Re: [ccp4bb] Rama-Z, Ramachandran plot validation in PDB-REDO
Rama-Z is implemented in CCTBX meaning it is available to CCP4 and Phenix. Also it is reported in validation and refinement in Phenix (you get the number every time you run real- or reciprocal-space refinement!). Pavel On Mon, Jan 18, 2021 at 1:58 PM Boaz Shaanan wrote: > Hi, > Will it be possible to include the rama-z analysis in Coot (perhaps as a > plugin)? > Boaz > > Boaz Shaanan, Ph.D. > Department of Life Sciences > Ben Gurion University of the Negev > Beer Sheva > Israel > > On Jan 18, 2021 22:47, Robbie Joosten wrote: > Dear all, > > During the last CCP4 meeting, Oleg presented our collaboration with the > Phenix team, about the Ramachandran plot Z-score (or Rama-Z). Since then, > some asked for a convenient way to get this score. You are now welcome to > use: https://pdb-redo.eu/tortoize > > This is a quick and easy way to check you model. Just upload your > structure model (and restraints if you have non-standard compounds) and > press "calculate". You get the Ramachandran Z-score with an error margin > and you get the side-chain equivalent (also known as the Chi-1/Chi-2 > Z-score in WHAT_CHECK) for free. > > There are two more ways to get the score, that might be relevant for > specialized use: > 1) use the webservice to get the same values and the per-residue values in > an easy-to-parse JSON file. For example through curl with the command: curl > -F data=@1cbs_final.pdb -F > dict=@/zata/ccp4-7.1/lib/data/monomers/a/ALA.cif > https://pdb-redo.eu/tortoize. Note that the "dict" value is optional. Any > other POST on https://pdb-redo.eu/tortoize would also work. > > 2) to analyse a very large group of models you are encouraged to install > tortoize locally. It's available on https://github.com/PDB-REDO/tortoize > with a BSD license. > > The scores are also of course available after each PDB-REDO run: the > Rama-Z is one of the model quality metrics. All methods take PDB and mmCIF > formatted files as longs as they are valid, i.e. fit the current format > specification (mmCIF) or contain at least a CRYST1 record (PDB). As always, > constructive feedback is appreciated. > > If you use Rama-Z, please do cite: > Sobolev et al. A Global Ramachandran Score Identifies Protein Structures > with Unlikely Stereochemistry; Structure; > https://doi.org/10.1016/j.str.2020.08.005 > > All the best on behalf of Team REDO, > Robbie > > > > 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 > 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] Rama-Z, Ramachandran plot validation in PDB-REDO
All the (library) code is open source with a BSD license, so yes this is possible. Cheers, Robbie > -Original Message- > From: Boaz Shaanan > Sent: Monday, January 18, 2021 22:57 > To: Robbie Joosten > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Rama-Z, Ramachandran plot validation in PDB-REDO > > Hi, > Will it be possible to include the rama-z analysis in Coot (perhaps as a > plugin)? > Boaz > > Boaz Shaanan, Ph.D. > Department of Life Sciences > Ben Gurion University of the Negev > Beer Sheva > Israel > > On Jan 18, 2021 22:47, Robbie Joosten > wrote: > > Dear all, > > During the last CCP4 meeting, Oleg presented our collaboration with the > Phenix team, about the Ramachandran plot Z-score (or Rama-Z). Since then, > some asked for a convenient way to get this score. You are now welcome to > use: https://pdb-redo.eu/tortoize > > This is a quick and easy way to check you model. Just upload your structure > model (and restraints if you have non-standard compounds) and press > "calculate". You get the Ramachandran Z-score with an error margin and you > get the side-chain equivalent (also known as the Chi-1/Chi-2 Z-score in > WHAT_CHECK) for free. > > There are two more ways to get the score, that might be relevant for > specialized use: > 1) use the webservice to get the same values and the per-residue values in > an easy-to-parse JSON file. For example through curl with the command: curl > -F data=@1cbs_final.pdb -F dict=@/zata/ccp4- > 7.1/lib/data/monomers/a/ALA.cif https://pdb-redo.eu/tortoize. Note that > the "dict" value is optional. Any other POST on https://pdb-redo.eu/tortoize > would also work. > > 2) to analyse a very large group of models you are encouraged to install > tortoize locally. It's available on https://github.com/PDB-REDO/tortoize with > a BSD license. > > The scores are also of course available after each PDB-REDO run: the Rama-Z > is one of the model quality metrics. All methods take PDB and mmCIF > formatted files as longs as they are valid, i.e. fit the current format > specification (mmCIF) or contain at least a CRYST1 record (PDB). As always, > constructive feedback is appreciated. > > If you use Rama-Z, please do cite: > Sobolev et al. A Global Ramachandran Score Identifies Protein Structures > with Unlikely Stereochemistry; Structure; > https://doi.org/10.1016/j.str.2020.08.005 > > All the best on behalf of Team REDO, > Robbie > > ### > # > > 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/ > <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] Rama-Z, Ramachandran plot validation in PDB-REDO
