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

[ccp4bb] Fw: [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: Re: Low resolution chain tracing
From: Jeff Lee jlee {- at -} SCRIPPS {- dot -} EDU
Date: 2007-06-15		Next message:
Subject: Re: microscope
From: Jens Kaiser kaiser {- at -} CALTECH {- dot -} EDU
Date: 2007-06-15


Subject: Fw: 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

----- Original Message -----
From: "deliang chen"
To: "George M. Sheldrick"
Sent: Friday, June 15, 2007 12:57 PM
Subject: Re: [ccp4bb] conversion of .fcf to 2fo-fc.map and fo-fc.map of ccp4
format


> Thanks George,
>
> Yes, COOT can open fcf.file and make beautiful maps. But I don't know
> whether COOT can generate different Fourier type maps like 2Fo-Fc,
> mFo-DFc, etc according to the fcf and pdb files I input. It seems to me
> COOT only generate Fo and Fo-Fc maps when the fcf file is loaded. Is this
> correct?
>
> many 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