July 2020 - Chimera-users - RBVI Mailing Lists

Select zone around COM
by Yasser Almeida 06 Jul '20

06 Jul '20

Hello, I have a trajectory of a water box and I want to select, show only, save the waters that move in a zone around the COM of the whole system. Any thoughts? Thanks in advance, Yasser

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Chimera add H to NAD
by Peter Palenchar 03 Jul '20

03 Jul '20

Hi, I have an NAD coming from a PDB file. When I add H to it, Chimera has issues with the nicotinamide ring. It isn't seeing the ring as aromatic. I've saved the NAD without adding H as a .mol2 file and tried to edit it so that it would be seen by Chimera as being aromatic, but it is still adding 2 H's to some of the C in the ring that only should one. I've attached the mol2 file that I've edited. I've also tried to edit the .mol2 file where I've changed the C in the ring to C.2 and changed the bonds to double bonds (e.g. N1N, atom 36, and C2N, atom 37, have a double bond, C2N also has a single bond to C3N, and C2N is assigned C.2, but when I add H Chimera still puts two H on C2N). I can add the H and then delete the extra ones in Chimera, but then the bond angle for the remaining H is wrong. Ideally, I'd get Chimera to see the system as aromatic. But I'll take any input on the best way to start with a structure like this and get Chimera to create something that is close to NAD. Thanks! Peter Palenchar

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Chimera help - attempted to do minimization
by Jia Hao Chen 02 Jul '20

02 Jul '20

Hello, I attempted to do minimization on my mutant protein but I get this error when I try to run it: AttributeError: '_molecule.Atom' object has no attribute 'gaffType' File "C:\Program Files\Chimera 1.14\share\MMMD\MMTKinter.py", line 695, in _addStandardResidue "amber_atom_type": a.gaffType, I've attached the reply log for more details. Please let me know if I need to fix anything, thank you. Best regards, Jay Chen

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Chimera Molecular Dynamics
by Benjamin Strickland 01 Jul '20

01 Jul '20

Hello, I have recently started playing around with the MD tool in chimera, however I have noticed something odd. I set up the simulation and begin running it however, upon completion of the initial minimization I reach the "MMTK updated coordinates" step and heating.nc files appear on the desktop. However, after this point the application has a (not responding) and there appears no be very little usage of the CPU. I am unsure if something is going wrong or I have to simply wait longer as I see no indication of any pending process or status. I am running Windows 10 and the CPU is a AMD Threadripper 3960x.

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(no subject)
by Rohan Marde 01 Jul '20

01 Jul '20

How can I make comments on specific residues in UCSF Chimera?

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