Hi Recently I transferred to ChimeraX from the old version. I found: 1. Some SMILE strings copied directly from ChemDraw cannot be recognized by ChimeraX, such as O=C1NC2=C(/C1=C3NC4=CC=CC=C4C/3=C\O)C=CC(Br)=C2 2. Correct me if I am wrong but ChimeraX seems not able to do molecule docking/ligand minimization like the old version, right? Thank you Joshua Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
Hi Joshua, ChimeraX is a new and different program, not a version of Chimera. So all the features have to be developed separately... it does have several completely new features and advantages compared to Chimera, but also it does not have all of the commonly used tools of Chimera (yet). ChimeraX is being actively developed and new features are being added constantly, however. ChimeraX does allow fetching structures for SMILES strings, but maybe the backslash in your example is causing a problem. I will make a bug report for that. ChimeraX does not have a general minimization tool for nonstandard residues like ligands, but there are "tug" and "minimize" mouse modes for openMM dynamics when the structure has hydrogens and only standard residues, see: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode> <http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> <http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html#openmm> There is no docking tool in ChimeraX, only ViewDockX for looking at results from docking done separately. <http://rbvi.ucsf.edu/chimerax/docs/user/tools/viewdockx.html> However, it is important to understand that Chimera does not do docking either; although it has an "Autodock Vina" tool, that only uses an outside web service that does a very short docking that is not suitable for most research purposes, as mentioned in the boxed warning in its help page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 4, 2020, at 6:11 PM, Yuhua Fang <fangy34@myumanitoba.ca> wrote:
Hi
Recently I transferred to ChimeraX from the old version. I found: • Some SMILE strings copied directly from ChemDraw cannot be recognized by ChimeraX, such as O=C1NC2=C(/C1=C3NC4=CC=CC=C4C/3=C\O)C=CC(Br)=C2 • Correct me if I am wrong but ChimeraX seems not able to do molecule docking/ligand minimization like the old version, right? Thank you
Joshua
If you can provide a parameter file for your ligand in OpenMM’s ffXML format, then you’ll be able to use it for MD simulations/settling in ISOLDE. The tools to generate the parameterisation aren’t yet available in ChimeraX, but if you can generate an AMBER .mol2 and .frcmod (e.g. using phenix.elbow —amber) it can be easily converted using ParmEd. Let me know if you want more info. - Tristan
On 6 Apr 2020, at 16:31, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Joshua, ChimeraX is a new and different program, not a version of Chimera. So all the features have to be developed separately... it does have several completely new features and advantages compared to Chimera, but also it does not have all of the commonly used tools of Chimera (yet). ChimeraX is being actively developed and new features are being added constantly, however.
ChimeraX does allow fetching structures for SMILES strings, but maybe the backslash in your example is causing a problem. I will make a bug report for that.
ChimeraX does not have a general minimization tool for nonstandard residues like ligands, but there are "tug" and "minimize" mouse modes for openMM dynamics when the structure has hydrogens and only standard residues, see: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode> <http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> <http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html#openmm>
There is no docking tool in ChimeraX, only ViewDockX for looking at results from docking done separately. <http://rbvi.ucsf.edu/chimerax/docs/user/tools/viewdockx.html>
However, it is important to understand that Chimera does not do docking either; although it has an "Autodock Vina" tool, that only uses an outside web service that does a very short docking that is not suitable for most research purposes, as mentioned in the boxed warning in its help page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 4, 2020, at 6:11 PM, Yuhua Fang <fangy34@myumanitoba.ca> wrote:
Hi
Recently I transferred to ChimeraX from the old version. I found: • Some SMILE strings copied directly from ChemDraw cannot be recognized by ChimeraX, such as O=C1NC2=C(/C1=C3NC4=CC=CC=C4C/3=C\O)C=CC(Br)=C2 • Correct me if I am wrong but ChimeraX seems not able to do molecule docking/ligand minimization like the old version, right? Thank you
Joshua
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participants (3)
-
Elaine Meng -
Tristan Croll -
Yuhua Fang