- Chimera-users - RBVI Mailing Lists

axes
by Hernando J Sosa 13 Jul '20

13 Jul '20

Dear Chimera, Is there a way to run a command within a python script equivalent to the chimera command 'define axis' to be able to retrieve the results (length,center, direction) ? Something like: (length,center,direction) = mydefineaxis(atomspec) Thanks Hernando

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Questions regarding measuring distances between atoms
by Sitbon, Yoel 10 Jul '20

10 Jul '20

Hello, My name is Yoel Sitbon and I am a Phd student at the University of Miami. I started using chimera recently and I am running into a couple problems. Hopefully, you can help. 1. I keep getting this error (please see picture attached). While it doesn't interfere with what I am doing in terms of analysis, it does pop up every 5 seconds. Is there any way to fix it? 1. I am using PDB file 5TBY, and I am trying to measure the distance between residues I788 in chain B and A57 in chain D. I am able to do that. However, when I mutate the residue 57 from Alanine to Glycine, the program cannot measure distances as it cannot locate atoms at 57. When I try to mutate to cysteine, it works. Do you know why it is not allowing me to perform this? Thank you for the help, Yoel.S

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Unlist me
by Robin 09 Jul '20

09 Jul '20

This has been great association with chimera. May I request you to remove my email from users list? Thank you. Robin Parmar

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Sequence-structure associations
by Hernando J Sosa 09 Jul '20

09 Jul '20

Dear Chimera, Chimera sequence-structure associations appears to be limited to one association per model. Is this right? and if not how do you modify this? E.g. with a model PDB structure containing 3 chains A,B and C you could open the multialign viewer and align the three sequences corresponding to A B and C. However, it appears that only one of the three sequences in the multialign viewer can be associated with their respective chain in the structure. You could change the association but it seem that you cannot add more associations. Here is a view of the associations dialogue windows. Note that it shows only one entry even when there are three sequences in the multialign viewer window. ?? [cid:45cbe218-a6f2-4490-be08-b52fbb7a30e2] Thanks Hernando ___________________________________

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Chimera X - Windows 7 home premium
by MONICA MESA CADAVID 08 Jul '20

08 Jul '20

I would like to use the new Chimera X. I installed and open the program easily. But the images did not appear. I attach the information of my computer because I would like to know if I can fix the problem. Thank you [image: image.png] *Monica Mesa Cadavid* Profesor Titular Instituto de Quimica Facultad de Ciencias Exactas y Naturales monica.mesa(a)udea.edu.co Grupo Ciencia de los Materiales Sede de Investigacion Universitaria, SIU -Torre 1, laboratorio 310 Cra 53 # 61 - 30 Tel. 574 - 219 6546 [image: http://www.udea.edu.co/] <http://www.udea.edu.co/> *Universidad de Antioquia* www.udea.edu.co Sede Principal: Cll 67 # 53 - 108 Medellín, Colombia "La información aquí contenida es para uso exclusivo de la persona o entidad de destino. Está estrictamente prohibida su utilización, copia, descarga, distribución, modificación y/o reproducción total o parcial, sin el permiso expreso de Universidad de Antioquia, pues su contenido puede ser de carácter confidencial y/o contener material privilegiado. Si usted recibió esta información por error, por favor contacte en forma inmediata a quien la envió y borre este material de su computador. Universidad de Antioquia no es responsable por la información contenida en esta comunicación, el directo responsable es quien la firma o el autor de la misma." -- "La información aquí contenida es para uso exclusivo de la persona o entidad de destino. Está estrictamente prohibida su utilización, copia, descarga, distribución, modificación y/o reproducción total o parcial, sin el permiso expreso de Universidad de Antioquia, pues su contenido puede ser de carácter confidencial y/o contener material privilegiado. Si usted recibió esta información por error, por favor contacte en forma inmediata a quien la envió y borre este material de su computador. Universidad de Antioquia no es responsable por la información contenida en esta comunicación, el directo responsable es quien la firma o el autor de la misma."

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Assigning id to a chain with no id
by Aleena Jose 08 Jul '20

08 Jul '20

Hi, I need help with chimera. In my pdb I have a chain with no id and I want to assign it a new id. I tried using 'changechain' command but I am getting error messages because I don't have any specific from-chain id. I don't know what exactly to give as from-chain id or is there any other command that could help me? Thanks, Aleena.

