October 2015 - Chimera-users - RBVI Mailing Lists

AM1-BCC: Question
by José Luis 26 Oct '15

26 Oct '15

Dears Devepolers: My name is José Luis. PhD student and to run docking and MD I was using Chimera 1.3 for AM1-BCC partial charges calculationwithour problem. Now, I´m using 1.10 and 1.10.2 but in the firt one the calculation doesn´t complete it and in the second one the following message appears: the system can´t find C:\Program Files\Chimera 1.10.2\share\chimeraInit.py", line 259, in CreateProcess current_directory, startup_info). Can you help me? Many thanks in advance. José Luis --- El software de antivirus Avast ha analizado este correo electrónico en busca de virus. https://www.avast.com/antivirus

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Access to "Match Align" programmatically
by Miguel Ortiz Lombardía 26 Oct '15

26 Oct '15

Hi, Is it possible to call "Match Align" from a script or a 'com' file without using the GUI? I would use that possibility, if it does exist, to check pair-wise rmsd's of previously superimposed structures. I guess people may have asked this question before, but I couldn't find an answer in the usual places... Cheers, Miguel

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Query on Cryo-EM map
by Aditya Padhi 25 Oct '15

25 Oct '15

Dear Chimera Users, I have a cryo-em map file and I would like to convert it into a PDB file. How can I do that? I tried saving the .pdb file but it throws an error saying “No model chosen to save”. Another question, If I open a .map file of a protein complex in Chimera, how can I select a subregion (a particular chain) and colour the surface of that part differently? I am not able to select the chain when I upload the .map file. Thank you, Aditya

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How to make a microtubule model
by Tom Goddard 22 Oct '15

22 Oct '15

The following page shows a “bent microtubule” model made with a Chimera Python script https://www.cgl.ucsf.edu/chimera/data/microtubule_aug2013/bent_mt.html <https://www.cgl.ucsf.edu/chimera/data/microtubule_aug2013/bent_mt.html> The bend makes it more complicated than a straight microtubule. Here is an explanation of how the Chimera “sym” command can make a straight microtubule model. These commands in Chimera (menu Favorites / Command-line to enter commands) make a straight microtubule from a PDB model as shown in the attached image. open 1jff sym #0 group h,9.8,27.7,13*shift,8,80.0 surf true axis x center 0,115,0 res 5 The sym command took the tubulin dimer (shown in red and blue in the image) and made copies in a helical pattern to look like a microtuble. The trick is to find the right helical parameters. I just did a few minutes trial and error to find the above. The “group” option says make a helix where each subunit is shifted 9.8 Angstroms from the previous one and by 27.7 degrees around the axis from the previous one, and make 13 copies (for a 13 protofilament microtubule). This makes a single turn of the microtubule. A microtubule does not have helical symmetry, the one turn achieves a shift of 1.5 subunits creating a seam where alpha and beta tubulin are touching in two adjacent protofilaments. So I just make one turn. Then the above command says shift that one turn by 80 Angstroms along the axis for each of 8 copies. The “surf true” option says show the copies as surfaces. Without that it will copy the atomic model and use a ton of memory. The helix axis is x (just judged by eye after opening tubulin dimer 1jff. The 1jff dimer seems to be centered not far from 0,0,0 so I shifted the helix axis 115 Angstroms along y to make the diameter about 23 nm. Here are the docs for the sym command: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/sym.html <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/sym.html> Here’s a web page where I did something more sensible to get better symmetry parameters — I fit the tubulin dimer to an EM map of a microtubule. http://www.cgl.ucsf.edu/chimera/data/cellcomplexity06/tcell-demo.html <http://www.cgl.ucsf.edu/chimera/data/cellcomplexity06/tcell-demo.html> Tom

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center of mass
by erik.laurini＠di3.units.it 21 Oct '15

21 Oct '15

Dear Chimera users, I would to plot the distance between the centers of mass of a ligand and a specific portion of its biologic target during the corresponding MD trajectory. I tried with the "MD plot" but it seems that it works only with atom selection. Do you have any advice? Thanks in advance! -erik- Dr. Erik Laurini Department of Engineering and Architecture University of Trieste, Via Valerio 10, 34127, Trieste (Italy) Tel. + 39 0405583440

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Calculating the total areaSAS from a series of PDB files
by ros 21 Oct '15

