defined in volume G of International Tables for Crystallography and
used for the .fcf file) would be a subset of all extended CIFs (like
MMCIF).
This explains why Coot first converts the .fcf file from CIF to MMCIF.
The reason that SHELXL writes CIF rather than MMCIF is that it was
originally intended for small molecules (for which CIF is the standard)
and SHELXL was written before MMCIF was invented.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
On Fri, 15 Jun 2007, U Sam wrote:
Deliang,
That's right, coot closes if you want to open map from shelxpro which is
readable only in O.
In order to read map in coot it is necessary to convert it into ccp4
format, but I am also unable to do it by mapman, although I increased
memory size (10-20 times) still I am having the error.
sam
________________________________
> Date: Thu, 14 Jun 2007 17:29:19 -0700
> From: [EMAIL PROTECTED]
> Subject: Re: [ccp4bb] conversion of .fcf to 2fo-fc.map and fo-fc.map of
> ccp4 format
> To: [email protected]
>
> Hi Inari,
> I just tried 2Fo-Fc map generated from fcf file in shelxpro. You know
> what happened when COOT opened this map? COOT automatically shut itself
> off! Maybe shelxpro only generates the map in a way COOT can't handle.
> Help, anybody!
> Deliang
> ----- Original Message -----
> From: Inari Kursula
> To: U Sam
> Cc: deliang
> Sent: Wednesday, June 13, 2007 11:12 PM
> Subject: Re: [ccp4bb] conversion of .fcf to 2fo-fc.map and fo-fc.map of
> ccp4 format
> Dear Sam,
> you can use shelxpro to calculate maps with different coefficients from
> your .fcf file. Have never used these maps in coot (only O and
> Xtalview), but I can't see a reason why they shouldn't work.
> Kind regards,
> Inari
> ====================================
> Inari Kursula, Ph. D.
> Div. of Molecular Structural Biology
> Dept. of Medical Biochemistry and Biophysics
> Karolinska Institutet
> 17177 Stockholm
> Sweden
> ====================================
> On Jun 13, 2007, at 6:12 PM, U Sam wrote:
> Hi
> I would like to create ccp4 format 2fo-fc and fo-fc map from .fcf file
> created in shelex.
> I can load .fcf file in coot to see the map. But I want to create map
> files manually by ccp4.
> I appreciate if anybody suggest the script of CCP4 or CCP4i to make
> such map files.
> Thanks
> Sam
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