- Chimera-users - RBVI Mailing Lists

binned color ranges for scolor?
by Oliver Clarke 11 Mar '15

11 Mar '15

Hi all, I was wondering whether it is possible to use binned ranges for scolor? Specifically, I would like to color one volume by the density values of a second volume, but rather than using a continuous color palette, I would like to highlight several discrete bins with particular colors - e.g coloring all values between 2 and 4 red, and all values between 6 and 8 green, while leaving other voxels uncolored (or colored gray, for example). Is this currently possible? I couldn’t figure it out - both cmap and map range seem to give continuous coloring. Best, Oliver.

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How to lower the map size
by 李智海 09 Mar '15

09 Mar '15

Hi, Now I have a density map with a dimension of 820*820*820, it is too large for me to perform image processes with Chimera. So I was wondering whether there is a way to decrease the map size rather than re-reconstruct the map with bined particle image. please help me out! Thank you in advance! Zhihai Li

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Re: [Chimera-users] Request for support - UCSF Chimera
by Eric Pettersen 04 Mar '15

04 Mar '15

On Mar 4, 2015, at 10:14 AM, Nishant Ray Velagapudi <nishray(a)uw.edu> wrote: > Hello Mr. Petterson, > > I was looking for some help with using UCSF chimera and I was wondering if I can directly email you my question. If this is not the appropriate address, my apologies, and could you point me in the appropriate direction for support? Hi Nishant, You should probably send questions like these to the chimera-users mailing list. That way other people can benefit from the answer, and it also allows others to answer in the cases where I'm not really the best person for the question. > My issue is that I want to automate the process of creating and saving structure based sequence alignments. It has been simple to open the file and align them, but I am not sure how to save the .fasta alignment file out. Here is what I have so far: > > for fn in file_names: > replyobj.status("Processing: " + fn) > rc("open " + fn) > rc(mm #0 #1 show true) > rc("close " + fn) > > The bold line is the problematic one - is there any way to write out the resulting alignment file in a programmatic fashion? Yes. You can locate the MultAlign Viewer (MAV) instance using the code in this previous chimera-users mail: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010017.html That message also describes how to save the alignment to a file, in conjunction with the info in this message: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010015.html You can search the chimera-users list from this page to see if your question has been asked previously: http://www.cgl.ucsf.edu/chimera/docs/feedback.html I hope this helps. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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concatenate
by sunyeping 04 Mar '15

04 Mar '15

Dear all,I am dealing with a EM map which is a double helical filament and composed of two protein chains winding each other. Each of the two chains is composed of multiple same protein subunits. Now I am trying to color one chain of the map with one color, and the other chain with another color. How should I do that?Besides, it is known that multiple such double helixes can constitute a longer helix by a head-to-tail way. I can open several helixes in chimera, but how to concatenate they correctly into a long helix?Could you help me with these questions?With many thanks! Yeping Sun Institute of Microbiology, Chinese Academy of Sciences

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Command for zooming in
by Anindito Sen 04 Mar '15

04 Mar '15

Dear All, What is the command for zooming into a portion of a density map ? This will be just using the command line for the zoom-in instead of using the middle mouse button. Thanks Andy

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Select residue by array index, not residue id
by Thomas Hrabe 03 Mar '15

03 Mar '15

Hi everyone, is there a way to select a residue by it’s array index, starting at 0 -> sequence length rather than using the residue id? Thank you in advance for your help, Thomas

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Re: [Chimera-users] rmsd calculation for pre aligned structures
by Elaine Meng 02 Mar '15