Hi, Will it be possible to include the rama-z analysis in Coot (perhaps as a plugin)? Boaz Boaz Shaanan, Ph.D. Department of Life Sciences Ben Gurion University of the Negev Beer Sheva Israel On Jan 18, 2021 22:47, Robbie Joosten wrote: Dear all, During the last CCP4 meeting, Oleg presented our collaboration with the Phenix team, about the Ramachandran plot Z-score (or Rama-Z). Since then, some asked for a convenient way to get this score. You are now welcome to use: https://pdb-redo.eu/tortoize This is a quick and easy way to check you model. Just upload your structure model (and restraints if you have non-standard compounds) and press "calculate". You get the Ramachandran Z-score with an error margin and you get the side-chain equivalent (also known as the Chi-1/Chi-2 Z-score in WHAT_CHECK) for free. There are two more ways to get the score, that might be relevant for specialized use: 1) use the webservice to get the same values and the per-residue values in an easy-to-parse JSON file. For example through curl with the command: curl -F data="" -F dict=@/zata/ccp4-7.1/lib/data/monomers/a/ALA.cif https://pdb-redo.eu/tortoize. Note that the "dict" value is optional. Any other POST on https://pdb-redo.eu/tortoize would also work. 2) to analyse a very large group of models you are encouraged to install tortoize locally. It's available on https://github.com/PDB-REDO/tortoize with a BSD license. The scores are also of course available after each PDB-REDO run: the Rama-Z is one of the model quality metrics. All methods take PDB and mmCIF formatted files as longs as they are valid, i.e. fit the current format specification (mmCIF) or contain at least a CRYST1 record (PDB). As always, constructive feedback is appreciated. If you use Rama-Z, please do cite: Sobolev et al. A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry; Structure; https://doi.org/10.1016/j.str.2020.08.005 All the best on behalf of Team REDO, Robbie 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
[ccp4bb] Rama-Z, Ramachandran plot validation in PDB-REDO
Dear all, During the last CCP4 meeting, Oleg presented our collaboration with the Phenix team, about the Ramachandran plot Z-score (or Rama-Z). Since then, some asked for a convenient way to get this score. You are now welcome to use: https://pdb-redo.eu/tortoize This is a quick and easy way to check you model. Just upload your structure model (and restraints if you have non-standard compounds) and press "calculate". You get the Ramachandran Z-score with an error margin and you get the side-chain equivalent (also known as the Chi-1/Chi-2 Z-score in WHAT_CHECK) for free. There are two more ways to get the score, that might be relevant for specialized use: 1) use the webservice to get the same values and the per-residue values in an easy-to-parse JSON file. For example through curl with the command: curl -F data=@1cbs_final.pdb -F dict=@/zata/ccp4-7.1/lib/data/monomers/a/ALA.cif https://pdb-redo.eu/tortoize. Note that the "dict" value is optional. Any other POST on https://pdb-redo.eu/tortoize would also work. 2) to analyse a very large group of models you are encouraged to install tortoize locally. It's available on https://github.com/PDB-REDO/tortoize with a BSD license. The scores are also of course available after each PDB-REDO run: the Rama-Z is one of the model quality metrics. All methods take PDB and mmCIF formatted files as longs as they are valid, i.e. fit the current format specification (mmCIF) or contain at least a CRYST1 record (PDB). As always, constructive feedback is appreciated. If you use Rama-Z, please do cite: Sobolev et al. A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry; Structure; https://doi.org/10.1016/j.str.2020.08.005 All the best on behalf of Team REDO, Robbie 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/
