Keitaro, Please disregard my previous email. After informing myself on how Refmac is executed from command line (via online websites & log files from GUI Refmac runs) and many trial and error executions, I was able to execute refmac5 from command line and was able to recycle the code for execution of refmacat.
Best, Nick Clark On Mon, May 29, 2023 at 1:48 PM Nicholas Clark <ndcla...@buffalo.edu> wrote: > Hi Keitaro, > > Thanks for the response. Is there documentation somewhere on how to run > refmacat (like an example for Crystallographic data refinement, I found the > one for CryoEM data but )? I have made multiple attempts to get this to run > on my end but when I input the command I get "Waiting for input.." as a > response and it just seems to hold here. I've tried this with multiple > different iterations but even the simplest of just coordinates & > reflections yields the same response. The command I'm running is, as a > simplified example with only coordinates & reflections: > > refmacat XYXIN /location/for/coordinates.pdb HKLIN > /location/for/reflections.mtz > > I've also tried passing a full list of the Refmac5 arguments but I still > get a hold at "waiting for input". I'm sure I'm not passing something > appropriately, but I'm not very familiar with running CCP4 programs on the > command line. Any assistance would be appreciated! > > Interestingly, when I use the "LINK" and change the type to "peptide" in > Coot only the linkage to the preceding residue is broken during refinement, > the subsequent residue remains bonded. I can "circumvent" this issue by > adding an alternate conformation to the preceding residue (i.e., both > covalent linkages remain). > > Best, > > Nick Clark > > On Sat, May 27, 2023 at 4:03 PM Keitaro Yamashita < > kyamash...@mrc-lmb.cam.ac.uk> wrote: > >> Because of non-standard atom names, group names of some monomers were >> changed to NON-POLYMER. In this case the hydrogen atom is only the >> problem, so changing group to peptide works unless you have hydrogen. >> Moreover, in CSO, the problematic hydrogen is removed when forming a >> peptide link. The details are described in the paper Paul mentioned. >> >> Refmac would work, if "refmacat" (explained in the paper) is used. The >> command is already available in the latest CCP4 update, but not from >> the interfaces at the moment. >> >> Best regards, >> Keitaro >> >> On Sat, 27 May 2023 at 04:02, Nicholas Clark <ndcla...@buffalo.edu> >> wrote: >> > >> > Hi Paul, >> > >> > Thank you for providing that information. Editing the restraints for >> CSO corrected the issue! Your assistance is greatly appreciated. I figured >> I was missing something :) >> > >> > Best, >> > >> > Nick Clark >> > >> > On Fri, May 26, 2023 at 10:55 PM Paul Emsley <pems...@mrc-lmb.cam.ac.uk> >> wrote: >> >> >> >> >> >> On 27/05/2023 03:46, Nicholas Clark wrote: >> >> >> >> Paul, >> >> >> >> Yes, it appears that the upper level group is "NON-POLYMER". However, >> there is an alias at the bottom that does state polymer. >> >> >> >> >> >> Hi Nick, >> >> >> >> >> >> In Coot: Edit -> Restraints... -> CSO -> OK -> Change "Non-POLYMER" to >> "peptide" and press enter in the entry, then "Apply" >> >> >> >> Now you can refine your CSO in Coot. >> >> >> >> Paul. >> >> >> >> >> >> >> >> Best, >> >> >> >> Nick Clark >> >> >> >> >> >> On Fri, May 26, 2023 at 10:37 PM Paul Emsley < >> pems...@mrc-lmb.cam.ac.uk> wrote: >> >>> >> >>> >> >>> On 27/05/2023 03:23, Nicholas Clark wrote: >> >>> >> >>> Hey Paul, >> >>> >> >>> I found the dictionary entry for CSO, it appears to be in the >> "peptide" group (under CCP4-8.0->lib->data->monomers->c->CSO.cif): >> >>> >> >>> "loop_ >> >>> _chem_comp_alias.comp_id >> >>> _chem_comp_alias.group >> >>> _chem_comp_alias.atom_id >> >>> _chem_comp_alias.atom_id_standard >> >>> CSO peptide HN2 H2" >> >>> >> >>> I've attached the file I have for your reference, as I may not be >> looking in the correct place. Also, if I'm looking in the wrong file >> location, please let me know. >> >>> >> >>> >> >>> Due to other priorities, Coot is not up to speed with the >> developments of my colleagues: >> >>> >> >>> >> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC10167671%2F&data=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7Cd20ae1e11ae4471a826c08db5eed6835%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638208146360356901%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=JXhA8CQjRF0V%2BMDfmIeegB%2Bc2rvKjT6dEofU7gcVjt4%3D&reserved=0 >> (Section 2) >> >>> >> >>> What is the value of _chem_comp.group ? That is (for the moment) what >> Coot cares about. >> >>> >> >>> >> >>> Paul. >> >>> >> >>> >> >> >> >> >> >> -- >> >> Nicholas D. Clark (He/Him) >> >> PhD Candidate >> >> Malkowski Lab >> >> University at Buffalo >> >> Department of Structural Biology >> >> Jacob's School of Medicine & Biomedical Sciences >> >> 955 Main Street, RM 5130 >> >> Buffalo, NY 14203 >> >> >> >> Cell: 716-830-1908 >> >> >> >> ________________________________ >> >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> >> >> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7Cd20ae1e11ae4471a826c08db5eed6835%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638208146360356901%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=muO6FI75NWneFDirpnv3BOUH3C%2Fat3VcNpUPKq0JIGI%3D&reserved=0 >> > >> > >> > >> > -- >> > Nicholas D. Clark (He/Him) >> > PhD Candidate >> > Malkowski Lab >> > University at Buffalo >> > Department of Structural Biology >> > Jacob's School of Medicine & Biomedical Sciences >> > 955 Main Street, RM 5130 >> > Buffalo, NY 14203 >> > >> > Cell: 716-830-1908 >> > >> > ________________________________ >> > >> > To unsubscribe from the CCP4BB list, click the following link: >> > >> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7Cd20ae1e11ae4471a826c08db5eed6835%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638208146360356901%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=muO6FI75NWneFDirpnv3BOUH3C%2Fat3VcNpUPKq0JIGI%3D&reserved=0 >> > > > -- > Nicholas D. Clark (He/Him) > PhD Candidate > Malkowski Lab > University at Buffalo > Department of Structural Biology > Jacob's School of Medicine & Biomedical Sciences > 955 Main Street, RM 5130 > Buffalo, NY 14203 > > Cell: 716-830-1908 > -- Nicholas D. Clark (He/Him) PhD Candidate Malkowski Lab University at Buffalo Department of Structural Biology Jacob's School of Medicine & Biomedical Sciences 955 Main Street, RM 5130 Buffalo, NY 14203 Cell: 716-830-1908 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