02 Mar '15

Hi Oliver, In that case, you can just show the sequence of one protein, then use the sequence window menu: Structure… Associations to associate both structures with that one sequence, then sequence window Headers menu to show the RMSD of interest, etc. This would work even if the sequences of the structures were slightly different, as long as they were both similar enough to the sequence in Multalign Viewer that Chimera could figure out the association accurately. Elaine On Mar 2, 2015, at 3:12 PM, Oliver Clarke <olibclarke(a)gmail.com> wrote: > Hi Elaine, thanks for the reply! This sounds like exactly the right solution. However, when I try to add a sequence in the sequence dialog, Chimera hangs on “running Needleman-Wunsch”. > > I suspect this is because my sequences are so long (~5000 residues). > > But I don’t actually need to align them - they are already aligned as they are actually the same sequence, because I am looking at different conformations of the same protein. > > I guess I can create a dummy sequence alignment, with two identical sequences, but it would be nice to have some way of telling chimera not to align the sequences, or to allow for manual alignment in cases such as these - perhaps a “Do not align” or “align manually” checkbox in the add sequence dialog would do the trick. > > Thanks again, > Oliver.

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rmsd calculation for pre aligned structures
by Oliver Clarke 02 Mar '15

02 Mar '15

Hi, I have two structures that are pre-aligned in another program, and I would like to calculate a per-residue rmsd between the two structures and assign this to an attribute that I can use to color one of the structures. Is there any way to do this at present? The mavRMSD attribute only seems to be calculated after matchmaker, not after using the regular “rmsd” command. Perhaps there is a way to do a dummy run of matchmaker, somehow forcing both structures to remain fixed? Best, Oliver.

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explicit parentheses in atom selections
by Oliver Clarke 02 Mar '15

02 Mar '15

Hi all, Would it be possible at some point to allow the use of explicit parentheses when grouping selections on the command line? It would make it much easier/clearer when using multiple boolean operations (e.g "ligand z<5 &~ ligand &~ solvent” could be “ligand z<5 &~(ligand | solvent)”). Is there a reason why this kind of syntax is not used at the moment? Also, just a random thought for a future version - it would be really handy to have something like the “Macro recorder” function of ImageJ or similar programs. This records whatever the user does using the GUI (while the recorder is active) and spits out the equivalent scripting commands to a dialog, where they can be saved and reused, or turned into a script. This can be a very powerful tool for learning the command line functionality of a complex application in an interactive manner. Cheers, Oliver.

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Embed chimera into my gui code
by hy liao 26 Feb '15

26 Feb '15

Hi, I am creating a GUI using tkinter, and I would like to embed chimera into it. Specifically, I would like to display a 3D molecule density map using chimera and inside my GUI. Chimera would be activated while the GUI is on. Is there documentation to accomplish this? Thanks! Stu

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Inverse volume-erasing
by kzhang＠mrc-lmb.cam.ac.uk 25 Feb '15

25 Feb '15

Dear Chimera users, Dose anyone know how to do inverse volume-erasing? Normally we use the eraser to erase density we don't want to keep. However, what shall I do if I want to keep the density within the eraser while getting rid of other parts? Many thanks Kai

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Re: [Chimera-users] Inverse volume-erasing
by kzhang＠mrc-lmb.cam.ac.uk 25 Feb '15

25 Feb '15

Thanks! This is a good solution. But I wonder if there's an interactive way just like the eraser, but doing the opposite thing. It might help on difficult cases when you want a real time feedback what you are erasing and keeping just in Chimera without external command. Kai > difference ma p > <kzhang(a)mrc-lmb.cam.ac.uk>于2015年2月25日星期三写道： >> Dear Chimera users, >> Dose anyone know how to do inverse volume-erasing? Normally we use the eraser to erase density we don't want to keep. However, what shall I do if >> I want to keep the density within the eraser while getting rid of other parts? >> Many thanks >> Kai >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu <javascript:;> >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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about model coordinates
by Tat Cheung Cheng 20 Feb '15

20 Feb '15

Hi, I recently got a ~4.4A EM map and built a improved model using MDFF. The map and model is well aligned when loaded in Chimera. But it is off when I hit "center" in the volume viewer, as the origin is shifted. As I try to improve the model in Coot, the map and model isn't aligned at all in Coot, seemingly by the same offset when "center" button was hit. And also the values in the original index in the volume viewer is different from the values in the header in the density map. So I wonder what determines the origin index? and is it possible to find the shift and transform the coordinates in the model so as to align the model with the map in coot? Thanks a lot. Tc

