- Chimera-users - RBVI Mailing Lists

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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Re: [Chimera-users] Euler Angles
by Tom Goddard 30 Jun '20

30 Jun '20

Hi Gabriella, Euler angles are not rotations about x, y, and z. Rotations about x,y,z and also Euler angles are generally not very useful for explaining relative orientations of domains because they are hard for a person to comprehend and depend on the coordinate system. It is particularly tricky because the order of the rotations matters, for instance, a rotation of 30 degrees about x followed by 30 degrees about y is different from 30 degrees about y followed by 30 degrees about x. So usually just the total rotation about the axis of rotation is reported and that is what Chimera tells you, If you still want Euler angles or x,y,z rotations Chimera does not produce those and you will need to find other software to do it. Tom > On Jun 30, 2020, at 7:06 AM, Gabriella Angiulli <gab.ang87(a)hotmail.com> wrote: > > Hi Tom, > > What I need to do is calculating the transformation (rotation and translation) of the same domain in two different conformations. Particularly, I would like to describe the rotation as rotational angles around the three axis (x,y and z). I know that Chimera provide for the rotational angle, but what I would like to know is the Euler angels. > Thank you so much, > Gabriella > > >> On Jun 29, 2020, at 4:45 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Gabriella, >> >> Chimera does not output and does not use Euler angles as described in this previous message >> >> http://www.cgl.ucsf.edu/pipermail/chimera-users/2017-November/014102.html <http://www.cgl.ucsf.edu/pipermail/chimera-users/2017-November/014102.html> >> >> What software are you using that wants Euler angles? There are different conventions in how Euler angles are defined. >> >> Tom >> >> >>> On Jun 29, 2020, at 8:36 AM, Gabriella Angiulli <gab.ang87(a)hotmail.com <mailto:gab.ang87@hotmail.com>> wrote: >>> >>> Hi, >>> >>> I’m trying to calculate the transformation between two Cterminal domains in two different conformations and I’ve been using the command “measure rotation”. The rotation is reported in the first three columns of a 4x3 matrix in the log file window and my question is: do I have a way to get the Euler angles of my transformation from that matrix ? >>> >>> Thank you so much, >>> Gabriella >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >>> >> >

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Icosaedron coordinates
by Yasser Almeida 30 Jun '20

30 Jun '20

Hello, I am using the icosahedron surface tool to build a triangulated sphere cage around a model. How can I write its coordinates? Thanks in advance, Yasser

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Euler Angles
by Gabriella Angiulli 29 Jun '20

29 Jun '20

Hi, I’m trying to calculate the transformation between two Cterminal domains in two different conformations and I’ve been using the command “measure rotation”. The rotation is reported in the first three columns of a 4x3 matrix in the log file window and my question is: do I have a way to get the Euler angles of my transformation from that matrix ? Thank you so much, Gabriella

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Intallation
by Joakin Mori 29 Jun '20

29 Jun '20

Hello, I am having trouble with opening the application. I keep getting error message. Please see attached. [cid:447FFFA4-4784-499C-80AC-B4D90E44938F@GuestNet.Tuskegee.Edu]

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adding residues to an existing protein or joining a protein to a small peptide.
by brody deming 26 Jun '20

26 Jun '20

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AutoDock Vina Help
by Ali 23 Jun '20

23 Jun '20

Hi Everyone, As of the end of April 2020, the webserver to opal is no longer working. I have tried to build the PDB2PQR programme locally but have been struggling. Basically, need to align a RNA molecule to a sight within the pdb. If anyone can help, please assist. Thank you, Ali from Cape Town

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New instance opened with each new map
by Melody Campbell 23 Jun '20

23 Jun '20

Hi, Since I installed the 64-bit UCSF Chimera version for Mac Catalina (10.15.5) each time I open a new map, a new instance of UCSF Chimera opens instead of opening the map in the same instance. Could you help me find where the setting is to change this so that by default all new maps and models opened (via double clicking icons) is done in the same instance of Chimera? (I tried re-installing/ restoring all factory settings and deleting my /Users/user/.chimera/preferences file, but still by default, a new session opens for each map). Thanks so much! Melody

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