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