June 2020 - Chimera-users - RBVI Mailing Lists

(no subject)
by Thirumurugan Prakasam 30 Oct '21

30 Oct '21

Hi, I am trying to make metal coordination bond as a dotted line and also I need to make electron clouds around the atoms as in the picture below (Please provide me short guidelines on how to make nice cartoon). Please help me sort this two issues. Looking forward to hearing from you, Many thanks, Thiru [image: image.png] -- Thirumurugan Prakasam, Research Scientist, New York University Abu Dhabi, Experimental Research Building Building C1, Saadiyat Island Abu Dhabi, UAE Phone no: +971-561976358

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Fitting structure in rescaled map
by Ahmad Khalifa 23 Sep '20

23 Sep '20

Hello, How to fit an atomic model after downscaling my map (map shrinks)? Are atomic models built to scale?! Regards.

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Fw: Open MTZ file
by Williams, Joanne 20 Aug '20

20 Aug '20

Hello! Can you help with the inquiry below? thanks, Jo ________________________________ From: Sharyn Endow, Ph.D. <sharyn.endow(a)duke.edu> Sent: Thursday, February 22, 2018 5:01 AM To: chimera(a)cgl.ucsf.edu Subject: Open MTZ file Is it possible to open an .mtz file in Chimera? ~~~~~~~~~~~~~~~~~~~~~~~~~~ Sharyn A. Endow, PhD Professor of Cell Biology, DUMC Professor of NBD, Duke-NUS PO Box 3709 450 Sands Bldg/Research Drive Durham, NC 27710 USA T 919 684-4311 F 919 681-9929 ~~~~~~~~~~~~~~~~~~~~~~~~~~~

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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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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 24 Jun '20

24 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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Chimera-users June 2020