- Chimera-users - RBVI Mailing Lists

How to get the best references
by temban billyhp 28 May '19

28 May '19

HiI used UCSF chimera for MOLECULAR DOCKING. Are these citations below enough for me to cite. Could you please help me with more citations. 1.Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., and Ferrin, T.E., UCSF Chimera--a visualization system for exploratory research and analysis, J. Comput. Chem., 2004, vol. 25, p. 1605. 2. Maier, J.A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K.E., and C. Simmerling, ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB, J. Chem. Theory Comput., 2015, vol. 11, p. 3696. 3. Shapovalov, M.V. and Dunbrack, R.L., A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions, Structure, 2011, vol. 19, p. 844. 4. Trott, O. and Olson, A.J., AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry, 2010, vol. 31, p. 455. Best regards. Sent from Yahoo Mail on Android

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(no subject)
by MARIA CLARA BLANES MIRA 24 May '19

24 May '19

Dear Chimera users, I have a .psf and multiple .dcd files for a peptide movement and I need to make a movie combining certain frames for each dcd file. First, I have tried to load more than one dcd file in the MD movie interface but my computer hungs. I think I should use a metafile in this situation. Something like this: namd(psf/dcd) pam.psf pam1.dcd But I have all the other pam2.dcd, pam3.dcd, etc until 40, each having 3000 frames. How could I include them in the same metafile to be able to open one, record 20-30 frames, open the second, record some other frames and so on? And how could I include the frames number? Thank you in advance, Clara Blanes

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Re: [Chimera-users] Question on chimera app
by Elaine Meng 22 May '19

22 May '19

On May 21, 2019, at 4:38 PM, temban billyhp <btemban(a)yahoo.com> wrote: > > Hi > During the auto dock vina operation, when building the grid box. What is the unit of the dimensions. I will equally like to know how to find the grid spacing value. > Best regards. Chimera questions should be sent to chimera-users(a)cgl.ucsf.edu (CC’d here). The Autodock Vina tool in Chimera does not have a grid spacing setting. It only has the box center and size, which are in X,Y,Z coordinates of your atomic structure. Atomic structures are generally in Angstrom units. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> Maybe there is a setting to control grid spacing if you downloaded and used the Autodock Vina program directly (not using the tool in Chimera) but I do not know. You would have to look at the Autodock Vina website for that information. <http://vina.scripps.edu/> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Fwd: Re: ImportError: /lib/x86_64-linux-gnu/libfontconfig.so.1: undefined symbol: FT_Done_MM_Var
by Greg Couch 20 May '19

