Hi Tom I forgot to add, in addition to the non-standard protein residues, there are also a couple of errors, attributed to terminal OH group not added. The ChimeraX version here is: 1.2.dev202102050202 (2021-02-05). The commands I used were:
open 5gup; open 9539 from emdb coulombic #1 surface #2
After this, I get this error (the residue list below is not complete, but I have left a few to help gauge the error): The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: /2 SER 79... ... /v GLU 452 /x MET 289 Using Amber 20 recommended default charges and atom types for standard residues Traceback (most recent call last): File "/Users/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/cmd_line/tool.py", line 275, in execute cmd.run(cmd_text) File "/Users/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 2852, in run result = ci.function(session, **kw_args) File "/Users/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/coulombic/cmd.py", line 90, in cmd_coulombic assign_charges(session, needs_assignment, his_scheme, charge_method, File "/Users/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/coulombic/coulombic.py", line 86, in assign_charges add_charges(session, charged_residues, method=charge_method, status=status) File "/Users/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/add_charge/charge.py", line 19, in add_charges uncharged_res_types = add_standard_charges(session, residues, status=status, query_user=query_user, File "/Users/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/add_charge/charge.py", line 176, in add_standard_charges for res_type, residues in uncharged_res_types.items(): RuntimeError: dictionary changed size during iteration RuntimeError: dictionary changed size during iteration File "/Users/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/add_charge/charge.py", line 176, in add_standard_charges for res_type, residues in uncharged_res_types.items(): See log for complete Python traceback. Thanks Yaikhomba ________________________________ From: Y. Mutum <ym337@cam.ac.uk> Sent: 14 February 2021 11:02 To: Tom Goddard <goddard@sonic.net> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Coloring Atoms by Hydrohpobicity and Electrostatic potential Hi Tom Thanks for this. I've realised that the electrostatic calculation doesn't work, if there are posttranslationallymodified residues. In the case of pdb:6g2j for example, there's 2MR (dimethylated arginine). Could we please have a fix for this too? Thanks Yaikhomba Get Outlook for Android<https://aka.ms/ghei36> ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Saturday, February 13, 2021 9:06:59 PM To: Y. Mutum <ym337@cam.ac.uk> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Coloring Atoms by Hydrohpobicity and Electrostatic potential You can color a cryoEM map surface #2 directly using coulombic #1 surface #2 and also mlp should work mlp #1 surface #2 but the mlp command has a bug that prevents that from working -- I will fix it next week. Tom On Feb 13, 2021, at 6:07 AM, Y. Mutum <ym337@cam.ac.uk<mailto:ym337@cam.ac.uk>> wrote: Hi I tried looking up on colouring atoms by hydrophobicity/ electrostatic potential, but couldn't find a way to work in my current model. So, please excuse me if this is redundant. I am working with a pdb: 6j5k and was thinking of a way to color the atoms by hydrophobicity. From this, the idea is to also use this atomic model to color a map (a cryoEM map MRC format) based on hydrophobicity, using the command 'color zone'. First, I tried to generate a 'mlp' using the command:
mlp #1 map true color true
Even after saving the volumes in .mrc format, I am not sure how to load them up to 'color the atoms by hydrophobicity'; the command 'color sample' only seems to accept the surfaces for colouring. I also looked up coloring by attribute - but the hydrophobicity/ electrostatic doesn't seem to be a part of it. Also, there are lots of subunits/ chains, so is there a more straightforward way to load these hydrophobic-potential-maps later and color the atoms by hydrophobicity? In this particular case, I am trying to color the 'whole' pdb model and the cryo-EM map by hydrophobicity EMD-0667<https://www.emdataresource.org/EMD-0667>. Any workaround suggestions would be helpful for electrostatic too. Thanks Yaikhomba _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users