- Chimera-users - RBVI Mailing Lists

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

2 1

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

1 0

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

2 1

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

2 1

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

2 1

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.

1 0

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.

3 2

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.

2 2

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

2 1

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

3 2

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

1 0

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

2 1

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

3 2

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.

3 4

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

2 2

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

2 1

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>

2 5

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

1 0

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

2 1

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 >

1 0

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

3 2

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

2 4

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

2 2

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

2 1

radial density map
by Jian Guan 09 Feb '15

09 Feb '15

Hi all, I have a mrc map of virus, T=7 icosahedron. Does anyone know how to make radial density map (averaged radial density VS radius of virion)? I tried chimera method of shortcut rd. It took long time but return one result. For the rd result, is it make along x, y or z axis? Or along assigned axis, like 5 fold symmetric axis? I have asymmetric extra density around 5-fold axis. What will happen in my case if use rd? Are there any other ways to make the plot besides of rd? Thank you so much. Sincerely yours, Jian

2 1

CHIMERA movie with parm7/dcd
by Francesco Pietra 09 Feb '15

09 Feb '15

Hello: In the recent past, issues in running movie with parm7 files were solved. Now, with ambertools14 problems come out again, unless I dropped into a silly mistake. That is, parm7/dcd was refused because no top file was found. Renaming the prm7 extension prmtop led to File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line 354, in SetupFrame raise IOError, "Trajectory/Restart header line is greater than 80 characters -- invalid!!" Thanks for your kind attention francesco pietra

2 1

command line
by Dieter Blaas 09 Feb '15

09 Feb '15

Hi, sorry for asking again an old question but I lost the solution: how do I show single solid planes of several volumes? I tried: 'vol all style solid plane one axis z' and many combinations thereof but it always tells me: 'volume invalid planes argument "one": Value must be one of x,y,z, got "one" when I try ' vol all style solid plane z' it tells me: 'volume invalid planes argument "z"' and so on.... Thanks a lot for your patience, best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

2 2

Re: [Chimera-users] Ramachandran plot statistics
by Nadia Raboana 08 Feb '15

08 Feb '15

Hi, It works perfectly, thank you for helping me. Best regards, Nadia Sent from Windows Mail From: Elaine Meng Sent: ‎February‎ ‎8‎, ‎2015 ‎12‎:‎52‎ ‎AM To: Nadia Raboana CC: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Ramachandran plot statistics Hi Nadia, You would have to decide for yourself what probability cutoff you want to use as the boundary between allowed and disallowed. First assign the probabilities to the residues: in the Ramachandran Plot dialog, click the button at the bottom to “Assign Residue Probabilities” (or use the ramachandran command option “assign”): <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ramachandran/rama…> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ramachandran.html> Then in Select by Attribute (Chimera menu: Select… By Attribute Value) choose attributes of “residues” with Attribute: ramaProb … that will show a histogram of the probability values. Then you can move the green bars to enclose the range of probabilities you want to select. After you use that dialog to select everything above your cutoff probability, then you can get a count of the selected residues by clicking the green magnifying glass at the bottom right corner of the Chimera window to show the Selection Inspector. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.htm…> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html> Then you would divide by the total number of amino acid residues to get the percentage. You could count the total number of amino acid residues, for example, by using command “select protein” and then clicking the green magnifying glass. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Feb 7, 2015, at 4:49 AM, Nadia Raboana <nadia_raboana(a)hotmail.fr> wrote: > Hello, > I am using UCSF Chimera to generate Ramachandran plot related to my protein structure. I would like to know how to get the statistics about the analysis. I would precisely know the percentage values of residues in most favored regions, allowed regions and disallowed regions. > Thank you for answering me. > Best regards, > Nadia Raboanatahiry

1 0

Change selection mode programatically
by Mario J. Borgnia 07 Feb '15

07 Feb '15

Hi, I am trying to find a way to split a complex selection pattern among a number of lines in a script. I was expecting that this would be an option to the select command, but apparently it is not. I know that I can combine "select" commands by changing the selection mode to "append" in the GUI, but I am struggling to find the way of doing this from command line or from a script. Is there a way to change the selection mode to "append" without using the GUI? Thanks Mario -- +---------------------------------+ | Mario J. Borgnia, Ph. D. | | | | Lab of Cell Biology | | NIH NCI/CCR | | 50 South Drive Rm 4306 MSC 8008 | | Bethesda MD 20892-8008 | | | | Tel: (301) 594 0563 | | mborgnia(a)nih.gov | +---------------------------------+

2 2

Ramachandran plot statistics
by Nadia Raboana 07 Feb '15

07 Feb '15

Hello,I am using UCSF Chimera to generate Ramachandran plot related to my protein structure. I would like to know how to get the statistics about the analysis. I would precisely know the percentage values of residues in most favored regions, allowed regions and disallowed regions.Thank you for answering me.Best regards, Nadia RaboanatahirySchool of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan, CHINA

