- ChimeraX-users - RBVI Mailing Lists

How to hide a chain and overly the shown chain with another model
by McClean, Phillip 13 Oct '22

13 Oct '22

I have a .pdb file obtained from ColabFold. The model was developed with AlphaFold2 Multimer. It has two chains. How can I 1) hide only one chain and then 2) add a second model. The second model will be the visualized chain developed only on its own. I am looking for regions that might be different between the model with a second protein and by itself. I tried hide /c but that didn't work. Phil McClean

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Loading density files
by Tianming Qu 12 Oct '22

12 Oct '22

Dear Chimerax developers: I have a lot of density files, is there anyway I can load them at the same time and view then like a protein traj? Best, Tianming

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Problem reading ccp4 maps
by Luca Pellegrini 11 Oct '22

11 Oct '22

When I try to read ccp4 maps from Phenix Resolve_cryoEM into ChimeraX, I’ve started getting the following message: "MRC file is truncated. Failed reading 1 values, type int32” It’s ChimeraX version 1.5.dev202210110346 (2022-10-11)/ macOS Monterey/MacBook Pro 2021, M1 Pro. Best wishes, Luca

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Can you do convex hull on ChimeraX?
by Tianming Qu 10 Oct '22

10 Oct '22

Hi dear ChimeraX-Users and developers, Is ChimeraX available for drawing the convex hull of protein structures? Best, Tianming

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Fit in map, save new coords of map
by Nebojsa Bogdanovic 10 Oct '22

10 Oct '22

Hello, I open two maps and I fit #2 into #1. I need to save map #2 at it's new position, but there is no option "relative to model or map". By doing "volume resample #1 onGrid #1, I match the box sizes but the new position is not maintained after saving that new map. Is there any command/function I could do that with? Thank You and regards, Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University

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Re: [chimerax-users] alphafold contacts between 3 and more subunits
by Tom Goddard 10 Oct '22

10 Oct '22

Hi André, I added two options "replace" (default true) and "name" (default "PAE Contacts") to the alphafold contacts command. The replace option determines if existing contact pseudobonds (in the group with the specified or default name) are deleted. If replace is false the new contacts are just added to any existing ones. The name option gives the pseudobond model the specified name. So you could use alphafold contacts /A to /B alphafold contacts /B to /C replace false alphafold contacts /A to /C replace false to put all the contacts in one pseudobond submodel. If instead you wanted them in 3 different models you could use alphafold contacts /A to /B name "AB contacts" alphafold contacts /B to /C name "BC contacts" alphafold contacts /A to /C name "AC contacts" This will be in tomorrow's (Oct 11) ChimeraX daily builds. Tom > On Oct 10, 2022, at 12:38 PM, Michaelis, Andre Clemens <michaelis(a)biochem.mpg.de> wrote: > > Awesome, > Thank you so much! > > Best > André > > > —————————————————— > > >> Am 10.10.2022 um 20:50 schrieb Tom Goddard <goddard(a)sonic.net>: >> >> Hi André, >> >> The "alphafold contacts" command creates a submodel of the atomic structure containing pseudobonds with the submodel named "PAE Contacts". If you rename that submodel then it won't replace it when you do the second alphafold contacts command on the same structure. For instance, if the structure is model #1. >> >> alphafold contacts /A to /B >> rename #1.1 "AB contacts" >> alphafold contacts /B to /C >> rename #1.2 "BC contacts" >> alphafold contacts /A to /C >> >> This should be easier to do. I should add an option to the alphafold contacts command "replace false" that automatically uses new names for each group of pseudobonds. I've made a request for this. >> >> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7770 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7770> >> >> Tom >> >>> On Oct 10, 2022, at 5:47 AM, Michaelis, Andre Clemens via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Hi, >>> >>> Is it possible to draw contacts (PAE, alphafold) between more than just 2 subunits? >>> e.g.: >>> alphafold contacts /A to /B >>> AND >>> alphafold contacts /B to /C >>> AND >>> alphafold contacts /A to /C >>> >>> Righ now, a new command deletes the old contacts. Not sure about a syntax that would combine/add those >>> >>> Thank you very much! >>> >>> Best André >>> >>> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >>> Manage subscription: >>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>

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alphafold contacts between 3 and more subunits
by Michaelis, Andre Clemens 10 Oct '22

10 Oct '22

Hi, Is it possible to draw contacts (PAE, alphafold) between more than just 2 subunits? e.g.: alphafold contacts /A to /B AND alphafold contacts /B to /C AND alphafold contacts /A to /C Righ now, a new command deletes the old contacts. Not sure about a syntax that would combine/add those Thank you very much! Best André

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mrc to pdb
by Tianming Qu 07 Oct '22

07 Oct '22

Hi, is there any way I can convert a .mrc file to .pdb file in chimera? Best, Tianming

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A question about the level option in volume viewer
by Qu Tianming 06 Oct '22

06 Oct '22

Hi ChimeraX-developers, I got a question about the level option in volume viewer. I think the level represent the isovalue for the density map. So when I set the level as 0.03, I got a density map as following : [?? ???????] When I set the level as 0.01, the density map as following: [?? ???????] So my question is that, does level 0.03 or 0.01 means, all grids with a density value lower than 0.03 or 0.01 will be present? Means when I set the level as 0.01, everything left in the density map is the density value lower than 0.01? Best, Tianming

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Moving molecules in VR
by Dr. Eddie 06 Oct '22

06 Oct '22

Hello, I'm trying to move some waters away from a ligand (and eventually some lipids as well) as they overlap too much for minimization to fix it. I can't seem to figure out how to select an entire (water) molecule. The select atom lets me select one atom, but I cannot chain or add more atoms. Some atoms seem to refuse to move even when I try to move one at a time using the "Move atoms" right mouse option. Any help would be appreciated as I can't find much about translating molecules (the bond rotation works perfectly!). Thanks! Eddie

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