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problem installation on linux 64 bit
by Chiara Parravicini 20 Feb '15

20 Feb '15

<chimera-users(a)cgl.ucsf.edu>Dear Chimera Users, After installing Chimera from the precompiled version chimera-1.10.1-linux_x86_64.bin (the installation completed without any error), I get the following error when I run the binary: libGL error: unable to load driver: nouveau_dri.so libGL error: driver pointer missing libGL error: failed to load driver: nouveau libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast X Error of failed request: GLXBadContextTag Major opcode of failed request: 156 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1455 Current serial number in output stream: 1455 I would appreciate any help or suggestion! Many Thanks in advance Chiara

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Restricting "select by conservation" to a subset of sequences in a multiple alignment
by Oliver Clarke 18 Feb '15

18 Feb '15

Hi, I very much like the sequence tools within Chimera - I find the capacity to load in multiple alignments and select by conservation particularly handy. I have two suggestions that I would love to see in a future version of chimera (or maybe they are already in there and I don’t know about them!): 1. Selection of sub-groups of sequences within a multiple alignment for selecting residues by conservation. This would enable the easy selection/identification of residues that are specifically conserved within individual families with different functions or substrates - for example, a position that is an arginine, and always an arginine, in one subgroup of proteins that we know have a particular function, and always a glutamate in another group of proteins that we know possess a different but related function. It is possible to do this currently by loading in multiple different sequence alignments and saving and intersecting selections, but having a popup menu in the select/render by attribute tab where you could select or deselect sequences that contribute to the analysis of conservation would make it much easier. 2. Optional addition of sequence similarity, as well as identity, to the analysis of sequence conservation would make analysis of alignments including quite divergent sequences much more meaningful. Even better would be if the definition of similar groups for this purpose was user-adjustable and had allowance for overlapping groups of similar residues. Cheers, Oliver Clarke.

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MD movie export from per frame script
by Ankit Agrawal 18 Feb '15

18 Feb '15

Hi all I want to write a script which can create movie (.mp4) from per frame script. Because I want to show all models in movie. Please help Thanks Ankit Agrawal Department of Chemical Science IISER Mohali, India

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showing shapes in only selected Chimera animation scenes
by Michael Oldham 17 Feb '15

17 Feb '15

Chimera users, I am making an animation that needs to include either a box generated with an opened .bild file using a .box command or a rectangle generated by "shape rectangle” I wish the box or rectangle to appear in some scenes but not in others. My problem is, if I choose to show the box or rectangle in the first scene then it is shown in all subsequent scenes even if they were created in which the box or rectangle were not shown. Any suggestions on how to show the box or rectangle in only selected scenes of the animation. Thanks Mike Oldham Rockefeller University

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Fwd: Problem running chimera through a command script
by Christos Deligkaris 17 Feb '15

