Re: [ccp4bb] cryptic error message trying to use LigPlot on an unknown ligand
Dear Fred,
the error message looks like ligplot was started through a script, that
uses an environment variable, which is not set, soemthing like
${MYLIGPLOTDIR}/components.cif
In case MYLIGPLOTDIR is not set, you would get this sort of error
messages.
Best,
Tim
On Tue, 6 Apr 2021 15:47:21 +0200 Fred Vellieux
wrote:
> Hi folks,
>
> I'm trying to run Ligplot on a PDB file that contains a residue with
> type UNL (Unknown Ligand). I hadn't been using LigPlot for perhaps 2
> years now (which means that I had to reinstall, with an expired
> license, and get familiar with it again). I get the following error
> message (rather cryptic):
>
> Calling HBADD ...
> Running HBADD
> Het Group Dictionary: /components.cif
> Temporary PDB file: /tmp/lig7141158588178475829/ligplus.pdb
> Command: /LigPlus/lib/exe_linux/hbadd
> /tmp/lig7141158588178475829/ligplus.pdb /components.cif -wkdir
> /tmp/lig7141158588178475829/
> java.io.IOException: Cannot run program
> "/LigPlus/lib/exe_linux/hbadd": error=2, No such file or directory
> Other event: state
>
> Would anyone know what to make out of this message ? Otherwise is
> there another piece of software (called "app" nowadays) that could
> provide me with similar drawings ?
>
> At some stage I ran PRODRG, introduced the cif file in the file
> components.cif used by LigPlot (LigPlus). I also replaced the
> coordinate files by those returned by the PRODRG run. Always with the
> same cryptic error message provided by the software (oops, app).
>
> Thanks,
>
> Fred.
>
--
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna
Phone: +43-1-4277-70202
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Re: [ccp4bb] cryptic error message trying to use LigPlot on an unknown ligand
Hi Fred Ligplot diagram is part of PDBsum output - maybe that will work for you. Bostjan -- Bostjan Kobe FAA Australian Research Council Laureate Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) and Centre for Infectious Disease Research Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe Office: Building 76 Room 329 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland. On 6/4/21, 11:48 pm, "CCP4 bulletin board on behalf of Fred Vellieux" wrote: Hi folks, I'm trying to run Ligplot on a PDB file that contains a residue with type UNL (Unknown Ligand). I hadn't been using LigPlot for perhaps 2 years now (which means that I had to reinstall, with an expired license, and get familiar with it again). I get the following error message (rather cryptic): Calling HBADD ... Running HBADD Het Group Dictionary: /components.cif Temporary PDB file: /tmp/lig7141158588178475829/ligplus.pdb Command: /LigPlus/lib/exe_linux/hbadd /tmp/lig7141158588178475829/ligplus.pdb /components.cif -wkdir /tmp/lig7141158588178475829/ java.io.IOException: Cannot run program "/LigPlus/lib/exe_linux/hbadd": error=2, No such file or directory Other event: state Would anyone know what to make out of this message ? Otherwise is there another piece of software (called "app" nowadays) that could provide me with similar drawings ? At some stage I ran PRODRG, introduced the cif file in the file components.cif used by LigPlot (LigPlus). I also replaced the coordinate files by those returned by the PRODRG run. Always with the same cryptic error message provided by the software (oops, app). Thanks, Fred. -- MedChem, 1st F. Medicine, Charles University BIOCEV, Vestec, Czech Republic 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] cryptic error message trying to use LigPlot on an unknown ligand
