Dear Nick, Sorry for this. Refmacat is a replacement for the refmac5 command, so it is totally unfriendly to the people who never used Refmac as a command. But it is great you managed to use it!
Best regards, Keitaro On Mon, 29 May 2023 at 22:11, Nicholas Clark <ndcla...@buffalo.edu> wrote: > > 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/
