isolde write phenixRsrInput – how to restrain ligands?
Hi Tristan, I am trying to phenix real-space refine a structure containing AMPPNP, which I have modelled very accurately with ISOLDE. I create inputs using the isolde write phenixRsrInput command, including the restrainPositions true and includeHydrogens true arguments (which normally works perfectly). However, in this case, the Rsr output yields AMPPNPs with bond-length RMSZs > 2, although this is not the case in the input model itself. Would you be able to advise as to how I can potentially restrain the AMPPNP heavy atoms from the ISOLDE model as well? I am not a phenix expert, so not having to create these manually would be ideal. Perhaps a phenix command that will automatically generate an appropriate restraints file (to append to the isolde write phenixRsrInput command or phenix.real_space_refine itself), and/or lines that may be added to the real_space_refine.eff file created by ISOLDE? Any help would be immensely appreciated. Best regards, Taha
Hello Taha, Not sure why position restraints are not sufficient to keep the ligand atoms from moving too much. You could also try reference-model restraints, using the starting model as reference (but maybe this is already how ISOLDE sets up the parameter file for phenix.real_space_refine, I don’t remember). If this ligand needs custom restraints, you should be able to generate them either with the eLBOW tool in the Phenix suite (I haven’t tried it) or with the Grade2 server if you know the 3-letter code for this molecule: https://grade.globalphasing.org/cgi-bin/grade2_server.cgi I have never needed this, but I guess you can then edit the parameter file to add a parameter pointing to this restraint file. I hope this helps, Guillaume On 6 Nov 2024, at 14:33, Shahid, Taha (Dr.) via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hi Tristan, I am trying to phenix real-space refine a structure containing AMPPNP, which I have modelled very accurately with ISOLDE. I create inputs using the isolde write phenixRsrInput command, including the restrainPositions true and includeHydrogens true arguments (which normally works perfectly). However, in this case, the Rsr output yields AMPPNPs with bond-length RMSZs > 2, although this is not the case in the input model itself. Would you be able to advise as to how I can potentially restrain the AMPPNP heavy atoms from the ISOLDE model as well? I am not a phenix expert, so not having to create these manually would be ideal. Perhaps a phenix command that will automatically generate an appropriate restraints file (to append to the isolde write phenixRsrInput command or phenix.real_space_refine itself), and/or lines that may be added to the real_space_refine.eff file created by ISOLDE? Any help would be immensely appreciated. Best regards, Taha VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
(Guillaume’s reply made me realise this was an email to the chimerax-users list… re-sending my reply) Hi Taha, Hmm... the most likely explanation for this is a mismatch between Phenix's built-in restraints for AMPPNP (found in $PHENIX/modules/chem_data/geostd/a/data_ANP.cif) and the reference values used by the PDB (based on Mogul: https://www.wwpdb.org/validation/FAQs#ligand-geometry-validation). If you have a Mogul license you could consider generating your own restraints using phenix.elbow (reach out to Nigel Moriarty for help with that)... but in all honesty, if you check by eye and the ligand still looks fine, I'd consider just not sweating too much about this level of detail. Best, Tristan On Thu, 7 Nov 2024 at 10:33, Guillaume Gaullier via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello Taha,
Not sure why position restraints are not sufficient to keep the ligand atoms from moving too much. You could also try reference-model restraints, using the starting model as reference (but maybe this is already how ISOLDE sets up the parameter file for phenix.real_space_refine, I don’t remember).
If this ligand needs custom restraints, you should be able to generate them either with the eLBOW tool in the Phenix suite (I haven’t tried it) or with the Grade2 server if you know the 3-letter code for this molecule: https://grade.globalphasing.org/cgi-bin/grade2_server.cgi I have never needed this, but I guess you can then edit the parameter file to add a parameter pointing to this restraint file.
I hope this helps,
Guillaume
On 6 Nov 2024, at 14:33, Shahid, Taha (Dr.) via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Tristan,
I am trying to phenix real-space refine a structure containing AMPPNP, which I have modelled very accurately with ISOLDE.
I create inputs using the *isolde write phenixRsrInput *command, including the *restrainPositions true* and * includeHydrogens true* arguments (which normally works perfectly).
However, in this case, the Rsr output yields AMPPNPs with bond-length RMSZs > 2, although this is not the case in the input model itself.
Would you be able to advise as to how I can potentially restrain the AMPPNP heavy atoms from the ISOLDE model as well? I am not a phenix expert, so not having to create these manually would be ideal.
Perhaps a phenix command that will automatically generate an appropriate restraints file (to append to the *isolde write phenixRsrInput* command or *phenix.real_space_refine* itself), and/or lines that may be added to the* real_space_refine.eff* file created by ISOLDE?
Any help would be immensely appreciated.
Best regards,
Taha
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Hi Tristan and Guillaume, Many thanks to you both for your immensely helpful replies. I didn’t have a Mogul license - but I managed to get Mogul restraints for ANP from the Grade Web Server. I reran phenix.real_space_refine using this ANP restraints file as an additional argument, and the RMSZ scores for the ligands now come out fine in the validation report. Visually they look identical and as good as each other though. Best, Taha On 7 Nov 2024, at 10:38, Tristan Croll <tcroll@altoslabs.com> wrote: ***CAUTION:*** This email was sent from an EXTERNAL source. Think before clicking links or opening attachments. (Guillaume’s reply made me realise this was an email to the chimerax-users list… re-sending my reply) Hi Taha, Hmm... the most likely explanation for this is a mismatch between Phenix's built-in restraints for AMPPNP (found in $PHENIX/modules/chem_data/geostd/a/data_ANP.cif) and the reference values used by the PDB (based on Mogul: https://www.wwpdb.org/validation/FAQs#ligand-geometry-validation). If you have a Mogul license you could consider generating your own restraints using phenix.elbow (reach out to Nigel Moriarty for help with that)... but in all honesty, if you check by eye and the ligand still looks fine, I'd consider just not sweating too much about this level of detail. Best, Tristan On Thu, 7 Nov 2024 at 10:33, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hello Taha, Not sure why position restraints are not sufficient to keep the ligand atoms from moving too much. You could also try reference-model restraints, using the starting model as reference (but maybe this is already how ISOLDE sets up the parameter file for phenix.real_space_refine, I don’t remember). If this ligand needs custom restraints, you should be able to generate them either with the eLBOW tool in the Phenix suite (I haven’t tried it) or with the Grade2 server if you know the 3-letter code for this molecule: https://grade.globalphasing.org/cgi-bin/grade2_server.cgi I have never needed this, but I guess you can then edit the parameter file to add a parameter pointing to this restraint file. I hope this helps, Guillaume On 6 Nov 2024, at 14:33, Shahid, Taha (Dr.) via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hi Tristan, I am trying to phenix real-space refine a structure containing AMPPNP, which I have modelled very accurately with ISOLDE. I create inputs using the isolde write phenixRsrInput command, including the restrainPositions true and includeHydrogens true arguments (which normally works perfectly). However, in this case, the Rsr output yields AMPPNPs with bond-length RMSZs > 2, although this is not the case in the input model itself. Would you be able to advise as to how I can potentially restrain the AMPPNP heavy atoms from the ISOLDE model as well? I am not a phenix expert, so not having to create these manually would be ideal. Perhaps a phenix command that will automatically generate an appropriate restraints file (to append to the isolde write phenixRsrInput command or phenix.real_space_refine itself), and/or lines that may be added to the real_space_refine.eff file created by ISOLDE? Any help would be immensely appreciated. Best regards, Taha VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT
participants (3)
-
Guillaume Gaullier -
Shahid, Taha (Dr.) -
Tristan Croll