Quick navigation: Home   |    Site Map   ||    References   |    Biography   ||    Copyright   |    Other copyright   |    Contact us   |    Advert   |   
 

Re: [ccp4bb] conversion of .fcf to 2fo-fc.map and fo-fc.map of ccp4 format
- Protein crystallography

Main steps:

   - Protein purification
   - Crystallisation

Special:

   - Programs for crystallography
   - X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

   - CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous message:
Subject: conversion of .fcf to 2fo-fc.map and fo-fc.map of ccp4 format
From: "George M {- dot -} Sheldrick" gsheldr {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2007-06-15		Next message:
Subject: Re: Fw: conversion of .fcf to 2fo-fc.map and fo-fc.map of ccp4 format
From: Paul Emsley emsley {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-06-16


Subject: Re: conversion of .fcf to 2fo-fc.map and fo-fc.map of ccp4 format
From: deliang chen deliangc {- at -} UCI {- dot -} EDU
Date: 2007-06-15

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"
To:
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: deliangc@UCI.EDU
>> > Subject: Re: [ccp4bb] conversion of .fcf to 2fo-fc.map and fo-fc.map of
>> > ccp4 format
>> > To: CCP4BB@JISCMAIL.AC.UK
>> >
>> > 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
>> > ________________________________
>> > Play free games, earn tickets, get cool prizes! Join Live Search Club.
>> > Join Live Search Club!
>>
>> _________________________________________________________________
>> Hotmail to go? Get your Hotmail, news, sports and much more! Check out
>> the New MSN Mobile!
>> http://mobile.msn.com
>



ProteinCrystallography.org: Copyright 2006-2010 by Quid United Ltd