Dear David, Thank you for your help. It seems the problem is due to the Pymol program. I could only see 3 chains in Pymol from the assembly PDB downloaded from the RCSB website (biological assembly 1 PDB file). If I use UCSF Chimera, I can see 18 chains. With others' help, I can also use "sym" command in UCSF Chimera to generate assembly in UCSF Chimera, but Pymol just could not do the job.
Best, Xiao On Fri, May 21, 2021 at 6:50 AM David Armstrong <dav...@ebi.ac.uk> wrote: > Dear Xiao, > > For public entries in the PDB archive, it is possible to download the > coordinates of the assemblies defined in the PDB entry. > > If you visit the page for the entry at PDBe (pdbe.org/5l93) and select > 'Downloads' you have the option to download various data, including mmCIF > files containing the full assemblies. In this case, "Assembly 1 (mmCIF; > gz)" would give you the full structure. > > Kind Regards, > David Armstrong > > On 21/05/2021 11:33, Xiao Lei wrote: > > Dear Community, > > I wonder if there is a way to generate symmetry mates of EM structures? > For example for PDB code 5L93, I tried PISA assembly server and Pymol to > generate assembly (18 chains) but failed because it is not a crystal > structure. I tried to download assembly directly from RCSB databank but > after I opened the downloaded structure in Pymol, I can only see 3 chains, > although the RCSB databank indicates the assembly should contain 18 chains. > > Best wishes and thank you in advance, > > Xiao > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > -- > David Armstrong > Outreach and Training Coordinator > PDBe > European Bioinformatics Institute (EMBL-EBI) > European Molecular Biology Laboratory > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD UK > Tel: +44 1223 492544 > > ######################################################################## 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/