17 Feb '15

Dear all, I have a python script that creates a .com command script for chimera and then attempts to run the chimera script. Here is the python script: ************** #!/usr/bin/env python import re,os,sys,math, decimal, subprocess from copy import deepcopy from openeye.oechem import * from decimal import * script_file=open("chimera_script_for_" + "ligand" +".com", 'w') script_file.write("open "+ "127D" +"\n") script_file.write("open " + "127D" +"\n") script_file.write("open "+ "ligand.pdb" +"\n") script_file.write("match #0:"+ "6" + " " + "#1:"+ "18" +"\n") script_file.write("write format pdb 2 "+ "flipped_" + "ligand" + "\n") script_file.write("stop") script_file.close print script_file.name chimera=subprocess.call(["chimera", " --nogui ", " chimera_script_for_ligand.com"]) print chimera #delete the script, leaving just the flipped ligand #os.remove(script_file.name) ******************* When I run the script, it successfully generates the .com chimera script. However, I get the following error message: ******************* [christos@biophysics Desktop]$ ./script.py chimera_script_for_ligand.com Traceback (most recent call last): File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/share/__main__.py", line 69, in <module> value = chimeraInit.init(sys.argv) File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/share/chimeraInit.py", line 638, in init splash.create() File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/share/chimera/splash.py", line 25, in create sync=chimera.debug) File "/share/apps/PROGRAMS/CHIMERA/CHIMERA-1.9/lib/python2.7/lib-tk/Tkinter.py", line 1747, in __init__ self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use) _tkinter.TclError: no display name and no $DISPLAY environment variable 1 ********************** The python script successfully creates the .com script: ****************************** [christos@biophysics Desktop]$ more chimera_script_for_ligand.com open 127D open 127D open ligand.pdb match #0:6 #1:18 write format pdb 2 flipped_ligand stop *************************** and if I manually execute this chimera script, everything works out well: ************************** [christos@biophysics Desktop]$ chimera --nogui chimera_script_for_ligand.com Fetching 127D from web site www.rcsb.org 0 Kbytes received Fetch 127D: finished Done fetching 127D; verifying... Opening 127D... #0, chain A: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') #0, chain B: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') Opening VRML model in 127D - Nucleotides... 127D opened Opened VRML model in 127D - Nucleotides Opened 127D containing 1 model, 639 atoms, and 146 residues Fetching 127D from web site www.rcsb.org 88 Kbytes received 80 Kbytes received Fetch 127D: finished Done fetching 127D; verifying... Opening 127D... #1, chain A: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') #1, chain B: dna (5'-D(*cp*gp*cp*gp*ap*ap*tp*tp*cp*gp*cp*G)- 3') Opening VRML model in 127D - Nucleotides... 127D opened Opened VRML model in 127D - Nucleotides Opened 127D containing 1 model, 639 atoms, and 146 residues Opening ligand.pdb... ligand.pdb opened Opened ligand.pdb containing 1 model, 32 atoms, and 1 residues Executing match ['#0:6', '#1:18'], no iteration RMSD between 21 atom pairs is 0.630 angstroms Wrote flipped_ligand into /home/christos/Desktop ***************************** Why do I get the error message when I attempt to run chimera through script.py? Is this a python issue or a chimera issue? I appreciate any thoughts on solving this problem....thank you, Christos Deligkaris, PhD Assistant Professor of Physics, Drury University 900 N Benton Ave, Springfield MO, 65802 Office Phone: (417) 873-7234 www2.drury.edu/christos <http://www2.drury.edu/christos/index.html> @DeligkarisGroup <https://twitter.com/DeligkarisGroup> +ChristosDeligkaris <http://google.com/+ChristosDeligkaris>

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Announcement: Release of DOCK 6.7
by Scott Brozell 12 Feb '15

12 Feb '15

We are pleased to announce the release of DOCK 6.7. DOCK is a suite of programs for molecular docking. The source code for DOCK 6.7 is available for download and free for academic users at http://dock.compbio.ucsf.edu/. In version 6.7 the default values for several input parameters were updated based mainly on a performance assessment using large data sets and employing multiple metrics including pose reproduction, cross-docking, and database enrichment For full information on what is new in DOCK 6.7, please visit: http://dock.compbio.ucsf.edu/DOCK_6/new_in_6.7.txt Sincerely, The DOCK Team Please visit us at the DOCK Web site. http://dock.compbio.ucsf.edu

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UnitCell.molecule_center(): Attribute does not exist
by Alejandro Virrueta 11 Feb '15

