- Chimera-users - RBVI Mailing Lists

Write a PDB with Python API
by Jaime Rodríguez-Guerra Pedregal 02 Dec '15

02 Dec '15

Hi again! So in my quest to use OpenMM from Chimera, my first proof-of-concept attempts consist of using a PDB file as intermediate to convert chimera.Molecule objects to OpenMM Topologies (using openmm.app.PDBFile loader). While not ideal yet, it'd be convenient to use StringIO() as a memory file, and I have been more or less successful. This is my strategy: memfile = StringIO() m = chimera.openModels.list() chimera.pdbWrite(m, m[0].openState.xform, memfile) memfile.seek(0) # pass memfile to openmm.app.PDBFile and do OpenMM stuff memfile.close() It works, but some residues are not properly recognised... I dumped the converted PDB to an actual file and saw that the problematic residue (an ARG) is totally messed up! I've attached the results: original file is the mol2, the converted one is the pdb, and also a Chimera session with both superimposed. What's the recommended method to convert a chimera.Molecule to a PDB file (if possible, in-memory) with Chimera Python API? Thanks a lot!

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Matchmaker 'restrict to selection' not working as expected.
by Oliver Clarke 01 Dec '15

01 Dec '15

Hi all, When using Matchmaker, the ‘Further restrict to matching selection’ option does not seem to improve the speed of alignment as much as expected under certain circumstances (when the selection is a subset of a larger chain, as opposed to being an individual chain in a multi chain structure). It seems to still restrict the selection correctly for the final alignment (it is still only aligned on the selected domain), but the “test match” step seems to be conducted on the entire chain, rather than the selection - this makes a big difference to speed for large proteins. For example - I tried aligning two conformations of a protein complex consisting of one chain A ~100 residues, and chain B ~5000 residues. If I select chain A of both structures, and then select ‘Further restrict to matching selection’ for both the reference and the structure to match, the alignment is almost instantaneous - less than 2s. If I perform the same operation, but this time selecting the first 100 residues of chain B in each structure, the alignment takes 3min20s, regardless of whether I leave automatic chain pairing on or select the specific chains to use for alignment manually. It takes only marginally longer - 5 min - if I select the entirety of chain B, a selection that is 50X the size. Incidentally I still get the “test match” message in the status bar even when the selection only contains one chain from each structure, or when I manually select (using the chain pairing options) which chains to align - maybe Chimera is still running test match on the whole chain when it should only do so on the selection (or not at all if the selection only includes one possible match). This seems like a bug? Or am I missing something? Cheers, Oliver.

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domain angel
by Smith Liu 01 Dec '15

01 Dec '15

Dear All, Is any way to calculate the angel between 2 domains by Chimera? Smith

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Installing OpenMM in Chimera
by Jaime Rodríguez-Guerra Pedregal 01 Dec '15

01 Dec '15

Hello, I am trying to install OpenMM in Chimera to script some molecular dynamics. However, I am struggling to make it work, since the build fails with this error: g++ -pthread -fPIC -mtune=generic -m64 -I/home/chimera/chimeraBuild_X11/build/build/include -L/home/chimera/chimeraBuild_X11/build/build/lib -DUSE_DYLD_GLOBAL_NAMESPACE -shared -Wl,--hash-style=both build/temp.linux-x86_64-2.7/src/swig_doxygen/OpenMMSwig.o -L/lib -R/lib -lOpenMM -lOpenMMAmoeba -lOpenMMRPMD -lOpenMMDrude -o build/lib.linux-x86_64-2.7/simtk/openmm/_openmm.so g++: error: unrecognized command line option '-R' which is probably not related to Chimera at all. What I've done so far: 1. Download precompiled binaries for Linux from their site: https://simtk.org/project/xml/downloads.xml?group_id=161 2. Extract that file and merge the contents of the directories "include" and "lib" with those in Chimera root path. 3. Cd into the python directory of the extracted file and run: chimera --nogui --script "setup.py install". Has somebody been successful with this package? I know it seems more of a compiler issue, but maybe Chimera is doing some trickery with the build mechanism too. Thank you in advance, Jaime.

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inserting missing residue
by Francesco Pietra 30 Nov '15

30 Nov '15

Hi: II would like to insert a single non-terminal missing amino acid in a big peptide. By using MODELLER with CHIMERA, I don't find any option for NOT modeling loops. Just inserting the missing residue without moving the adjacent residues. In the sequence that appears by invoking modeling, the missing residue is not marked in any way, the sequence just continues as if no non-terminal residue were missing. thanks francesco pietra

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Re: [Chimera-users] calculating dipole moment of a protein in pdb
by Eric Pettersen 25 Nov '15

25 Nov '15

Hi Ajay, Okay I have attached a script that also shows the dipole vector as an arrow on the structure. It will also be listed in the model panel so you can easily hide it or change its color. If you want it to be a different length, change the setting of the “vectorScale” variable in the script itself. The updated script is also available via the scripts page. —Eric > On Nov 25, 2015, at 12:11 PM, Pande, Ajay K <apande(a)albany.edu> wrote: > > I really do need it for many structures, and I am reasonable certain many other people will too. What would be nice is that the dipole vector shows as an arrow on the pdb structure. If you can change the script file, it would be very useful. > > Thanks > > Ajay > > > > > > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Sent: Wednesday, November 25, 2015 2:50 PM > To: Pande, Ajay K > Cc: chimera List > Subject: Re: [Chimera-users] calculating dipole moment of a protein in pdb > > >> On Nov 23, 2015, at 10:37 AM, Pande, Ajay K <apande(a)albany.edu <mailto:apande@albany.edu>> wrote: >> >> Hi Eric, >> >> It does give me the numerical value of the dipole moment, but how do I generate the dipole vector in the pdb structure? >> >> Thanks >> >> Ajay > > If you add the following two lines to the script it will print out the center of mass and dipole vector: > > print “center of mass:”, com.data() > print “dipole:”, dipole.data() > > Make sure the lines are indented to the same level as the final print statement in the original script. With those values you can easily write a BILD format file that will draw an arrow from the center of mass to the (center of mass + dipole) and open that file to show the arrow. The BILD format is described here: > > http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/bild.html <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/bild.html> > > If you are doing this for many structures, it would be possible to modify the script itself to create/open the BILD file, but that would be significantly more work. But if you really need it let me know. > > —Eric > >> >> >> >> >> >> >> From: Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> >> Sent: Thursday, November 19, 2015 7:56 PM >> To: Pande, Ajay K >> Cc: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Subject: Re: [Chimera-users] calculating dipole moment of a protein in pdb >> >> Hi Ajay, >> The script referenced in this chimera-users archive message will compute it: >> >> http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-February/004780.html <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-February/004780.html> >> [Chimera-users] BCC CHARGES >> I've attached a script that if you run it (File->Open, or "open ~/ dipole.py" [if it's in your home directory]) will print the dipole moments of all open molecular ... >> Read more... <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-February/004780.html> >> >> Extracting the script from that message may be challenging, so I’m attaching it again. It’s also available from our Chimera Scripts page: >> >> http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> >> >> Like it says in the original message you have to assign partial charges before running the script (Tools->Structure Editing->AddCharge, or the “addcharge” command). >> >> —Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>

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calculating dipole moment of a protein in pdb
by Pande, Ajay K 25 Nov '15

25 Nov '15

Could you please tell me how to calculate the dipole moment of a protein in Chimera, given its pdb file? Thanks Ajay

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on ligand
by Smith Liu 25 Nov '15

25 Nov '15

Dear All, When we display a protein-ligand complex by chimera, the sidechains of residues around the ligand will be displayed. Will you please tell me by which criteria chimera select the residues arond the ligand for display? And how to change this criteria in the command input format? SMith

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feature request - add "save relative to model" as optional default?
by Oliver Clarke 25 Nov '15

25 Nov '15

Hi, Nitpick-y request for a future version but one that would make life easier... in the “Save PDB" dialog, would it be possible (when the option is present) to default (perhaps optionally) to having the “Save relative to model” box checked (and have the selected model default to the starting model)? I often save a manipulated pdb, or one that has been rigid-body fit to a density map, then open it up in coot or another program and realize that the map and model are no longer aligned because I forgot to check this box, and I can’t think of many cases when I would deliberately uncheck it. Cheers, Oliver.

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Re: [Chimera-users] scale problem
by Yaowang Li 24 Nov '15

24 Nov '15

Dear all, I faced a scale problem when I was trying to fit the density map. A density map was reconstructed from a set of projections which their magnitude are 1.055A/pixel, with a reference model that is 1.055 A/voxel and 5 A in resolution. However the pdb file cannot fit into the map because the map is too much small. So I have to change the voxel size to double and then can be fitted. Here I changed the voxel size, I think it changed the scale for the density. So i just worried about the fitting result. thanks On Sun, Nov 22, 2015 at 10:07 AM, Yaowang Li <liyaowang2911(a)gmail.com> wrote: > Dear all, > > > I faced a scale problem when I was trying to fit the density map. > > A density map was reconstructed from a set of projections which their > magnitude are 1.055A/pixel, with a reference model that is 1.055 A/voxel > and 5 A in resolution. However the pdb file cannot fit into the map > because the map is too much small. So I have to change the voxel size to > double and then can be fitted. > > Here I changed the voxel size, I think it changed the scale for the > density. So i just worried about the fitting result. > > thanks > > yaowang > > > > >

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Re: [Chimera-users] Calculation of the average isoelectric point of a proteins solvation shell
by Elaine Meng 23 Nov '15

23 Nov '15

> On Nov 21, 2015, at 11:54 AM, Csaba Nagy <csaba.nagy(a)utu.fi> wrote: > > Dear Elaine, > > thank you for your kind reply, and for the instructions regarding the surface charge of the protein. I just realized, that I phrased my question wrong, actually I wanted to calculate the average isoelectric constant of the proteins surface-amino acids in order to apply the most optimal buffer system to solubilize my protein. > Thank you again. > > Best wishes, > Csaba > Dear Csaba, Sorry, Chimera does not calculate isoelectric points or constants, it only estimates charge in aqueous solution near neutral pH. You would need to find some other program to do what you want. It is best to send Chimera questions to the chimera-users(a)cgl.ucsf.edu list, CC’d here. Apologies if you got this message more than once, I was having trouble sending the e-mail. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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How to insert a morph into a movie command file?
by Christina Bourne 23 Nov '15

23 Nov '15

Dear all, Is there a straightforward way to insert a morph within a larger movie? We are working from command scripts but see that the command "morph" is not recognized.Any help is appreciated,Christina

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Dock prep with multiple structures - endless loop?
by Oliver Clarke 20 Nov '15

20 Nov '15

Hi, Would it be possible to add a progress bar (with ETA) for Dock prep at some point? I ran it overnight to fill partial sidechains on six structures (each ~6000aas), and it still isn’t finished, but I can’t tell whether it is just taking a really long time or whether something has gone wrong. The status bar is still updating with “Matching donors”, “finding acceptors” and “building search tree” messages, but it seems to be giving these messages multiple times for each structure - is that normal? Cheers, Oliver.

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Inter-molecular H-bonds between water molecules not displayed in per-frame script
by George Green 20 Nov '15

20 Nov '15

Hi, I'm trying to get a per-frame script going which shows the inter-molecular H-bonds within a protein binding site. It is working in that all H-bonds show apart from water-water h-bonds. Is there any fix for this at all? My code is below: Water molecules are residues :159-162 I would be very grateful for any assistance. :) sg ################################################ #################### # per-frame H-bond repr bs :158 color hot pink :158 color byhet :158 # disp :60,37,85,112,109,35,158,84,60,40,38,114,69,90,58,61-68,56,21,45,52,101,15,92,40,105,116,24,42,54,40,24,10,97,120,159,160,161,162 disp :WAT # select :1-162; hbonds intramodel true intermodel true line 5 color gold ; ~select select :90 ################################################

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Calculation of the average isoelectric point of a proteins solvation shell
by Csaba Nagy 20 Nov '15

20 Nov '15

Dear Chimera Developers and -Users, I am struggling with the overexpression and purification of a cytoplasmic protein that looks to be soluble only in a very narrow pH range. I know the average isoelectric point of the whole protein, but there would be much more informative, to know what is the average isoelectric point of the proteins solvation shell, I think. Therefore I modeled the 3D structure of the protein and I tried several other visualization programs to calculate this pI value, but I was not successful. Could you tell me please, if there is any option to make this estimation in Chimera? Thank you very much in advance! Best regards, Csaba Nagy ------------------------------- Csaba I. Nagy, PhD Postdoctoral Researcher, PharmaCity, Itäinen Pitkäkatu 4 C, 6th floor, room 6049 Molecular Plant Biology University of Turku FI-20014 TURKU, Finland Phone +358 2 333 7914 Fax +358 2 333 8075 Email csaba.nagy(a)utu.fi --------------------------------