20 May '19

Yes, this bug was fixed after the 1.13.1 release. -- Greg On 5/17/2019 6:52 AM, Thomas Evangelidis wrote: > Strangely, the alpha version (May 09, 2019) works fine! > > On Fri, 17 May 2019 at 12:19, Thomas Evangelidis <tevang3(a)gmail.com > <mailto:tevang3@gmail.com>> wrote: > > Greetings, > > I did a fresh installation of Chimera on Ubuntu 19.04 but although > the installation finished successfully, I get this error message > whenever I launch the executable: > > > Traceback (most recent call last): > File > "/home2/thomas/Programs/Chimera-1.13.1/share/__main__.py", > line 73, in <module> > value = chimeraInit.init(sys.argv) > File > "/home2/thomas/Programs/Chimera-1.13.1/share/chimeraInit.py", > line 666, in init > import chimera > File > "/home2/thomas/Programs/Chimera-1.13.1/share/chimera/__init__.py", > line 2777, in <module> > from SimpleSession import BEGIN_RESTORE_SESSION, > END_RESTORE_SESSION > File > "/home2/thomas/Programs/Chimera-1.13.1/share/SimpleSession/__init__.py", > line 14, in <module> > from save import saveSession, sessionID, noAutoRestore, > autoRestorable, \ > File > "/home2/thomas/Programs/Chimera-1.13.1/share/SimpleSession/save.py", > line 13, in <module> > from chimera import replyobj, selection, SessionPDBio, version > File > "/home2/thomas/Programs/Chimera-1.13.1/share/chimera/replyobj.py", > line 24, in <module> > import Tkinter > File > "/home2/thomas/Programs/Chimera-1.13.1/lib/python2.7/lib-tk/Tkinter.py", > line 39, in <module> > import _tkinter # If this fails your Python may not be > configured for Tk > ImportError: /lib/x86_64-linux-gnu/libfontconfig.so.1: > undefined symbol: FT_Done_MM_Var > > > What is strange is that the following works without error: > > /home2/thomas/Programs/Chimera-1.13.1/bin/python2.7 -c 'import > _tkinter' > > > Any idea what might be wrong? > > Best, > Thomas > > > -- > > ====================================================================== > > Dr. Thomas Evangelidis > > Research Scientist > > IOCB - Institute of Organic Chemistry and Biochemistry of the > Czech Academy of Sciences > <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague, > Czech Republic > > & > CEITEC - Central European Institute of Technology > <https://www.ceitec.eu/>, Brno, Czech Republic > > email: tevang3(a)gmail.com <mailto:tevang3@gmail.com>, Twitter: > tevangelidis <https://twitter.com/tevangelidis>, LinkedIn: Thomas > Evangelidis > <https://www.linkedin.com/in/thomas-evangelidis-495b45125/> > > website: https://sites.google.com/site/thomasevangelidishomepage/ > > > > > > > -- > > ====================================================================== > > Dr. Thomas Evangelidis > > Research Scientist > > IOCB - Institute of Organic Chemistry and Biochemistry of the Czech > Academy of Sciences > <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague, Czech > Republic > > & > CEITEC - Central European Institute of Technology > <https://www.ceitec.eu/>, Brno, Czech Republic > > email: tevang3(a)gmail.com <mailto:tevang3@gmail.com>, Twitter: > tevangelidis <https://twitter.com/tevangelidis>, LinkedIn: Thomas > Evangelidis <https://www.linkedin.com/in/thomas-evangelidis-495b45125/> > > website: https://sites.google.com/site/thomasevangelidishomepage/ > > > > > > _______________________________________________ > Chimera-users mailing list:Chimera-users@cgl.ucsf.edu > Manage subscription:http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Help in validation of Mutant Structure
by carlo cast 20 May '19

20 May '19

Good Morning to everyone, it’s my first time here writing at you, I hope I’m doing right. The point is that I’m working with a wild type enzyme from which I got mutant versions by using swap aa command. My goal is to look at the effects that mutations have on the structure by superimposing the mutant form with the wild type one. When I perform matchmaker command, RMSD is equal to 0 and the structures overlap perfectly; thus I thought to minimize structure before superimposing and in this way I see a little difference in RMSD but it could be due to the different steps of the minimize process (e.g. adding protons) than the actual effect of mutations. Moreover when I perform multiple sequence alignment, the amminoacids I swapped actually are not different from the Wild type ones. If I point the cursor on the swapped aa I see the difference in name and side chain but by doing multiple sequence alignment they do not appear. Any suggestions? Inviato da Posta<https://go.microsoft.com/fwlink/?LinkId=550986> per Windows 10

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Re: [Chimera-users] Contact area between 2 Proteins
by Elaine Meng 17 May '19

