Secondary structure display - pdb and cif
Dear ChimeraX users and developers, I am having an issue with secondary structure display. I am real-space refining a set of 120 chains in phenix. Of these, only 10 are unique, the rest is symmetry-related. Thus, I define secondary structure elements for the 10 unique chains only. The output pdb file header contains the secondary structure elements as imposed during refinement. Displaying this pdb file in ChimeraX shows the right secondary structure. The mmcif file instead, whether I use the phenix output or generate it from the pdb myself, displays different, non-sensical structures. Secondary structure is shown in loop regions, and some actual strands and helices not recognized at all. This artifact is only shown for the 10 subunits with secondary structure definitions, the other subunits show no secondary structure at all, thus something is read in, but not correctly, apparently. Any idea what the problem could be? Could the size of the complex be an issue? The attachments show the lines from the two file types concerning secondary structure definitions. Kind regards, Stephan
Dear all, I am having an issue with secondary structure display. I am real-space refining a set of 120 chains in phenix. Of these, only 10 are unique, the rest is symmetry-related. Thus, I define secondary structure elements for the 10 unique chains only. The output pdb file header contains the secondary structure elements as imposed during refinement. Displaying this pdb file in ChimeraX shows the right secondary structure. The mmcif file instead, whether I use the phenix output or generate it from the pdb myself, displays different, non-sensical structures. Secondary structure is shown in loop regions, and some actual strands and helices not recognized at all. This artifact is only shown for the 10 subunits with secondary structure definitions, the other subunits show no secondary structure at all, thus something is read in, but not correctly, apparently. Any idea what the problem could be? Could the size of the complex be an issue? The attachments show the lines from the two file types concerning secondary structure definitions. Kind regards, Stephan
Hi Stephan I am not an expert at all but I think I was having similar problems as you are mentioning... In our case uploading the file to the pdb validation/deposition systems and getting back either of the generated files was nicely fixing our problems... Maybe you have already tried this simple thing or maybe is worthy to give it a trial * (validation is quicker: upload summary "converted file name") * (deposition requires to fill in stuff with whole sequence: re-upload files "converted file name") (Although the pdb_ extract tool was not useful for us right now as somehow some weird stuff in the loops was appearing...) Regards Marta P.D. Also working here with huge molecules On 04/03/2020 09:58, Tetter Stephan wrote:
Dear all,
I am having an issue with secondary structure display. I am real-space refining a set of 120 chains in phenix. Of these, only 10 are unique, the rest is symmetry-related. Thus, I define secondary structure elements for the 10 unique chains only. The output pdb file header contains the secondary structure elements as imposed during refinement. Displaying this pdb file in ChimeraX shows the right secondary structure. The mmcif file instead, whether I use the phenix output or generate it from the pdb myself, displays different, non-sensical structures. Secondary structure is shown in loop regions, and some actual strands and helices not recognized at all. This artifact is only shown for the 10 subunits with secondary structure definitions, the other subunits show no secondary structure at all, thus something is read in, but not correctly, apparently. Any idea what the problem could be? Could the size of the complex be an issue?
The attachments show the lines from the two file types concerning secondary structure definitions.
Kind regards,
Stephan
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Phenix used to have, and maybe still does, a problem with generating mmCIF files. In several places, it outputted the author sequence number, auth_seq_id, where it should put the label sequence number, label_seq_id. Tristan Croll has already reported one version of this bug to Phenix about 5 months ago, https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2483. Perhaps there is a newer version of Phenix that has the bug fixed? And is that the mistake you make when you generate the mmCIF from the PDB file yourself? You should be able to tell by looking at the atom_site table and the label_seq_id's for the various residues and see how that matches up to the beg_label_seq_id and end_label_seq_id values in the struct_conf table. The size of the complex is not an issue. If that's not the bug, then send me the complete mmCIF file and I'll guess what the bug is. HTH, Greg On 3/4/2020 12:58 AM, Tetter Stephan wrote:
Dear all,
I am having an issue with secondary structure display. I am real-space refining a set of 120 chains in phenix. Of these, only 10 are unique, the rest is symmetry-related. Thus, I define secondary structure elements for the 10 unique chains only. The output pdb file header contains the secondary structure elements as imposed during refinement. Displaying this pdb file in ChimeraX shows the right secondary structure. The mmcif file instead, whether I use the phenix output or generate it from the pdb myself, displays different, non-sensical structures. Secondary structure is shown in loop regions, and some actual strands and helices not recognized at all. This artifact is only shown for the 10 subunits with secondary structure definitions, the other subunits show no secondary structure at all, thus something is read in, but not correctly, apparently. Any idea what the problem could be? Could the size of the complex be an issue?
The attachments show the lines from the two file types concerning secondary structure definitions.
Kind regards,
Stephan
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participants (3)
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Greg Couch -
Marta Perez Illana -
Tetter Stephan