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command line issues
by liz kellogg 19 Nov '15

19 Nov '15

Hi, I've been using chimera quite happily for the past couple of years. I especially like the command line, as it makes operations much faster to complete (once you know the commands!) I've been using the command-line, in chimera, on my mac (osx yosemite version 10.10.3) for a while now, but just today my command-line would not display the text I'm entering into the command-line bar. This is odd, I've never seen this before, and I don't know what the problem is due to. I tried restarting chimera, I tried restarting my computer, and I tried re-installing chimera, but the command-line prompt is the same.. it doesn't display the text as I'm entering it.. though if I type a command, it does execute it and it shows up in the command history.. so it looks like a problem in displaying text as it's being entered. Has anyone else run into this problem? And how do you fix it? I'd be so much happier if I could see what I'm typing! thanks Liz

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Uploading to Microsoft Word
by Austin Brown 19 Nov '15

19 Nov '15

Hello, I am working on a project that involves uploading 10-15 Chimera images to a Microsoft Word document. The first time I got all of them on there, they looked great. However, upon opening my project the next morning, all the images were blank with a small red X in the corner. There was an error message that read "The image part with relationship ID rld5 was not found in the file." I am not sure what went wrong, but it's just a .png picture that I saved through Chimera. I am running on a Mac with Microsoft Word 2013. Any help is appreciated. Thanks, Austin

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Calculation of the average isoelectric point of a proteins solvation shell
by Csaba Nagy 19 Nov '15

19 Nov '15

Dear Chimera Developers, I am struggling with the overexpression and purification of a cytoplasmic protein that looks to be soluble only in a very narrow pH range. I know the average isoelectric point of the whole protein, but there would be much more informative, to know what is the average isoelectric point of the proteins solvation shell, I think. Therefore I modeled the 3D structure of the protein and I tried several other visualization programs to calculate this pI value, but I was not successful. Could you tell me please, if there is any option to make this estimation in Chimera? Thank you very much in advance! Best regards, Csaba Nagy ------------------------------- Csaba I. Nagy, PhD Postdoctoral Researcher, PharmaCity, Itäinen Pitkäkatu 4 C, 6th floor, room 6049 Molecular Plant Biology University of Turku FI-20014 TURKU, Finland Phone +358 2 333 7914 Fax +358 2 333 8075 Email csaba.nagy(a)utu.fi --------------------------------

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Re: [Chimera-users] RMSD script
by Elaine Meng 18 Nov '15

18 Nov '15

Yes, as described in more detail in the “RMSD Analysis” description you can select specific atoms (for example command “select protein & @n,ca,c,o” to select the peptide backbone atoms) and use the “Restrict map to current selection, if any” option. That option is on by default. If it was on and you didn’t select any atoms, it used all atoms. > See MD Movie manpage, especially sections “Startup and Input” and “RMSD Analysis" > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.…> More about selection: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> Best, Elaine On Nov 18, 2015, at 2:47 PM, Ruth Nelson <Ruth.Nelson.180(a)nd.edu> wrote: > Hi Elaine, thank you for your response. > > Using MD Movie worked to calculated the RMSDs, but I am unsure if the output values are full atom or for the backbone (Ca, C, N, O) only. Is there some way I can specify this? > > Thank you very much, > Ruthie > > On Wed, Nov 18, 2015 at 5:06 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Ruthie, > If all of the PDB files have exactly the same atoms with the same names, and no END lines, you could try opening all of them as one trajectory in MD Movie. That tool has an all-by-all RMSD calculation option and you can save the results to a text file. You would still have to process that file into CSV, however, as there is no CSV output option, but this would greatly decress the number of steps you have to script yourself, and it would be done outside of Chimera in whatever type of scripting you prefer. > > I.e. you would start MD Movie ( in menu under Tools… MD/Ensemble Analysis) and then choose to open the trajectory as PDB, multiple files. They have be named similarly with numbers but the numbers don’t have to be consecutive. If loading the trajectory is successful, the MD Movie playback dialog will appear, and from that dialog you could choose Analysis…RMSD Map. The RMSD can be calculated from all atoms or only specify ones that you have selected. Then there is a button to “Save RMSDs” on the resulting map window. > > See MD Movie manpage, especially sections “Startup and Input” and “RMSD Analysis" > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.…> > > 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 Nov 18, 2015, at 9:38 AM, Ruth Nelson <Ruth.Nelson.180(a)nd.edu> wrote: > > > Hello, > > > > I have a matrix of 10x10 .pdb files, and I need to calculate the RMSD from each PDB file to every other PDB file in that matrix. When I do this in the command line of Chimera, I type something like "match #0 #1" or "match #0 #2" for each of my PDB files, but I would like to automate this process so that it does not take as long. I have hundreds of files and they are all are named similarly (file_1.pdb, for example) but they are not numbered consecutively (file_1.pdb, file_17.pdb, file_43.pdb, for example). If possible, I would like the RMSD values to be output into a CSV file so that I can open it in excel. > > > > I have very little experience writing scripts and no idea where to begin to write this one, so I would greatly appreciate any help. I have been reading some of the responses given to other people regarding similar scripts, but I am having a hard time translating that to what I would like to do. > > > > Thank you very much, > > Ruthie > > > > > > > -- > Ruth Nelson, Graduate Student > Department of Chemistry and Biochemistry > University of Notre Dame > rnelson9(a)nd.edu

