Hi Nigel, Search and replace was _probably_ to done as an abstract syntax tree replacement - but I would be surprised if “O” was replaced with “self” (surprised, but not impossible) Do you have the commit I could check? Evidently if people did not notice for 2 years the code is not well tested… but equally I am surprised. Oh, found it https://github.com/cctbx/cctbx_project/commit/c0ac70cab55b41b874bdb2ec1a97d5... looking... Thanks Graeme On 21 Apr 2021, at 16:48, Nigel Moriarty mailto:[email protected]> wrote: Hi, Not sure if this message was posted earlier or not, that is why I am reposting it. I had a couple of questions about sampling backrub and sidechains using the building or refinement modules in cctbx_project/mmtbx. 1) In the file: mmtbx.building.alternate_conformations.conformer_generation.pyhttp://mmtbx.building.alternate_conformations.conformer_generation.py/ In the function def __call__: the if statements for checking whether the sampled side chain conformation is a rotamer outlier or not, the check in the if statement is for "selfUTLIER". Also in the function set_up_backrub(self): the atom "O" for the previous residue is not included in the backrun motion, as a result this atom is not moved when the backrub is implemented. I was just wondering if this is a mistake (possibly all instances of "O" being replaced by "self" which would explain both these things, and some other instances throughout the file), or is this code old and not used anymore? This is exactly the case. It appears that Graeme Winter did a search and replace two years ago. I did a git blame and it shows that the original code was written by Nat Echols 5 years ago. The fact that the code is broken would indicate that the code is not used or tested well. Feel free to correct it and submit a pull request. 2) When trying to run fit_residues.py and tst_fit_residues* scripts in mmtbx.refinement.real_space, I encountered errors mainly related to chem_data/rotamer_chi_angles/ not being present. Looks like this data is not distributed with cctbx. Is this correct, or maybe there is some other known issue ? You may need the chem_data directory from a Phenix installation. Nigel I look forward to hearing from you. Thanks, Swati _______________________________________________ cctbxbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/cctbxbb _______________________________________________ cctbxbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/cctbxbb -- 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

I just did a git blame and saw you committed the line with "selfUTLIER". This answered one question. Bugs are a different matter. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464 On Wed, Apr 21, 2021 at 8:59 AM Winter, Graeme (DLSLtd,RAL,LSCI) < [email protected]> wrote:

OK, I checked the diffs and it really is just a load of fixing

function ( args ) :

type stuff

Are you sure I made the change here?

Thanks Graeme

On 21 Apr 2021, at 16:53, Winter, Graeme (DLSLtd,RAL,LSCI) < [email protected]> wrote:

Hi Nigel,

Search and replace was _probably_ to done as an abstract syntax tree replacement - but I would be surprised if “O” was replaced with “self” (surprised, but not impossible)

Do you have the commit I could check? Evidently if people did not notice for 2 years the code is not well tested… but equally I am surprised.

Oh, found it

https://github.com/cctbx/cctbx_project/commit/c0ac70cab55b41b874bdb2ec1a97d5...

looking...

Thanks Graeme

On 21 Apr 2021, at 16:48, Nigel Moriarty wrote:

...

Hi,

Not sure if this message was posted earlier or not, that is why I am reposting it.

I had a couple of questions about sampling backrub and sidechains using the building or refinement modules in cctbx_project/mmtbx.

1) In the file: mmtbx.building.alternate_conformations.conformer_generation.py

In the function def __call__: the if statements for checking whether the sampled side chain conformation is a rotamer outlier or not, the check in the if statement is for "selfUTLIER".

Also in the function *set_up_backrub*(self): the atom "O" for the previous residue is not included in the backrun motion, as a result this atom is not moved when the backrub is implemented.

I was just wondering if this is a mistake (possibly all instances of "O" being replaced by "self" which would explain both these things, and some other instances throughout the file), or is this code old and not used anymore?

This is exactly the case. It appears that Graeme Winter did a search and replace two years ago. I did a git blame and it shows that the original code was written by Nat Echols 5 years ago. The fact that the code is broken would indicate that the code is not used or tested well. Feel free to correct it and submit a pull request.

...

2) When trying to run fit_residues.py and tst_fit_residues* scripts in mmtbx.refinement.real_space, I encountered errors mainly related to chem_data/rotamer_chi_angles/ not being present. Looks like this data is not distributed with cctbx. Is this correct, or maybe there is some other known issue ?

You may need the chem_data directory from a Phenix installation.

Nigel

...

I look forward to hearing from you.

Thanks, Swati _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

--

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

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

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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

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Hi everyone, Thanks a lot for the information. Seems like you all agree that this code is old and not tested. Regarding the chem_data question, I don't have a phenix license. I was able to get some chem_data information (geostd from sourceforge and mon_lib and rama and rota evaluation information from the Richardson lab), but not the directory that is needed for the fit_residue* functions. However, the individual_sites real space refinement seems to be working fine, both the test script as well as when I try it myself. Am I correct is assuming that it does not require any additional data (apart from the openly available data I was able to get) or the code is not throwing any errors and just skipping steps? Thanks a lot, Swati On Wed, Apr 21, 2021 at 9:18 PM Nigel Moriarty wrote:

Hi,

...

Not sure if this message was posted earlier or not, that is why I am reposting it.

I had a couple of questions about sampling backrub and sidechains using the building or refinement modules in cctbx_project/mmtbx.

1) In the file: mmtbx.building.alternate_conformations.conformer_generation.py

In the function def __call__: the if statements for checking whether the sampled side chain conformation is a rotamer outlier or not, the check in the if statement is for "selfUTLIER".

Also in the function *set_up_backrub*(self): the atom "O" for the previous residue is not included in the backrun motion, as a result this atom is not moved when the backrub is implemented.

I was just wondering if this is a mistake (possibly all instances of "O" being replaced by "self" which would explain both these things, and some other instances throughout the file), or is this code old and not used anymore?

This is exactly the case. It appears that Graeme Winter did a search and replace two years ago. I did a git blame and it shows that the original code was written by Nat Echols 5 years ago. The fact that the code is broken would indicate that the code is not used or tested well. Feel free to correct it and submit a pull request.

...

2) When trying to run fit_residues.py and tst_fit_residues* scripts in mmtbx.refinement.real_space, I encountered errors mainly related to chem_data/rotamer_chi_angles/ not being present. Looks like this data is not distributed with cctbx. Is this correct, or maybe there is some other known issue ?

You may need the chem_data directory from a Phenix installation.

Nigel

...

I look forward to hearing from you.

Thanks,

Swati _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb