Re: [COOT] Reading .cif files from PDB

[Eleanor Dodson]

Does coot care? Coot Auto read mtz just looks for FWT and DELFWT etc...
Will test it ...
E

On Sat, 24 Aug 2019 at 09:03, John Berrisford  wrote:

> Hi Eleanor
>
> It this case that won't work as the CIF files we produce don't have F and
> sigF columns.
>
> John
>
> On 24 Aug 2019 07:44, Eleanor Dodson  wrote:
>
> You can read your cif file and convert it to an mtz - easy with the GUI -
> import merged data task - then read it into coot as always..
> eleanor
>
> On Fri, 23 Aug 2019 at 21:17, John Berrisford  wrote:
>
> Dear Mark
>
>
>
> In the mean time please see the instructions at
>
> https://www.wwpdb.org/validation/2017/FAQs#convert-edmap-coef
>
>
>
> Regards
>
>
>
> John
>
>
>
> *From:* Mailing list for users of COOT Crystallographic Software <
> COOT@JISCMAIL.AC.UK> *On Behalf Of *Paul Emsley
> *Sent:* 23 August 2019 19:07
> *To:* COOT@JISCMAIL.AC.UK
> *Subject:* Re: Reading .cif files from PDB
>
>
>
>
>
> On 23/08/2019 17:05, Mark Saper wrote:
>
> The sf-annotate_P1.cif file that I have generated for PDB submission
> contains the map coefficients along with the observed structure factors.
>
> _refln.pdbx_FWT
>
> _refln.pdbx_PHWT
>
> _refln.pdbx_DELFWT
>
> _refln.pdbx_DELPHWT
>
>
>
> Is there any way that Coot can read these columns from a CIF file and
> calculate a map?
>
>
>
>
>
> Not at the moment. It's on the list. Actually, it's a feature that needs
> to be added to Clipper. Once it's done, many CCP4 programs will be able to
> read such cif files also.
>
> Paul.
>
>
>
>
> --
>
> To unsubscribe from the COOT list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT=1
>
> --
>
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>
>
>



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Re: [COOT] Reading .cif files from PDB

[John Berrisford]

Hi EleanorIt this case that won't work as the CIF files we produce don't have F and sigF columns. JohnOn 24 Aug 2019 07:44, Eleanor Dodson  wrote:You can read your cif file and convert it to an mtz - easy with the GUI - import merged data task - then read it into coot as always..eleanorOn Fri, 23 Aug 2019 at 21:17, John Berrisford  wrote:Dear Mark In the mean time please see the instructions athttps://www.wwpdb.org/validation/2017/FAQs#convert-edmap-coef Regards John From: Mailing list for users of COOT Crystallographic Software  On Behalf Of Paul EmsleySent: 23 August 2019 19:07To: COOT@JISCMAIL.AC.UKSubject: Re: Reading .cif files from PDB  On 23/08/2019 17:05, Mark Saper wrote:The sf-annotate_P1.cif file that I have generated for PDB submission contains the map coefficients along with the observed structure factors. _refln.pdbx_FWT _refln.pdbx_PHWT _refln.pdbx_DELFWT _refln.pdbx_DELPHWT  Is there any way that Coot can read these columns from a CIF file and calculate a map?  Not at the moment. It's on the list. Actually, it's a feature that needs to be added to Clipper. Once it's done, many CCP4 programs will be able to read such cif files also.Paul.  To unsubscribe from the COOT list, click the following link:https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT=1 


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Re: [COOT] Reading .cif files from PDB

[Eleanor Dodson]

You can read your cif file and convert it to an mtz - easy with the GUI -
import merged data task - then read it into coot as always..
eleanor

On Fri, 23 Aug 2019 at 21:17, John Berrisford  wrote:

> Dear Mark
>
>
>
> In the mean time please see the instructions at
>
> https://www.wwpdb.org/validation/2017/FAQs#convert-edmap-coef
>
>
>
> Regards
>
>
>
> John
>
>
>
> *From:* Mailing list for users of COOT Crystallographic Software <
> COOT@JISCMAIL.AC.UK> *On Behalf Of *Paul Emsley
> *Sent:* 23 August 2019 19:07
> *To:* COOT@JISCMAIL.AC.UK
> *Subject:* Re: Reading .cif files from PDB
>
>
>
>
>
> On 23/08/2019 17:05, Mark Saper wrote:
>
> The sf-annotate_P1.cif file that I have generated for PDB submission
> contains the map coefficients along with the observed structure factors.
>
> _refln.pdbx_FWT
>
> _refln.pdbx_PHWT
>
> _refln.pdbx_DELFWT
>
> _refln.pdbx_DELPHWT
>
>
>
> Is there any way that Coot can read these columns from a CIF file and
> calculate a map?
>
>
>
>
>
> Not at the moment. It's on the list. Actually, it's a feature that needs
> to be added to Clipper. Once it's done, many CCP4 programs will be able to
> read such cif files also.
>
> Paul.
>
>
>
>
> --
>
> To unsubscribe from the COOT list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT=1
>
> --
>
> To unsubscribe from the COOT list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT=1
>



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Re: [COOT] Reading .cif files from PDB

[John Berrisford]

Dear Mark

 

In the mean time please see the instructions at

https://www.wwpdb.org/validation/2017/FAQs#convert-edmap-coef

 

Regards

 

John

 

From: Mailing list for users of COOT Crystallographic Software
 On Behalf Of Paul Emsley
Sent: 23 August 2019 19:07
To: COOT@JISCMAIL.AC.UK
Subject: Re: Reading .cif files from PDB

 

 

On 23/08/2019 17:05, Mark Saper wrote:

The sf-annotate_P1.cif file that I have generated for PDB submission
contains the map coefficients along with the observed structure factors. 

_refln.pdbx_FWT 

_refln.pdbx_PHWT 

_refln.pdbx_DELFWT 

_refln.pdbx_DELPHWT 

 

Is there any way that Coot can read these columns from a CIF file and
calculate a map?

 

 

Not at the moment. It's on the list. Actually, it's a feature that needs to
be added to Clipper. Once it's done, many CCP4 programs will be able to read
such cif files also.

Paul.

 

 

  _  

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 =1 




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Re: [COOT] Reading .cif files from PDB

[Paul Emsley]

On 23/08/2019 17:05, Mark Saper wrote:
The sf-annotate_P1.cif file that I have generated for PDB submission 
contains the map coefficients along with the observed structure factors.

_refln.pdbx_FWT
_refln.pdbx_PHWT
_refln.pdbx_DELFWT
_refln.pdbx_DELPHWT

Is there any way that Coot can read these columns from a CIF file and 
calculate a map?




Not at the moment. It's on the list. Actually, it's a feature that needs 
to be added to Clipper. Once it's done, many CCP4 programs will be able 
to read such cif files also.


Paul.





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[COOT] Reading .cif files from PDB

[Mark Saper]

The sf-annotate_P1.cif file that I have generated for PDB submission contains 
the map coefficients along with the observed structure factors.
_refln.pdbx_FWT 
_refln.pdbx_PHWT 
_refln.pdbx_DELFWT 
_refln.pdbx_DELPHWT 

Is there any way that Coot can read these columns from a CIF file and calculate 
a map?

Thanks,
Mark
___
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, U-M Medical School
Room 3220B, MSRB III   sa...@umich.edu   +1 (734) 764-3353 mobile: (734) 
276-6505




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