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RMSD script
by Ruth Nelson 18 Nov '15

18 Nov '15

Hello, I have a matrix of 10x10 .pdb files, and I need to calculate the RMSD from each PDB file to every other PDB file in that matrix. When I do this in the command line of Chimera, I type something like "match #0 #1" or "match #0 #2" for each of my PDB files, but I would like to automate this process so that it does not take as long. I have hundreds of files and they are all are named similarly (file_1.pdb, for example) but they are not numbered consecutively (file_1.pdb, file_17.pdb, file_43.pdb, for example). If possible, I would like the RMSD values to be output into a CSV file so that I can open it in excel. I have very little experience writing scripts and no idea where to begin to write this one, so I would greatly appreciate any help. I have been reading some of the responses given to other people regarding similar scripts, but I am having a hard time translating that to what I would like to do. Thank you very much, Ruthie

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Changing default framerate of Animation tool
by Eiros Zamora, Juan 17 Nov '15

17 Nov '15

Dear Chimera experts, I would like to know if there’s a way to increase the default 25 fps framerate when using the ‘Animation' tool to make movies. I tried increasing it from the ‘Movie Recorder’ menu, but it’s still producing the video at 25 fps. Also, I am not sure about what does the ‘Nth frame for discrete transitions’ property of items in the timeline mean. Should I increase this to get more FPS? I would like to do this because I am trying to do a video of an MD trajectory showing at the beginning the water box (and then hiding it), but at the moment the videos that I am getting feel very ‘clunky’ Cheers Juan

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how to prepare ligand by command line?
by Albert 17 Nov '15

17 Nov '15

Hello: I've got a ligand in 2D .sdf format without any hydrogens. I am just wondering how can we prepare this compound for docking? Is it possible to run it by command from Chimera? Thanks a lot Albert

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Problem using Chimera
by BRUXELLES Tatiana (ETU VIE) 17 Nov '15

17 Nov '15

Dear Sir, dear Madam I am a Master student at the Université de Strasbourg in France and I am currently doing an internship in a bioinformatics lab : the LBGI in Strasbourg. One of my tasks during this internship is to make Chimera read about 80 files with the extensions .scf. The problem is that software doesn't to be able to read my command file. I can't even make it read a print instruction. To execute those files I use the command : read File_name in command line on chimera. I am gonna join the files so you can see. Could you suggest a solution to my problem ? Kind regards, Bruxelles Tatiana

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helices
by A G Szabo 17 Nov '15

17 Nov '15

I sent a message yesterday regarding how I can change helices from ribbons to smooth wires. I am pleased that I can indicate that I figured it out.. Arthur G Szabo Professor Emeritus Wilfrid Laurier University

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smooth backbones
by A G Szabo 16 Nov '15

16 Nov '15

I have no problems with ribbons. However I would like to show some helices as backbones only. How can I achieve the result shown on the attachment for this helix. Don't know where to start looking. Any " Actions" only gave me this. Thank you Arthur G. Szabo Professor Emeritus Wilfrid Laurier University

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