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/
