While to answering the question on mtz availability or conversion, I do find 
the “Fetch PDB and Maps from PDB-REDO…” option in Coot’s “File” menu the 
easiest way to get maps for inspection (with some fixes to the structure as 
well), even if not quite the same as the authors would have looked at.

Best, Marko

From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Yong Wang
Sent: 14 January 2025 17:07
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [EXTERNAL] [ccp4bb] access to the electron density maps 
of a PDB entry

We also recently found out that mtz files are no longer available for download 
from RCSB and structure factor cif files may or may not contain map 
coefficients, depending on the entry.

For this particular entry, 8hbk, the map coefficients are actually contained in 
the 8hbk-sf.cif file.  You may not be able to display the map from cif directly 
in Coot but converting to mtz first works.

Yong

From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Yong Tang
Sent: Tuesday, January 14, 2025 9:38 AM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: [EXTERNAL] [ccp4bb] access to the electron density maps of a PDB entry

Dear all, Taking a random PDB entry 8hbk as an example, at one point of time, 
we have access to a phase file called 8hbk_phases. mtz under the download 
section in https: //www. rcsb. org/structure/8hbk However that option doesn't 
seem to be

Dear all,

Taking a random PDB entry 8hbk as an example, at one point of time, we have 
access to a phase file called 8hbk_phases.mtz under the download section in 
https://www.rcsb.org/structure/8hbk<https://urldefense.com/v3/__https:/www.rcsb.org/structure/8hbk__;!!A_kSX19cfVk!HdgsgNwhr6a_jzlMwNUyo6YabEgda94JJF6faMTvEEMz0w50x6bHOLGn3_zWVoUWKNFT1XWdjGZcawnuv5kllA$>
 However that option doesn't seem to be available anymore in general.

I do understand PDBe offers electron density maps (8hbk.ccp4 and 8hbk_diff.ccp4 
separately)- is that our go-to nowadays when we would like to inspect the maps 
of any particular PDB entry 
https://www.ebi.ac.uk/pdbe/entry/pdb/8hbk<https://urldefense.com/v3/__https:/www.ebi.ac.uk/pdbe/entry/pdb/8hbk__;!!A_kSX19cfVk!HdgsgNwhr6a_jzlMwNUyo6YabEgda94JJF6faMTvEEMz0w50x6bHOLGn3_zWVoUWKNFT1XWdjGZcawmmWc483g$>

Please help – maybe I have missed something obvious?

Thank you! -yong

________________________________

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.com/v3/__https:/www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!A_kSX19cfVk!HdgsgNwhr6a_jzlMwNUyo6YabEgda94JJF6faMTvEEMz0w50x6bHOLGn3_zWVoUWKNFT1XWdjGZcawlHQW3fsQ$>

________________________________

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

########################################################################

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Reply via email to