July 2020 - Chimera-users - RBVI Mailing Lists

Solvent Exposure of Amino Acids HELP
by Narine Vapuryan 15 Jul '20

15 Jul '20

Hi! I hope this email finds you well and healthy. I have a question regarding relative solvent excluded surface area (relSESA) calculations using Chimera. I am able to calculate the relative solvent excluded surface areas of residues using the following Chimera guide: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html. Although I am able to perform the calculations and get an output, I am having trouble understanding those values. I would have expected lower relSESA values to mean more residue exposure to solvent (surface residues), and high relSESA to mean less residue exposure to solvent (buried residues). Is my interpretation incorrect? Are lower relSESA values are to be interpreted as lower exposure to solvent (buried residues) and higher relSESA values as more exposed to the solvent (surface residues)? I would really appreciate any help or insight on this matter considering that I have been trying to figure this out for the past week. Please feel free to reach out to me if you need clarification on my question. Best, Narine

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Creating a Volume Viewer Preset
by MICHAEL M ARISTOV 15 Jul '20

15 Jul '20

Hello All, I'm hoping to get some inset in setting up a preset for New Surface. Ideally, I'd Like it to do the following: Firstly, I'd like to open the surface with a predefined Level -0.05 -> 0.05 (regardless of range) (The value set in volume viewer) Secondly, I'd like to set the color of the surface to Red for Negative and Blue for Positive Lastly, I'd like any additional surfaces opened in the same session to have the above parameters as well. If anyone could provide me some tips to make the above settings default, I would greatly appreciate it! Thank you for your time and insight. -Mike Aristov

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Re: [Chimera-users] [chimerax-users] re-assignment of mousemode
by piskacek＠post.cz 14 Jul '20

14 Jul '20

Dear Elaine, thank you very much for your assistance, but I do everything correctly, but it just did not work = see figure I would like to rotate tryptofan in my figure, so as first I need to set pivot on the C-atom (designated here as CB) and than rotate with right mouse the tryptofan -- Martin Piskacek Laboratory of Cancer Biology and Genetics www.piskacek.org Department of Pathological Physiology Faculty of Medicine Masaryk University Brno Kamenice 5 625 00 Brno Czech Republic ---------- Původní e-mail ---------- Od: Elaine Meng <meng(a)cgl.ucsf.edu> Komu: <piskacek(a)post.cz> <piskacek(a)post.cz> Datum: 14. 7. 2020 0:29:28 Předmět: Re: [chimerax-users] re-assignment of mousemode "You have to display the atoms (e.g. command "show") and click on an atom. You said "on amino acid" which makes me think you are clicking on the ribbon instead, which is not the same as clicking on an atom and will not set the pivot. If you are displaying atoms and after clicking the Right Mouse "set pivot" icon, clicking the atom with the right mouse button doesn't make that atom the center of rotation, then you can use menu: Help... Report a Bug to submit a bug report that includes more information about your specific type of computer. If you don't want to show atoms, you can select ribbon of the amino acid with Ctrl-click (which will draw a green outline for that residue) and then use the Actions menu method described in my second message to set the pivot to the whole selected residue instead of to a single atom. Elaine > On Jul 13, 2020, at 2:48 PM, <piskacek(a)post.cz> <piskacek(a)post.cz> wrote: > > exactly all as you described all this is not working > > I assigned what my wright mouse should execute, > but if I try to apply this function on amino acid from my protein it is not working > > Should I need to activate my mousemode somehow? > > I suppose, that ChimeraX is not working properly on windows in my case > I need some correction of some script to solve some hidden conflict in windows > > thank you very much for you help > -- > Martin Piskacek > Laboratory of Cancer Biology and Genetics > www.piskacek.org > Department of Pathological Physiology > Faculty of Medicine > Masaryk University Brno > Kamenice 5 > 625 00 Brno > Czech Republic > > > ---------- Původní e-mail ---------- > Od: Elaine Meng <meng(a)cgl.ucsf.edu> > Komu: <piskacek(a)post.cz> <piskacek(a)post.cz> > Datum: 13. 7. 2020 22:45:47 > Předmět: Re: [chimerax-users] re-assignment of mousemode > > Another way to set pivot (without changing mouse-button functions) is by: > > (1) selecting an atom (Ctrl-click on the atom in the graphics window) that you want as the center of rotation > (2) using menu: Actions... Set Pivot > > Elaine > > > On Jul 13, 2020, at 1:00 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > > Hi Martin, > > It is not clear what you mean by "no response." Do you have a mouse with a right button, or can you use trackpad + Alt as the right button? If you click any other icons in the Right Mouse tab of the Toolbar, can you successfully assign any of those other functions to the right mouse button? > > > > Maybe it is a misunderstanding of how the icons work: > > If it is working correctly, nothing will happen when you click a RIght Mouse icon, except that there will be a light green box around that icon. Clicking the icon only reassigns the function of the right mouse button, but does not perform any action at that time. However, if you reassign to pivot by clicking the Right Mouse pivot icon, for example, then later clicking with the right mouse button (if you have one) on an atom will make that atom the pivot point. > > > > <http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> > > > > If you do not have a right mouse button, you can use the "mousemode" command (instead of icons) to assign the function to a different mouse button. > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode> > > > > I hope this helps, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > >> On Jul 13, 2020, at 9:02 AM, <piskacek(a)post.cz> <piskacek(a)post.cz> wrote: > >> > >> Dear Authors of ChimeraX, > >> > >> I load and start to use your very useful program ChimeraX on Windows 10 > >> (Alienware 17 x64, I7-4900MQ 2.8GHz, RAM 32GB, GeForce GTX 780M), > >> > >> I could do the same and more as in PyMol, but > >> I have trouble with re-assignment of mousemode in window "Right Mouse" > >> as result is no response for re-assignment into Pivot or Rotate model > >> > >> I tried ChimeraX versions 0,93, 1.0 and 1.1 (daily version) w/o improvement > >> > >> Please, could you help me > >> Thank you very much for support > >> "

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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 08 Jul '20

08 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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