21 Oct '15

Hello! I would like to measure the SAS from a series of PDB files to see how the surface value changes over time (the PDB files are from an MD simulation). I know that If I open a PDB file and calculate the surface, I get the areaSAS value, but I do not want to do this 5000 times. I am making progress on a python script to automate the process, which is: -------------------------------------------- import os from chimera import runCommand as rc from chimera import replyobj os.chdir("/home/tmp/pdb") file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")] for fn in file_names: replyobj.status("Processing " + fn) rc("open " + fn) rc("surf") rc("sel :1-6") from chimera.selection import currentResidues residues = currentResidues() outf = open("/home/tmp/sas.dat", "w") for r in residues: print>>outf, r, r.areaSAS rc("stop now") -------------------------------------------- The PDB's consist of only 6 residues (DNA residues). With this script, I get the output: #1 DA 1 320.8377808 #2 DC 3 277.614161432 #2 DG 4 323.883637217 #1 DC 3 284.934065707 #2 DT 6 221.04715555 #0 DA 1 321.883850728 #1 DC 5 345.231659889 #0 DC 2 179.379177183 #2 DC 5 350.455405176 #0 DC 3 285.785918236 #1 DT 6 245.048330456 #0 DG 4 303.501165912 #1 DG 4 314.409510799 #0 DC 5 352.639633257 #1 DC 2 193.509086639 #0 DT 6 214.883334659 #2 DC 2 183.766654447 #2 DA 1 344.369126737 using 3 test pdb's. Is there a way to get the total value of areaSAS of each model and not for each residue? I am interested in having a file just like (using for example 3 pdb's): Model # total areaSAS value #0 123123.123122 #1 123123.12312 #3 123123.12312 ... etc. I have tried deleting the residues loop, but I do not know how the total areaSAS attribute is stored or how to assign it to a variable. Thank you for your help! Rodrigo. PS. The main goal is to be able to do this without the PDB files and just reading an AMBER topology/trajectory...

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Change chain id of blank chain
by Tom Goddard 20 Oct '15

20 Oct '15

Hi Joshua, Eric looked at the code and said the changechains command can’t change the blank chain id because it won’t accept a quoted space character as the chain letter. It could be done with Python code, or as you mention you can do it with the change chain ids gui. Tom > On Oct 20, 2015, at 2:07 PM, Broyde, Joshua E. <wrote: > > Dear Tom, > Hope you are well. I am having an issue with redefining the chains in a pdb open in Chimera. If a model has two chains (A and B) then it is easy to reassign the chain ids using: > changechains A,B B,A > > However, if one of the chains does not have a chain id already, (what Chimera calls, the "principle chain"), how do I assign a chain id? This is easy to do in the GUI, but I cannot find a command for doing so. > > Sincerely, > Joshua Broyde

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Color blobs automatically
by Petr.Brazda＠seznam.cz 19 Oct '15

19 Oct '15

Hello, I have both periodically distributed blobs and blobs, which are randomly distributed in my volume data. I know the translational vectors of the periodic net of blobs and I would like to automatically color them to distinguish them from the rest of the blobs. Is there a way to tell Chimera to color the blobs, which contain voxel with particular x, y, z coordinates? Or is there some other way to do this job? Best regards, Petr

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mouse selection not working
by Joel Meyerson 19 Oct '15

19 Oct '15

Hi, I'm unable to click-and-drag to select objects in the latest version of Chimera. Specifically, when I hold 'ctrl' and drag over an object, no selection is made. This is something that worked just fine in previous versions of the program. Any suggestions on how to fix the issue? I'm using Chimera production version 1.10.2 (build 40686) and running Mac OS X 10.10.4. Thanks, Joel

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on movie command
by Smith Liu 18 Oct '15

18 Oct '15

Dear All, Suppose there is a 100-residue protein opened in chimera, and it was scaled to a windows which can hold 10 residues, for example residue 10-20. Is any good way we first center on residue 15, then smoothly center on residue 16 (window hold residue 11-21), then smoothly center on residue 17 (window hold residue 12-22), then smoothly center on residue 18 (window hold residue 13-23), ......., until we center on residue 100? Here I emphasize "smoothly" so that the residue "move" was not too sudden to the eye. Best regards. Smith

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Chimera-users October 2015