2 1

Help in writing python code
by Ankit Agrawal 06 Feb '15

06 Feb '15

Hi I am doing trajectory analysis which has 40000 frames. So for all frames I wanted to calculate the all three inertia axes. That I did. But problem is that when I run the python code it starts making all the three axes for each frames that becomes messy. So I want a little change in my code so that during trajectory analysis it should create axes but should delete or hide the previous axes also. So during run I will see only the axes which are related to that frame. Here is the python code in per-frame analysis. from chimera import runCommand frame = mdInfo['frame'] runCommand("measure inertia #1:0-120 color yellow") runCommand("measure inertia #1:120-237 color green") Thanks. Ankit

2 2

Help in executing python script in per-frame analysis
by Ankit Agrawal 05 Feb '15

05 Feb '15

Hi I am analysing a protein molecule (MD simulations). I wrote a python script to calculate inertia for the protein and ran it over 40000 frames. I got a data in log file but it is creating a ellipsoid around the molecule. I want 3 axes of the ellipsoid to be shown in that protein molecule not the ellipsoid as it covers the whole protein molecule. So that I can easily visualize the movement of all 3 axes of ellipsoid over the 40000 frames (means how the axes are changing during trajectory run). Thanks Ankit Department of Chemical Science IISER-Mohali, India

2 1

multiple Chimera sessions on Mac
by Vladimir Yarov-Yarovoy 03 Feb '15

03 Feb '15

Hello, Is it possible to open multiple Chimera sessions on Mac OS X Yosemite? I tried to start multiple chimera sessions from different terminal windows that was recommended in this thread - http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003231.html - but it doesn't work. Thank you, Vladimir

2 3

Command line problem
by Luca Pellegrini 03 Feb '15

03 Feb '15

Hi, I am having the following problem when I try to use the command line. When I select ‘Command line’ from the ‘Favorites’ menu, the command line window appears, but I can’t type anything in it. Or rather, I can type in it, because if I hit return the command gets executed, but I can’t see what I type. Any idea of what’s going on? I suspect that it might be something to do with Yosemite 10.10.2, since this problem arose after upgrading the MacOSX operating system. I am using Chimera 1.10.1, build 40415. Thanks for any advice. Kind regards, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

2 2

Error: UnboundLocalError: local variable 'i' referenced before assignment
by Letizia Meregalli 03 Feb '15

03 Feb '15

Hi, I have a tRNA molecule and I would like to measure the angles between two nitrogenous bases. I created two planes, each for each base. When I select both planes, in order to measure the angles between them (Structure Measurements Axes/Planes/Centroids) I get following message: <type 'exceptions.UnboundLocalError'> Exception in Tk callback Function: <bound method SortableTable._browseCmd of <CGLtk.Table.SortableTable instance at 0x117990638>> (type: <type 'instancemethod'>) Args: ('1',) Traceback (innermost last): File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/Applications/Chimera.app/Contents/Resources/share/CGLtk/Table.py", line 1043, in _browseCmd self.userBrowseCmd(self.selected()) File "/Applications/Chimera.app/Contents/Resources/share/StructMeasure/Geometry.py", line 268, in _tableCB self.feedback(sels) File "/Applications/Chimera.app/Contents/Resources/share/StructMeasure/Geometry.py", line 113, in feedback diff = " ".join(words2[i:]) <type 'exceptions.UnboundLocalError'>: local variable 'i' referenced before assignment UnboundLocalError: local variable 'i' referenced before assignment File "/Applications/Chimera.app/Contents/Resources/share/StructMeasure/Geometry.py", line 113, in feedback diff = " ".join(words2[i:]) See reply log for Python traceback. I really don’t know how can I solve this problem.. I’d be really grateful if you could help me or give me some hints! thank you a lot Letizia

2 1

Help Needed
by angshu＠klyuniv.ac.in 03 Feb '15

03 Feb '15

Hi, I need a small help. I need to find out the amino acid residues from one chain of a protein which are within 5A of a specific amino acid residue of some another chain of the same protein. For example: Say I have a protein 1XYZ.pdb containing A, B, C chains. I want to find which amino acids from chain B and C are within 5A distance from ALA 78 belonging to chain A. Please let me know. Thanks. Angshuman

2 1

Using Chimera to measure voxel densities
by Noble, Alex 30 Jan '15

30 Jan '15

Hi all, I have a pdb fit into an EM density in Chimera and I would like to be able to see what the nearest voxel densities are at specific atomic coordinates. Is there any way to do this in Chimera? Best, -Alex Noble

