Greetings, Chimera's ViewDock tool does not read .crd format. The help page for that tool lists the formats it can use: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html> However, the SwissDock website may also give you other files that you could open in Chimera. The "old" SwissDock website would give you an output file for Chimera (not .crd). See their old website including a video with instructions of how to view the results in Chimera: <http://old.swissdock.ch/> But maybe you tried the "new" website: <https://www.swissdock.ch/> I have not tried the new website but their own help page explains their output files: <https://www.swissdock.ch/FAQ.php> See answer to #2," What can I find in the results folder?" "Once you untar the results.tar.gz file you obtain a results folder, in which you can find, for Attracting Cavities: • parameters: the file containing your query parameters • result.dock4: the result file containing ligand poses • extra.par: the parameter file for the ligand and small molecules present • ligand.pdb: the ligand coordinate file • extra.rtf: the topology file for the ligand and small molecules present • receptor.crd: the receptor coordinate file • receptor.pdb: the receptor PDB file • receptor.psf: the receptor protein structure file For AutoDock Vina: • parameters: the file containing your query parameters • ligand.pdbqt: the pdbqt file of your ligand used for Vina • system.pdbqt: the pdbqt file of your target used for Vina • vina_out.pdb: the result file containing different ligand poses • vina_out.pdbqt: the result file in pdbqt format containing different ligand poses • and your query files" So there is no reason to open .crd anyway, since you could open receptor.pdb instead of receptor.crd if you need to show it. Also that is not even the results anyway, it is only the receptor. If you were using the AutoDock Vina option, you can view the vina_out.pdbqt file with Chimera's ViewDock tool. If you were using the Attracting Cavities option, it seems like the output is "result.dock4" ... I don't know what format that is, so I don't know if you can view that in Chimera or not. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 2, 2024, at 3:09 AM, safi ch via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Greetings, hope you are doing well. I want your guidance on how can I open a .crd file on UCSF Chimera. I am working on a protein and its mutants and performed their docking via Swiss Dock, it gave results in form of .crd file that I cannot open. My supervisor also has no idea how to open it, so please help me in this regard, I need to open it to work further on my research. Waiting for your kind response please.