PS: CIF can be converted to PDB easily using (for instance) gemmi:
$ gemmi convert OEX.cif OEX.pdb
All available options can be listed using:
$ gemmi convert -h
Be aware that an output PDB file will have issues for 5-letter-code
monomers as the PDB format can accommodate only monomer codes up to 3
characters.
Cheers,
Martin
On 14/11/2024 12:41, Martin Malý wrote:
Dear Guenter,
The old CCP4i interface is not supported. Please try to use AceDRG in
CCP4i2 or CCP4Cloud or run it from command line. There have been
actually many changes in the last years related to ligands in general
(e.g. monomer codes with 5 characters, necessity of the mmCIF file
format, monomer library updates, ...). So it is worth using up-to-date
software when dealing with ligands. You can contact me directly if you
are not happy with the current AceDRG implementation in CCP4i2 as I
participate in its maintenance in the last months.
Best wishes,
Martin
On 14/11/2024 11:23, Fei Long wrote:
Dear Guenter,
Acedrg has stopped producing the final output files of pdb format
since CCD/PDB introduced 5-letter ligand code, because pdb format
could not handle with that. However, it seems there are still strong
requests for the output pdb files, acedrg will produce pdb files when
the ligand codes are 3 letters or no ligand codes are input, in the
coming new version.
What I talked here is about running acedrg via command lines. I do
not know what happens in gui.
Best wishes,
Fei
On 2024-11-13 18:41, Guenter Fritz wrote:
Dear all,
I have a strange acedrg error. I usually run via command line for a
set of smiles.
If I run it from command line, the job runs, but acedrg writes only a
cif and not a pdb anymore.
If I run acedrg from the gui (ccp4i old gui) I get for any input
(smiles or cif) an error:
......
***************************************************************************
The program run with command:
/opt/software/CCP4/9.0/ccp4-9/bin/ccp4-python -m acedrg -c
/scratch/guenter/S100A9/glycine.cif -o
/home/guenter/PROJEKTE/NQR/152/152_14
has failed with error message
[19:31:32] non-ring atom 3 marked aromatic
***************************************************************************
#CCP4I TERMINATION STATUS 0 "[19:31:32] non-ring atom 3 marked
aromatic"
#CCP4I TERMINATION TIME 13 Nov 2024 19:31:35
#CCP4I MESSAGE Task failed
Any input is appreciated.
Thanks and best regards, Guenter
-------------------------
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
---
Dr. Fei Long
Structural Studies Division
UKRI Laboratory of Molecular Biology
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge
CB2 0QH UK
Email:fl...@mrc-lmb.cam.ac.uk
########################################################################
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/
########################################################################
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/
########################################################################
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/