3 4

Question
by Monete Rajão Gomes 28 Jan '15

28 Jan '15

Hi, I have some problem these days about superimpose templates with matchmaker. I followed this tutorial http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-August/006686.html. There are regions on aminoacids sequences which are identical. So, when I superimpose them, they stay separated. I am sending a screenshot attached. It would be great if you could help me. Best, Monete

2 2

Morph conformations - estimated time to completion in status bar?
by Oliver Clarke 26 Jan '15

26 Jan '15

Hi all - silly little feature suggestion, but I was wondering if it would be possible to add an live-updating “x % complete” or “estimated time to completion” entry in the status bar when running Morph Conformations? When morphing two structures with very large numbers of atoms, morph conformations can take a long time (hours) to complete, and it would be handy to know whether it is nearly done or not (currently it just shows “computing interpolation 1” until it is finished). On a related note, is there any way to speed up morph conformations for large structures? E.g calculating transformations using C-alpha atoms only? Best, Oliver.

2 1

modelling a dimer
by David Norman (Staff) 23 Jan '15

23 Jan '15

I am trying to model a symmetrical dimer using modeller within Chimera. I cannot work out how to present the alignment and pdb. files in oder to do this. Any hints please. Thanks David David Norman Ph.D Nucleic Acids Research Group School of Life Sciences MSI/WTB Complex Dow St. Dundee, DD1 5EH, Scotland, UK. phone +44(0)1382 384798 mobile +44(0)7808572788 E.mail d.g.norman(a)dundee.ac.uk Web site: http://www.lifesci.dundee.ac.uk/people/david-norman The University of Dundee is a Scottish Registered Charity, No. SC015096 The University of Dundee is a registered Scottish Charity, No: SC015096

2 1

how to find non-bonded interactions between a protein and a ligand?
by Sam Paul D. 22 Jan '15

22 Jan '15

Hi, I need to find non-bonded interactions between a protein and a ligand through command line. Could anyone please suggest which chimera command to use with the syntax? With regards, Sam

3 4

Find subsequence programatically
by Thomas Hrabe 22 Jan '15

22 Jan '15

Hi Chimera Team, How can I automate the Sequence View -> Edit -> Find Subsequence Tool programmatically with the Chimera shell or better within python? Thank you, Thomas

2 2

Coot capabilities in Chimera
by Mario J. Borgnia 22 Jan '15

22 Jan '15

Dear all, WIth the advent of atomic resolution maps in Cryo-EM, we find ourselves refining structures. The blunt question is, should I move to Coot and leave behind Chimera for that or are there overlapping functions and what will I be missing if I choose to stay with Chimera. I have some ideas about the answers but would like to read what the developers and power users have to say on the issue. Thanks!!!

2 1

How to predict/model the structure of two known structure proteins
by Phan Trong Hoang 22 Jan '15

22 Jan '15

Dear UCSF developers, I am Hoang, working in IPK in Germany. I am following your series online tutorials about how to use UCSF Chimera. This program is very useful for me. However, I did not see your video showing how to predict/model the structure of a fusion protein that is made by combination of two known structure proteins in PDB (for example gi|534286646|pdb|4KRN| and gi|390136394|pdb|4DDF|A). Is this function available in your software? If yes can you show me how to manipulate with it. I would like appreciate it very much Thank you for your attention and I am looking forward to hearing from you. Best regards Hoang Phan

2 3

SDF file
by Hernando J Sosa 22 Jan '15

22 Jan '15

I have an sdf file with a small ligand molecule in 2D (it looks flat when opened in chimera). What would be the best way to make it 3D (i.e. assign/minimize the proper bond angles & distances). Is it possible to do it in chimera? Thanks

3 3

How can one create a sculpted view of a cellular assembly?
by Kenward Vaughan 21 Jan '15

21 Jan '15

As I slowly approach the operational realization of my computational/visualization lab, I received your lovely holiday card. This seriously elevated my dreams of larger scale possibilities for chemistry and biology students through the cellPack resources. In playing with it, I found myself wanting a more robust version of a clipping plane which would have several characteristics: 3 dimensional - take a cell and hack out 1 or 2 adjoining octants relative to its center to give a sliced view similar to what is found in some texts (also often used in geology books to depict the earth's internal structure--see http://www.the-science-site.com/earths-interior.html for an example). Being able to leave the nucleus alone while the surface strips away the cytoplasm would be cool, much like the referenced image above showing the core of the earth. Likely a difficult one to actually implement? Have the clipped surface not be flat, but rather allow a component to stay visible as the surface is moved past it until some determined relationship at which point it vanishes (perhaps when it has passed entirely through the clipping surface?). The clipped surface would thus show structure of a sort. Have the choice of the clipping surface being static with the assembly (it could rotate with the assembly, keeping the same internal view), or separately static (how a clipping plane behaves now--as I know it--where rotating the structure causes things to move through the unmoving plane. One approach I can imagine would be the use of a spherical or ellipsoidal (?) surface of specific size at a specific distance from the center of the cellular assembly. Is this already implemented in a way that can be manipulated to achieve at least the major aspects of this effect (e.g. logical ANDing of clipping by 3 intersecting planes)? Sorry for the long question... ;-/ Kenward -- In a completely rational society, the best of us would aspire to be _teachers_ and the rest of us would have to settle for something less, because passing civilization along from one generation to the next ought to be the highest honor and the highest responsibility anyone could have. - Lee Iacocca