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Difference in alignment of cofactor between Chimera and ChimeraX
by Derek Harris 07 Jul '20

07 Jul '20

Hello, I am trying to reproduce an alignment I had previously done in Chimera in ChimeraX with matchmaker command. The protein alignment between the two programs is the same, but in ChimeraX the active-site cofactor of the matchstruct isn't aligning appropriately to the refstruct cofactor and is unreasonably placed in relation to even its own protein. In Chimera the two cofactors align nicely. The two structures I am trying to align are 3U7Q and 5N6Y. Thanks in advance for any assistance you can offer! Derek Harris Postdoctoral Fellow Seefeldt Lab Department of Chemistry and Biochemistry Utah State University

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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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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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convert .mod to .mrc
by Emmanuel Moebel 23 Jun '20

23 Jun '20

Dear Chimera community, I am visualising a tomogram segmentation with Chimera, the format of the file is .mod and has been obtained with the IMOD software. I would like to get a voxel map from it : a volume with integer values, for ex. '0' for background, '1' for membrane, '2' for filament. Output file format needs to be .mrc or .em. Is this possible to achieve with Chimera? Thanks in advance, Emmanuel Moebel, PhD

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ask a question about the chimera in windows
by Hai Li 22 Jun '20

22 Jun '20

Hi, officer, I am Hai Li at university of texas working on the protein structure and function. Recently I begin to use chimera to show the protein structure. I lean that I need to click and drag a residue in the list in order to show this residue’s sidechain in chimra. However, I have windows and I tried to do the click and drag a residue but it did not work. Could you please tell me how to visualize a residue in windows? Thank you. hai Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Structure Minimization and Molecule Movement (ChimeraX-1.0)?
by Ammar Jastaniah 20 Jun '20

20 Jun '20

Hi, I am not able to find the minimize feature function in ChimeraX-1.0. Is there an equivalent to the regular Chimera version, which is to be found under Tools ==> Structure Editing ===> Minimize Structure? Also. Are you able to move a PDB file ligand molecule around while keeping the other receptor PDB structure stationary/in its place in ChimeraX-1.0? Once again, this is achievable in Chimera by clicking on Tools ==> Movement ===> Movement Mouse Mode. Thank you. Ammar

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Re: [Chimera-users] [chimerax-users] ViewDock script
by Moustafa, Ibrahim M. 19 Jun '20

19 Jun '20

Hi Eric, I'm using Chimera. Is there an equivalent command to use in Chimera? Thanks, Ibrahim ________________________________ From: Eric Pettersen <pett(a)cgl.ucsf.edu> Sent: Friday, June 19, 2020 3:50 PM To: Moustafa, Ibrahim M. <ria2(a)psu.edu> Cc: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> Subject: Re: [chimerax-users] ViewDock script Hi Ibrahim, “ui tool hide ViewDockX” will hide all ViewDockX windows. --Eric Eric Pettersen UCSF Computer Graphics Lab On Jun 19, 2020, at 11:54 AM, Moustafa, Ibrahim M. <ria2(a)psu.edu<mailto:ria2@psu.edu>> wrote: Dear All, I'm trying to run ViewDock from a script using the following command in a loop: runCommand("viewdock " + filename + " AutoDock") It works fine. However, the ViewDock window remains opened after reading each file. For large number of files it is not practical to close them manually. Is there a command to close the opened ViewDock windows to add to the script? Thank you for your help. Ibrahim _______________________________________________ ChimeraX-users mailing list ChimeraX-users(a)cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl…>

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ViewDock in script
by Moustafa, Ibrahim M. 19 Jun '20

19 Jun '20

"re-sending question to the right bb" Dear All, I'm trying to run ViewDock, in Chimera, from a script using the following command in a loop: runCommand("viewdock " + filename + " AutoDock") It works fine. However, the ViewDock window remains opened after reading each file. For large number of files it is not practical to close them manually. Is there a command to close the opened ViewDock windows to add to the script? Thank you for your help. Ibrahim

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Saving volume surface in IMOD .mod
by Long Gui 18 Jun '20

18 Jun '20

Dear all, I was trying to save the surface data of a mrc file in Volume Viewer as the IMOD file type .mod so that it would be read in IMOD. I have searched but could only find the following link about opening IMOD .mod file in Chimera: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/imod… But I want to do the reserve operation. Is that possible that we could generate and save the surface data in Chimera and let it be read by IMOD? Thanks a lot, Long Gui, Ph.D. Postdoc Researcher, Nicastro Lab University of Texas Southwestern Medical Center Long.Gui(a)utsouthwestern.edu Tel: (214)-645-1561 ________________________________ UT Southwestern Medical Center The future of medicine, today.

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