May 2019 - Chimera-users - RBVI Mailing Lists

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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Fwd: Downloading HIV PDB 3j3q?
by Elaine Meng 13 Jan '20

13 Jan '20

> > From: Divjak Maja <Maja.Divjak(a)petermac.org> > Subject: Downloading HIV PDB 3j3q? > Date: April 1, 2019 at 5:23:39 AM PDT > To: Elaine Meng <meng(a)cgl.ucsf.edu> > > Hi Elaine, > > It's me again! Hope you had a nice weekend... > > I'm having some trouble downloading the HIV capsid file, PDB 3j3q. When I try to import it to Chimera it begins downloading, but the molecule never quite appears, even though it ends up in the entry list. The screen stays blue like it has yet to be uploaded. If I try to upload it from the list, again, nothing appears. I realise the molecule is very large, but I think I'm missing something important here? > > Thanks so much for your help, as always, > > Maja > > Dr Maja Divjak > BAppSc(Hons), PhD, Grad Cert 3D Animation (AFTRS) > Biomedical Animator > Office of Cancer Research > Hi Maja, (forwarding to the address that should be used for for Chimera questions) It is probably just too big for the memory on your computer to open this structure in Chimera. Depending on what you’re trying to do with this capsid, maybe you could try using ChimeraX instead of Chimera. It handles large structures much more efficiently, but it does not have the same set of features as Chimera. <http://www.rbvi.ucsf.edu/chimerax/index.html <http://www.rbvi.ucsf.edu/chimerax/index.html>> If you are just trying to get the atomic coordinates of the entire capsid, they are already in the file(s) you could download directly from the RCSB PDB without using any visualization program. <https://www.rcsb.org/structure/3j3q <https://www.rcsb.org/structure/3j3q>> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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animation commands in a morph movie
by Natesh Singh 31 May '19

31 May '19

Dear Chimera development team, I am trying to add a simple animation into the morphed trajectory that was developed using two unique conformations (protein and proten-ligand complex). I want the ligand to fly into the binding site (of course ligand is not considered in the morph since it was not a part of a chain), but I guess this could be done. contents of my model panel. ID 0 ligand surface ID 0 conformation A (protein-ligand complex) ID 1 conformation B (protein) ID 2 Morph (400 frames) I am adding the following commands into the perframe box of md movie: # Save bound view. savepos p1 # Move ligand away and save unbound view. move y -10 model #0 ; turn z -30 model #0 center #0 scale 0.2 savepos p2 #fly ligand into the binding site reset p1 100 wait But it's not working the way I want. I just want the ligand to fly slowly into its original position may be within 25-50 frames. Could we execute the commands at a specific frame number? Kindly let me know what would be the correct commands to achieve this effect. Many thanks for your help. Sincerely, Natesh University of Lille

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I forgot where I saved my Chimera session
by Ahmad Khalifa 31 May '19

31 May '19

Is there anyway I can know from logs, history etc where I had saved my session? Regards.

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Select by attribute value in a .psf file
by MARIA CLARA BLANES MIRA 29 May '19

29 May '19

Hello Chimera users, I am trying to see the movement of some phospholipids in a lipid bilayer when a peptide is anchoring to this membrane. I have a .pdb, .psf and several .dcd files. When I select one of these phospholipids I obtain four molecules selected (with the same name due to the segments). I have been trying with ’Select by attribute value’/atoms/pdbSegment and it works perfect because this way I can specify the segment where it is. But I can’t find the way to do the same with the .psf file. Could you tell me how should I do it?. Thank you very much, clara

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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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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 23 May '19

23 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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