3 3

Ringer/Chimera/IDLE
by Alejandro Virrueta 21 Jan '15

21 Jan '15

Hello, I am modifying some Ringer files for my own needs, but I am running into a weird issue. If I run Ringer via typical means: $RINGER/ringer/ringer -i ringer_in_${pdb_ID}.txt -o ringer_out_${pdb_ID}.txt it works fine. However, when I step through it in what I think is my version of IDLE ("$CHIMERA_HOME/bin/chimera --nogui --nostatus --script `which idle2.7` /usr/bin/idle2.7", with `which idle2.7` returning "/usr/bin/idle2.7"), I run into this error: Traceback (most recent call last): File "/Users/av376/ringer-2.0/ringer/main_copy.py", line 233, in <module> main() File "/Users/av376/ringer-2.0/ringer/main_copy.py", line 161, in main move_set, pdb = structureFile(parameters, path) File "/Users/av376/ringer-2.0/ringer/main_copy.py", line 65, in structureFile pdb = chimera.openModels.open(parameters.pdbfileName) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 1817, in open checkForChanges=False, noprefs=noprefs) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 1644, in add makePseudoBondsToMetals(realMolecules) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 1961, in makePseudoBondsToMetals cmPBG = mol.metalComplexGroup(issueHint=True) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 119, in _getMetalPbg am.color = preferences.get(MOLECULE_DEFAULT, MOL_COMPLEX_COLOR) File "/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", line 608, in get forPrefSave=forPrefSave) File "/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", line 179, in get return self._options[name].get(forPrefSave=forPrefSave) File "/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", line 80, in get return self.prefToVal(self.value) File "/Applications/Chimera.app/Contents/Resources/share/chimera/tkoptions.py", line 1229, in _prefToColor return getColorByName(pref) File "/Applications/Chimera.app/Contents/Resources/share/chimera/colorTable.py", line 87, in getColorByName color = chimera.MaterialColor(r/255.0, g/255.0, b/255.0) ValueError: missing default material Any suggestions? Cheers, Alex

2 1

Alternate conformations in residues
by Alejandro Virrueta 21 Jan '15

21 Jan '15

Hello all, Is there a way to get the all the information for an alternate conformation from a residue object? I have res.altLocs resulting in set([a,b]), but how can I get chi1-4 for conformation b for example? Thanks! Alex

2 1

Alternate conformations in residues
by Alejandro Virrueta 21 Jan '15

21 Jan '15

Hello all, Is there a way to get the all the information for an alternate conformation from a residue object? I have res.altLocs resulting in set([a,b]), but how can I get chi1-4 for conformation b for example? Thanks! Alex

1 0

Mesh defined by distance to selection
by R. Michael Sivley 21 Jan '15

21 Jan '15

I have a set of residues in a protein structure that each mark the center of a sphere over which a value has been calculated. I can select a subset of residues by value, but the values actually correspond to the sphere around that residue. I would like to visualize this by creating a mesh defined by being within 10A of any selected residue. If a selected residue isn't within 10A of any other selected residue, I would like this to produce two meshes, but if they are within 10A, I would like a single continuous mesh whose boundaries are defined as being 10A from either residue. Zone-selecting residues within 10A of the selection and then showing their surface as a mesh is a close approximation of what I'm trying to convey, but doesn't give me exactly what I'm looking for. I found this in the Chimera help pages, and it seems to be exactly what I need: http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html#z… I think I'm missing a first step, though, because I don't understand how to actually create the mesh. I select my residues, open the Volume Viewer, and define the zone radius, but then I'm stuck. How do I actually instantiate the mesh given those values? I've tried showing the surface for the selected residues, but the changes I make in the Volume Viewer don't appear to have any effect on the surface, so I'm assuming these are two separate features. There is no "apply" button in the Volume Viewer, and closing the window does not create a mesh. I've included a screenshot of where I'm stuck, should it be helpful. Could you help me identify the missing step in this process? Thanks! Mike Sivley PhD Student in Biomedical Informatics Center for Human Genetics Research Vanderbilt University

2 1