Re: [ccp4bb] Outlawed PDB files, what should a muggle do
Thanks David (and others who replied the same off list) Yes, this is exactly what I wanted thank you Agree that dimple should probably accept mmCIF, but for the moment I have the capacity to compute maps so jobsagoodun All the best Graeme From: David Waterman Sent: 20 September 2023 16:35 To: Winter, Graeme (DLSLtd,RAL,LSCI) Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] Outlawed PDB files, what should a muggle do gemmi convert --shorten 7qgf.cif foo.pdb ? -- David On Wed, 20 Sept 2023 at 15:57, Winter, Graeme (DLSLtd,RAL,LSCI) <6a19cead4548-dmarc-requ...@jiscmail.ac.uk<mailto:6a19cead4548-dmarc-requ...@jiscmail.ac.uk>> wrote: Looks like PDB files have been outlawed because mmCIF But dimple needs PDB files cif2pdb says nope Grey-Area work :( $ cif2pdb --help * ERROR * No cif file read on input Grey-Area work :( $ cif2pdb ~/Downloads/7qgf.cif * ERROR * No cif file read on input Grey-Area work :( $ cif2pdb CIFIN ~/Downloads/7qgf.cif * ERROR * No cif file read on input For someone who only used PDB files to get F^2 to validate processing, how best to get one *from the command line* ? Thanks Graeme -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk/>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] Outlawed PDB files, what should a muggle do
Of course the proper answer should be to fix dimple to read mmCIF (for which I would also recommend gemmi) -- David On Wed, 20 Sept 2023 at 16:35, David Waterman wrote: > gemmi convert --shorten 7qgf.cif foo.pdb > > ? > -- David > > > On Wed, 20 Sept 2023 at 15:57, Winter, Graeme (DLSLtd,RAL,LSCI) < > 6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote: > >> Looks like PDB files have been outlawed because mmCIF >> >> But dimple needs PDB files >> >> cif2pdb says nope >> >> Grey-Area work :( $ cif2pdb --help >> >> * ERROR * >> No cif file read on input >> >> Grey-Area work :( $ cif2pdb ~/Downloads/7qgf.cif >> >> * ERROR * >> No cif file read on input >> >> >> Grey-Area work :( $ cif2pdb CIFIN ~/Downloads/7qgf.cif >> >> * ERROR * >> No cif file read on input >> >> >> >> For someone who only used PDB files to get F^2 to validate processing, >> how best to get one *from the command line* ? >> >> Thanks Graeme >> >> >> -- >> This e-mail and any attachments may contain confidential, copyright and >> or privileged material, and are for the use of the intended addressee only. >> If you are not the intended addressee or an authorised recipient of the >> addressee please notify us of receipt by returning the e-mail and do not >> use, copy, retain, distribute or disclose the information in or attached to >> the e-mail. >> Any opinions expressed within this e-mail are those of the individual and >> not necessarily of Diamond Light Source Ltd. >> Diamond Light Source Ltd. cannot guarantee that this e-mail or any >> attachments are free from viruses and we cannot accept liability for any >> damage which you may sustain as a result of software viruses which may be >> transmitted in or with the message. >> Diamond Light Source Limited (company no. 4375679). Registered in England >> and Wales with its registered office at Diamond House, Harwell Science and >> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom >> >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ >> > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] Outlawed PDB files, what should a muggle do
gemmi convert --shorten 7qgf.cif foo.pdb ? -- David On Wed, 20 Sept 2023 at 15:57, Winter, Graeme (DLSLtd,RAL,LSCI) < 6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote: > Looks like PDB files have been outlawed because mmCIF > > But dimple needs PDB files > > cif2pdb says nope > > Grey-Area work :( $ cif2pdb --help > > * ERROR * > No cif file read on input > > Grey-Area work :( $ cif2pdb ~/Downloads/7qgf.cif > > * ERROR * > No cif file read on input > > > Grey-Area work :( $ cif2pdb CIFIN ~/Downloads/7qgf.cif > > * ERROR * > No cif file read on input > > > > For someone who only used PDB files to get F^2 to validate processing, how > best to get one *from the command line* ? > > Thanks Graeme > > > -- > This e-mail and any attachments may contain confidential, copyright and or > privileged material, and are for the use of the intended addressee only. If > you are not the intended addressee or an authorised recipient of the > addressee please notify us of receipt by returning the e-mail and do not > use, copy, retain, distribute or disclose the information in or attached to > the e-mail. > Any opinions expressed within this e-mail are those of the individual and > not necessarily of Diamond Light Source Ltd. > Diamond Light Source Ltd. cannot guarantee that this e-mail or any > attachments are free from viruses and we cannot accept liability for any > damage which you may sustain as a result of software viruses which may be > transmitted in or with the message. > Diamond Light Source Limited (company no. 4375679). Registered in England > and Wales with its registered office at Diamond House, Harwell Science and > Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
[ccp4bb] Outlawed PDB files, what should a muggle do
Looks like PDB files have been outlawed because mmCIF But dimple needs PDB files cif2pdb says nope Grey-Area work :( $ cif2pdb --help * ERROR * No cif file read on input Grey-Area work :( $ cif2pdb ~/Downloads/7qgf.cif * ERROR * No cif file read on input Grey-Area work :( $ cif2pdb CIFIN ~/Downloads/7qgf.cif * ERROR * No cif file read on input For someone who only used PDB files to get F^2 to validate processing, how best to get one *from the command line* ? Thanks Graeme -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
