Consider this: open 1pgb fromDatabase pdb format mmcifstyle sphereshow atoms 1. What is the command to hide all water? 2. How do I color charged amino acids, leaving uncharged one a neutral color (such as white)? I was hoping there was a menu item or command that would do something similar to this: color all whitecolor :lys,arg bluecolor :glu,asp redcolor :his lightblue without having to type all those commands. FirstGlance in Jmol and iCn3D have "one click" ways to do this, but I don't see one in ChimeraX or MolStar. Thanks, -Eric
Hi Eric, If you spend a little time learning the program you will be able to generalize a bit more. There are several tutorials. <https://www.rbvi.ucsf.edu/chimerax/tutorials.html>
On Dec 5, 2024, at 2:57 PM, Eric Martz via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Consider this:
open 1pgb fromDatabase pdb format mmcif style sphere show atoms
1. What is the command to hide all water?
hide solvent - or - hide :HOH Almost all commands use "atomspec" which has a lot of options, element (as in your previous question), residue name, category such as "solvent" etc. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> If you don't want to learn commands you can use the menu, Select... Residues... HOH Actions... Atoms/Bonds... hide
2. How do I color charged amino acids, leaving uncharged one a neutral color (such as white)?
I was hoping there was a menu item or command that would do something similar to this:
color all white color :lys,arg blue color :glu,asp red color :his lightblue
without having to type all those commands.
You can make your own presets which are sets of commands that are read from a file. Then you can just choose your custom entry from the Presets menu. See the "Startup" section of the preferences. <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup>
FirstGlance in Jmol and iCn3D have "one click" ways to do this, but I don't see one in ChimeraX or MolStar.
Thanks, -Eric
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
Thank you, Elaine! I have no problem learning command language. I have been doing that for 25 years starting with RasMol, then Chime, and now Jmol -- while I try to make protein structure more accessible through https://Proteopedia.org , http://FirstGlance.Jmol.Org , and tutorials http://molviz.org so that most users won't have to learn any command language. The problem is figuring out the exact syntax from the help documents of ChimeraX. Many ChimeraX commands offer numerous options, yet have no examples. But hey, we have exactly the same problem with Jmol. Even though I've been learning Jmol command language almost since the inception of Jmol, it often takes me over an hour and an email exchange before I understand the syntax well enough to succeed with a Jmol command I'm trying to use for the first time. -Eric http://martz.molviz.org On Thursday, December 5, 2024 at 06:33:59 PM EST, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Eric, If you spend a little time learning the program you will be able to generalize a bit more. There are several tutorials. <https://www.rbvi.ucsf.edu/chimerax/tutorials.html>
On Dec 5, 2024, at 2:57 PM, Eric Martz via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Consider this:
open 1pgb fromDatabase pdb format mmcif style sphere show atoms
1. What is the command to hide all water?
hide solvent - or - hide :HOH Almost all commands use "atomspec" which has a lot of options, element (as in your previous question), residue name, category such as "solvent" etc. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> If you don't want to learn commands you can use the menu, Select... Residues... HOH Actions... Atoms/Bonds... hide
2. How do I color charged amino acids, leaving uncharged one a neutral color (such as white)?
I was hoping there was a menu item or command that would do something similar to this:
color all white color :lys,arg blue color :glu,asp red color :his lightblue
without having to type all those commands.
You can make your own presets which are sets of commands that are read from a file. Then you can just choose your custom entry from the Presets menu. See the "Startup" section of the preferences. <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup>
FirstGlance in Jmol and iCn3D have "one click" ways to do this, but I don't see one in ChimeraX or MolStar.
Thanks, -Eric
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
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Eric Martz