What about coot? Have a look at https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/files/coot-may-2017-ligands-madrid-mcs2017-csic.pdf pp28-40 and Emsley P. (2017). Tools for ligand validation in Coot. Acta Crystallogr. D73, 203–210. https://doi.org/10.1107/S2059798317003382 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5349432/ It is called FLEV (Flatland Ligand Environment View) Regards, -Mitch Quoting Fred Vellieux : Hi folks, I'm trying to run Ligplot on a PDB file that contains a residue with type UNL (Unknown Ligand). I hadn't been using LigPlot for perhaps 2 years now (which means that I had to reinstall, with an expired license, and get familiar with it again). I get the following error message (rather cryptic): Calling HBADD ... Running HBADD Het Group Dictionary: /components.cif Temporary PDB file: /tmp/lig7141158588178475829/ligplus.pdb Command: /LigPlus/lib/exe_linux/hbadd /tmp/lig7141158588178475829/ligplus.pdb /components.cif -wkdir /tmp/lig7141158588178475829/ java.io.IOException: Cannot run program "/LigPlus/lib/exe_linux/hbadd": error=2, No such file or directory Other event: state Would anyone know what to make out of this message ? Otherwise is there another piece of software (called "app" nowadays) that could provide me with similar drawings ? At some stage I ran PRODRG, introduced the cif file in the file components.cif used by LigPlot (LigPlus). I also replaced the coordinate files by those returned by the PRODRG run. Always with the same cryptic error message provided by the software (oops, app). Thanks, Fred. -- MedChem, 1st F. Medicine, Charles University BIOCEV, Vestec, Czech Republic 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] cryptic error message trying to use LigPlot on an unknown ligand
Hi Fred, I'm currently making some similar figures and I came across PLIP https://plip-tool.biotec.tu-dresden.de/plip-web/plip/index It doesn't give the 1d plots but it gives a very nice pymol output to make 3d images. Hope that helps, Rob ce On 6/04/2021 15:47, Fred Vellieux wrote: Hi folks, I'm trying to run Ligplot on a PDB file that contains a residue with type UNL (Unknown Ligand). I hadn't been using LigPlot for perhaps 2 years now (which means that I had to reinstall, with an expired license, and get familiar with it again). I get the following error message (rather cryptic): Calling HBADD ... Running HBADD Het Group Dictionary: /components.cif Temporary PDB file: /tmp/lig7141158588178475829/ligplus.pdb Command: /LigPlus/lib/exe_linux/hbadd /tmp/lig7141158588178475829/ligplus.pdb /components.cif -wkdir /tmp/lig7141158588178475829/ java.io.IOException: Cannot run program "/LigPlus/lib/exe_linux/hbadd": error=2, No such file or directory Other event: state Would anyone know what to make out of this message ? Otherwise is there another piece of software (called "app" nowadays) that could provide me with similar drawings ? At some stage I ran PRODRG, introduced the cif file in the file components.cif used by LigPlot (LigPlus). I also replaced the coordinate files by those returned by the PRODRG run. Always with the same cryptic error message provided by the software (oops, app). Thanks, Fred. 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] cryptic error message trying to use LigPlot on an unknown ligand
Hi folks, I'm trying to run Ligplot on a PDB file that contains a residue with type UNL (Unknown Ligand). I hadn't been using LigPlot for perhaps 2 years now (which means that I had to reinstall, with an expired license, and get familiar with it again). I get the following error message (rather cryptic): Calling HBADD ... Running HBADD Het Group Dictionary: /components.cif Temporary PDB file: /tmp/lig7141158588178475829/ligplus.pdb Command: /LigPlus/lib/exe_linux/hbadd /tmp/lig7141158588178475829/ligplus.pdb /components.cif -wkdir /tmp/lig7141158588178475829/ java.io.IOException: Cannot run program "/LigPlus/lib/exe_linux/hbadd": error=2, No such file or directory Other event: state Would anyone know what to make out of this message ? Otherwise is there another piece of software (called "app" nowadays) that could provide me with similar drawings ? At some stage I ran PRODRG, introduced the cif file in the file components.cif used by LigPlot (LigPlus). I also replaced the coordinate files by those returned by the PRODRG run. Always with the same cryptic error message provided by the software (oops, app). Thanks, Fred. -- MedChem, 1st F. Medicine, Charles University BIOCEV, Vestec, Czech Republic 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/
