Splitting, addh, save only saves secondary structure for first model
Hi, It a multisubunit complex such as 2ast, Chimera will indicate it's better to split the model to add the hydrogens. However when after split and adding hydrogens I would like to save as 1 model which I can do but then I only get the secondary structure helices and sheets for first model. You will see there should be around 20-23 total "HELIX" for all 3 structures A,B,C in total (authors split continuous helices for some reason). However I only get the helices and sheets for model A (159 residue protein) when "saving multiple models in a single file". Is this a functionality request so that all HELIX from all models are included after split as in the original PDB file? Brian JHU
Hi Brian, Addh has nothing to do with splitting, so I'm somewhat mystified by your description. Just open the structure, addh, and save the single model as a single file. The only thing that might suggest splitting, as far as I know, is if there is an error in computing the molecular surface. However, that is just an error relating to the display of the surface and can be ignored for your purposes. Splitting does have some deficiencies as what data are duplicated, so avoid it unless there is some pressing reason to use it. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 2, 2020, at 10:33 AM, Brian Wiley <bwiley4@jhu.edu> wrote:
Hi,
It a multisubunit complex such as 2ast, Chimera will indicate it’s better to split the model to add the hydrogens. However when after split and adding hydrogens I would like to save as 1 model which I can do but then I only get the secondary structure helices and sheets for first model. You will see there should be around 20-23 total “HELIX” for all 3 structures A,B,C in total (authors split continuous helices for some reason). However I only get the helices and sheets for model A (159 residue protein) when “saving multiple models in a single file”. Is this a functionality request so that all HELIX from all models are included after split as in the original PDB file?
Brian JHU
Ah you know what. I had a surface on one of the chains (the b chain) before entering the "addh" command. You get the popup error indicating surface calculating failed when entering "addh" command if you have a surface in this case so I interpreted the error coming from the addh command. Thanks. -----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, August 3, 2020 5:04 PM To: Brian Wiley <bwiley4@jhu.edu> Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Splitting, addh, save only saves secondary structure for first model External Email - Use Caution Hi Brian, Addh has nothing to do with splitting, so I'm somewhat mystified by your description. Just open the structure, addh, and save the single model as a single file. The only thing that might suggest splitting, as far as I know, is if there is an error in computing the molecular surface. However, that is just an error relating to the display of the surface and can be ignored for your purposes. Splitting does have some deficiencies as what data are duplicated, so avoid it unless there is some pressing reason to use it. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 2, 2020, at 10:33 AM, Brian Wiley <bwiley4@jhu.edu> wrote:
Hi,
It a multisubunit complex such as 2ast, Chimera will indicate it’s better to split the model to add the hydrogens. However when after split and adding hydrogens I would like to save as 1 model which I can do but then I only get the secondary structure helices and sheets for first model. You will see there should be around 20-23 total “HELIX” for all 3 structures A,B,C in total (authors split continuous helices for some reason). However I only get the helices and sheets for model A (159 residue protein) when “saving multiple models in a single file”. Is this a functionality request so that all HELIX from all models are included after split as in the original PDB file?
Brian JHU
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Elaine Meng