17 May '19

Dear Fer Villa, (better to send questions to chimera-users(a)cgl.ucsf.edu, CC’d here) It is not really a matter of right and wrong. Instead it depends on what you want… If you want to measure buried solvent-accessible and solvent-excluded surface areas of atomic structures, use “measure buriedArea”. The “measure contactArea” command is similar but if the goal is measurement (rather than coloring for a figure), it is generally used for other kinds of surfaces that are not necessarily associated with any atoms, like density map isosurfaces. In that case, the appropriate cutoff value really depends on the judgment of the user based on what kinds of surfaces these are and what the user is trying to do. The tutorial you mention is for making a figure where the interaction surfaces of two proteins are colored, which is a different purpose than getting a measurement value. It explains that different cutoffs could be used with “measure contactArea", but the example has 2.5 because it gave similar appearance to using the other (buriedArea) method. The tutorial shows both methods because if you are making a figure, you could use either one as you like. It actually discusses three methods. For the other people on the list, here is that tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html> … 3 methods of coloring the interface: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html#in…> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 10, 2019, at 12:17 AM, Fernando Villa <fer.vdl1928(a)gmail.com> wrote: > > Dear Chimera users, > I would like to know which is the correct method to know what is the surface area of contact between two proteins: > measure contactArea or measure buriedArea? > When I apply the command: measure contactArea # 0.1 # 0.2 2.5 color yellow offset 0 that comes in the tutorial, it says that the cutting distance is equal to 2.5 A2 > But, is it correct? > How can I know that? > this example states that if this cut-off distance (2.5 A) is applied compared with a cut distance for measure buriedArea: > Command: measure buriedArea # 0.1 # 0.2 > Command: color yellow #0.1@/buriedSESArea> 1 > Command: color hot pink #0.2@/buriedSESArea> 1 > measure buried Area # 0.1 & protein # 0.2 & protein > atoms with> 1.0 Å2 > How can I know which is the correct contact area (protein protein interaction) of two models or crystals? > What is the correct cutting area that I should apply? > Could it be the default cut area of 1A? > Which method of calculation is better, measure contactArea or measure buriedArea? > I would thank you in advance for a possible solution to my problem. > > Best regards. > > Fer Villa. > Enviar comentarios > Historial > Guardadas > Comunidad > > <image.png> > > Command:open 1avx > Command: ~longbond > Command: split > Command: preset apply int 2 > Command: repr stick > Command: delete solvent > Command: color sea green #0.1 > Command: color medium purple #0.2 > Command: surface > Command: measure contactArea #0.1 #0.2 2.5 color yellow offset 0 > Command: measure contactArea #0.2 #0.1 2.5 color hotpink offset 0 > > > or > > Command: measure buriedArea #0.1 #0.2 > Command: color yellow #0.1@/buriedSESArea>1 > Command: color hot pink #0.2@/buriedSESArea>1 > > Command: measure buriedArea #0.1&protein #0.2&protein > > ATTE > Fernando Villa Díaz >

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display bond lengths and angles
by Thomas Evangelidis 17 May '19

17 May '19

Hello, Is it possible to load a small molecule in Chimera and display all bond lengths and angle values, pretty much as you can do using labelopt option for the atom names? If not directly, could you please give me some hints about how to write a Python script to do it? I thank you in advance for your help. Thomas -- ====================================================================== Dr. Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/>, Brno, Czech Republic email: tevang3(a)gmail.com, Twitter: tevangelidis <https://twitter.com/tevangelidis>, LinkedIn: Thomas Evangelidis <https://www.linkedin.com/in/thomas-evangelidis-495b45125/> website: https://sites.google.com/site/thomasevangelidishomepage/

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ImportError: /lib/x86_64-linux-gnu/libfontconfig.so.1: undefined symbol: FT_Done_MM_Var
by Thomas Evangelidis 17 May '19

17 May '19

Greetings, I did a fresh installation of Chimera on Ubuntu 19.04 but although the installation finished successfully, I get this error message whenever I launch the executable: > > Traceback (most recent call last): > File "/home2/thomas/Programs/Chimera-1.13.1/share/__main__.py", line 73, > in <module> > value = chimeraInit.init(sys.argv) > File "/home2/thomas/Programs/Chimera-1.13.1/share/chimeraInit.py", line > 666, in init > import chimera > File "/home2/thomas/Programs/Chimera-1.13.1/share/chimera/__init__.py", > line 2777, in <module> > from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION > File > "/home2/thomas/Programs/Chimera-1.13.1/share/SimpleSession/__init__.py", > line 14, in <module> > from save import saveSession, sessionID, noAutoRestore, > autoRestorable, \ > File > "/home2/thomas/Programs/Chimera-1.13.1/share/SimpleSession/save.py", line > 13, in <module> > from chimera import replyobj, selection, SessionPDBio, version > File "/home2/thomas/Programs/Chimera-1.13.1/share/chimera/replyobj.py", > line 24, in <module> > import Tkinter > File > "/home2/thomas/Programs/Chimera-1.13.1/lib/python2.7/lib-tk/Tkinter.py", > line 39, in <module> > import _tkinter # If this fails your Python may not be configured for > Tk > ImportError: /lib/x86_64-linux-gnu/libfontconfig.so.1: undefined symbol: > FT_Done_MM_Var > What is strange is that the following works without error: /home2/thomas/Programs/Chimera-1.13.1/bin/python2.7 -c 'import _tkinter' > Any idea what might be wrong? Best, Thomas -- ====================================================================== Dr. Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/>, Brno, Czech Republic email: tevang3(a)gmail.com, Twitter: tevangelidis <https://twitter.com/tevangelidis>, LinkedIn: Thomas Evangelidis <https://www.linkedin.com/in/thomas-evangelidis-495b45125/> website: https://sites.google.com/site/thomasevangelidishomepage/

