Thank you Johan, these are the same results I get in Wincoot. So there is a problem with either the cif file itself or the interpretation of the (maybe malformed) cif file by coot.
original post below. Thanks & best wishes, BR ---------------------------------------------------- Dear Cootiers, Wincoot version 0.9.6 When I read the PDB format file of 7PGU downloaded from PDBe, everything is fine. If I convert both the archive and updated cif from PDBe to PDB format, everything is fine. Fine means I see chains F and N in the Go-to menu, see the Zn links , and can display Ca/backbone normal as traces. If I open the archive or updated cfif file, I see an empty chain A and B in the go-to menu, the Zn links are gone, and if I display Ca/backbone, the chain F is interpreted/displayed as single hetero atoms (also the AA images are dislayed like ligands). I find nothing offensive in the cif, but if I remove from the cif the content of the (I believe correct) loop_ _struct_asym.id... # then the empty A,B chains are gone, ca/backbone is displayed correctly as backbone traces, but the Zn links are still missing. Can someone please verify if this finding is correct and happens on other versions? My suspicion is that some part of the chain assignment is interpreted incorrectly and causes the mess. Best regards, BR ----------------------------------------------------------------- Bernhard Rupp (Hofkristallrat a. D) 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ ----------------------------------------------------------------- The hard part about playing chicken is to know when to flinch ----------------------------------------------------------------- On Sat, Dec 18, 2021 at 2:45 PM Zeelen, Johan Philip < j.zee...@dkfz-heidelberg.de> wrote: > Coot 0.9.6. EL (ccp4) and Coot 0.8.9.2-pre EL (revision count 7607): > > pdb > > > > > cif > > Johan > > On 18 Dec 2021, at 22:43, Bernhard Rupp <hofkristall...@gmail.com> wrote: > > Perfect,same so far - now can you please - for the cif - select in display > manager the option Ca/backbone and compare that with Ca/backbone for the > PDB? > Thx, BR > ----------------------------------------------------------------- > Bernhard Rupp (Hofkristallrat a. D) > 001 (925) 209-7429 > +43 (676) 571-0536 > b...@ruppweb.org > hofkristall...@gmail.com > http://www.ruppweb.org/ > ----------------------------------------------------------------- > The hard part about playing chicken > is to know when to flinch > ----------------------------------------------------------------- > > > On Sat, Dec 18, 2021 at 1:18 PM Zeelen, Johan Philip < > j.zee...@dkfz-heidelberg.de> wrote: > >> Dear Bernhard, >> >> here the result from Coot 0.9.6 EL (ccp4) on Mac Catalina >> (I get the same result with Coot 0.8.9.2-pre EL (revision count 7607) on >> Mac Catalina) >> >> PDB: >> <PastedGraphic-5.png> >> <PastedGraphic-1.png> >> >> INFO:: Reading coordinate file: …./7pgu.pdb >> PDB file ….../7pgu.pdb has been read. >> INFO:: Found 1 models >> Model 1 had 8 links >> >> >> CIF >> <PastedGraphic-4.png> >> <PastedGraphic-2.png> >> >> INFO:: Reading coordinate file: …../7pgu.cif >> mmCIF file …./7pgu.cif has been read. >> INFO:: Found 1 models >> Model 1 had 0 links >> >> Johan >> >> On 18 Dec 2021, at 20:48, Bernhard Rupp <hofkristall...@gmail.com> wrote: >> >> Dear Cootiers, >> >> Wincoot version 0.9.6 >> >> When I read the PDB format file of 7PGU downloaded from PDBe, everything >> is fine. >> If I convert both the archive and updated cif from PDBe to PDB format, >> everything is fine. >> Fine means I see chains F and N in the Go-to menu, see the Zn links , and >> can display Ca/backbone normal as traces. >> >> If I open the archive or updated cfif file, I see an empty chain A and B >> in the go-to menu, the Zn links are gone, and if I display Ca/backbone, the >> chain F is interpreted/displayed as single hetero atoms (also the AA images >> are dislayed like ligands). >> >> I find nothing offensive in the cif, but if I remove from the cif the >> content of the (I believe correct) >> loop_ >> _struct_asym.id... >> # >> then the empty A,B chains are gone, ca/backbone is displayed correctly as >> backbone traces, but the Zn links are still missing. >> >> Can someone please verify if this finding is correct and happens on other >> versions? >> My suspicion is that some part of the chain assignment is interpreted >> incorrectly and causes the mess. >> >> Best regards, BR >> ----------------------------------------------------------------- >> Bernhard Rupp (Hofkristallrat a. D) >> 001 (925) 209-7429 >> +43 (676) 571-0536 >> b...@ruppweb.org >> hofkristall...@gmail.com >> http://www.ruppweb.org/ >> ----------------------------------------------------------------- >> The hard part about playing chicken >> is to know when to flinch >> ----------------------------------------------------------------- >> >> ------------------------------ >> >> To unsubscribe from the COOT list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 >> >> >> > ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