11 Feb '15

Hello all, I'm trying to execute the script to fill out the crystal unit cell found here: http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q13 However, I get the error that UnitCell does not have the 'molecule_center' attribute (code line ~12). I checked with dir(), and yeah, it's not there: ['ModelessDialog', 'Unit_Cell_Dialog', '__builtins__', '__doc__', '__file__', '__name__', '__package__', '__path__', 'chimera', 'dialogs', 'find_model_by_name', 'outline_box', 'place_molecule_copies', 'remove_extra_copies', 'show_unit_cell_dialog'] Where did the attribute go? Is there some other module I could use? Could someone explain (or direct me to some webpage that explains) the process of expanding the ASU and I can write my own script. Any help is greatly appreciated! Thanks! Alex

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Re: [Chimera-users] Problem using structureViz plugin for Cytoscape - Chimera
by Scooter Morris 11 Feb '15

11 Feb '15

Hi Juan, I've uploaded a new version of structureViz (1.0.1) that should fix your problem. Don't hesitate to let us know if there are other issues/enhancements you would like to see. -- scooter On Feb 9, 2015, at 6:39 AM, Juan Eiros Zamora <j.eiros-zamora14(a)imperial.ac.uk <mailto:j.eiros-zamora14@imperial.ac.uk>> wrote: > Hi all, > > I am using Chimera 1.10.1 and Cytoscape 3.2.0, and have installed the > structureViz2 plugin. > > I use structureviz to open chimera through cytoscape and load an MD > trajectory of a protein to create a RIN through Analysis --> Residue > interaction network... > > What I am trying to do is colour the nodes in cytoscape based on which > chain they belong to. My protein has three chains, and in chimera I > color each differently. In cytoscape, I go to apps --> structureviz--> > synchronize residue colors. Here I am given two options. The first one > is “Apply colors from current network view to associated Chimera > models”: This one works fine, but it is not what I want. What I want > to do is the second option: “Apply colors from associated Chimera > models to current network view”, but when I clik on OK it does nothing. > > Anybody having the same problem or some suggestions on how I might > solve this? > > Much appreciated, > > Juan Eiros >

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Manipulate individual hexagons/pentagons in cage builder
by vamsee 10 Feb '15

10 Feb '15

Hello Elaine, I am trying to build a cage but with incorrectly attached pentagons and hexagons to represent mis-assembly. Though I don't believe it is possible using the cage builder, I was wondering if the wonderfully brilliant chimera team would know of any other ways of doing this or even with the cage builder. Thank you yet again, Vamsee

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pymol get_view and set_view in Chimera?
by Jan Kosinski 10 Feb '15

10 Feb '15

Is there an equivalent of pymol get_view and set_view in Chimera? I am aware of savepos command, but I am looking for a feature like Pymol get_view command (http://www.pymolwiki.org/index.php/Get_View) which allows to copy the current view to a script as text and restore it using set_view (http://www.pymolwiki.org/index.php/Set_View) Thanks in advance, Jan

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adding morphs to scene animation in Chimera
by Michael Oldham 10 Feb '15

10 Feb '15

Chimera users, I want to use a combination of various scene selections and morphs in a Chimera animation. Can someone tell me how morphs and scenes be combined to make one movie. Thanks Mike Oldham Rockefeller University

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Problem using structureViz plugin for Cytoscape - Chimera
by Juan Eiros Zamora 09 Feb '15

09 Feb '15

Hi all, I am using Chimera 1.10.1 and Cytoscape 3.2.0, and have installed the structureViz2 plugin. I use structureviz to open chimera through cytoscape and load an MD trajectory of a protein to create a RIN through Analysis --> Residue interaction network... What I am trying to do is colour the nodes in cytoscape based on which chain they belong to. My protein has three chains, and in chimera I color each differently. In cytoscape, I go to apps --> structureviz--> synchronize residue colors. Here I am given two options. The first one is “Apply colors from current network view to associated Chimera models”: This one works fine, but it is not what I want. What I want to do is the second option: “Apply colors from associated Chimera models to current network view”, but when I clik on OK it does nothing. Anybody having the same problem or some suggestions on how I might solve this? Much appreciated, Juan Eiros

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