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Still won't work after libfreetype.so* and libz.so* removal
by Яцкевич Максим 14 May '19

14 May '19

Hi! I am running Fedora 29. Now I'm trying to install chimera-1.13.1-linux_x86_64.bin. After successful installation it failed to create a window in a desktop applecation menu. So I followed the instructions on the web-site (http://www.cgl.ucsf.edu/chimera/data/downloads/1.13.1/linux_x86_64.html) After running the command <dir_name>/bin/xdg-setup install it stumbled upon the same error that was discussed in this thread (https://www.cgl.ucsf.edu/pipermail/chimera-users/2018-November/015237.html) Traceback (most recent call last): File "/home/sec/.local/chimera/share/__main__.py", line 73, in <module> value = chimeraInit.init(sys.argv) File "/home/sec/.local/chimera/share/chimeraInit.py", line 666, in init import chimera File "/home/sec/.local/chimera/share/chimera/__init__.py", line 2777, in <module> from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION File "/home/sec/.local/chimera/share/SimpleSession/__init__.py", line 14, in <module> from save import saveSession, sessionID, noAutoRestore, autoRestorable, \ File "/home/sec/.local/chimera/share/SimpleSession/save.py", line 13, in <module> from chimera import replyobj, selection, SessionPDBio, version File "/home/sec/.local/chimera/share/chimera/replyobj.py", line 24, in <module> import Tkinter File "/home/sec/.local/chimera/lib/python2.7/lib-tk/Tkinter.py", line 39, in <module> import _tkinter # If this fails your Python may not be configured for Tk ImportError: /usr/lib64/libfontconfig.so.1: undefined symbol: FT_Done_MM_Var So I followed your advise and removed the corresponding files: > rm ~/.local/chimera/lib/libz.so* > rm ~/.local/chimera/lib/libfreetype.so* Unfortunately it didn't solve the problem. So after typing: > ~/.local/chimera/bin/xdg-setup install It complained that it cannot find the libz.so file! Traceback (most recent call last): File "/home/sec/.local/chimera/share/__main__.py", line 73, in <module> value = chimeraInit.init(sys.argv) File "/home/sec/.local/chimera/share/chimeraInit.py", line 659, in init initialize_ssl_cert_dir() File "/home/sec/.local/chimera/share/chimeraInit.py", line 309, in initialize_ssl_cert_dir import ssl File "/home/sec/.local/chimera/lib/python2.7/ssl.py", line 146, in <module> import base64 # for DER-to-PEM translation File "/home/sec/.local/chimera/lib/python2.7/base64.py", line 11, in <module> import binascii ImportError: libz.so: cannot open shared object file: No such file or directory I will be grateful for any help. Best regards, Maxim. PhD Student, Physical Faculty, Lomonosov Moscow State University

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Upload color scheme
by Cornelius Hunter 10 May '19

10 May '19

I am looking for a 3D protein viewer that allows me to visualize the protein tertiary structure using my own color assignments, for each residue (or alpha carbon). In other words I would upload a file, with a value for each residue, which would drive the color assignments. Thx

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