- Chimera-dev - RBVI Mailing Lists

(no subject)
by Kristen Eisenberg 10 Sep '11

10 Sep '11

[chimera-dev] Calculating RMSD Hi, I want to calculate the RMSD between two mol2 structures in place. The two structures are different forms of the same structure. I haver modified the mol2 so that the two of them have the same serialNumber in their respective atoms. The problem is that when I use the command rmsd #model1 #model2, it return an incorrect value of the rmsd, as the value showed is too high, about 5, when it should be about 1 (the two structures are very similar). Is there any way to calculate the RMSD value in place correctly or I am doing anything wrong? Thanks for your help. Kristen Eisenberg Billige Flüge Marketing GmbH Emanuelstr. 3, 10317 Berlin Deutschland Telefon: +49 (33) 5310967 Email: utebachmeier at gmail.com Site: http://flug.airego.de - Billige Flüge vergleichen

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Using Pmw widgets
by Mateusz Dobrychłop 01 Sep '11

01 Sep '11

Dear Chimera Dev Team, I am writing a Chimera extension and I use the Pmw toolkit in my GUI. I had no problems testing it and it worked great until I decided to reinstall my OS (Windows 7). After that, I installed Chimera 1.5.3, imported my extension and didn't face any problems at first. But then, after closing the viewer and running it again, an error occured right after importing the extension's gui: Traceback (most recent call last): File "<pyshell#5>", line 1, in <module> b=Pmw.EntryField(a,labelpos="w",label_text="asd") File "C:\Program Files (x86)\Chimera 1.5\bin\lib\site-packages\Pmw\Pmw_1_3\lib\PmwEntryField.py", line 73, in __init__ sequences = root.bind_class(tag) File "C:\Program Files (x86)\Chimera 1.5\bin\lib\lib-tk\Tkinter.py", line 1012, in bind_class return self._bind(('bind', className), sequence, func, add, 0) File "C:\Program Files (x86)\Chimera 1.5\bin\lib\lib-tk\Tkinter.py", line 947, in _bind return self.tk.splitlist(self.tk.call(what)) TclError: bad window path name ".94327912.94328912" I didn't change anything since the last succesful testing of my extension - something happened after closing Chimera for the first time, and I have no idea what it is. After that, I tried reinstalling Chimera, installing older versions - it's always the same story; everything works great on the first run, but after I close the viewer for the first time, I am not ever able to use Pmw anymore. The code that causes this error is simple: a=Tkinter.Tk() b=Pmw.EntryField(a,labelpos="w",labeltext="c") I tried to type the same thing in IDLE and I got the exact same error. Thank you for any help, best, Mateusz

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Re: [chimera-dev] Chimera-dev Digest, Vol 90, Issue 1
by Jean Didier Pie Marechal 29 Aug '11

29 Aug '11

HI everyone, just a small suggestion. When opening the match ->aling tool. All the models present in the session are selected. Could we have a pushing button somewhere for select all/none action? or that mouse sliding would select or unselect series of models. Thanks a lot JD Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://asklipio.qf.uab.es ----- Missatge original ----- De: chimera-dev-request(a)cgl.ucsf.edu Data: Dimarts, Agost 16, 2011 9:00 pm Assumpte: Chimera-dev Digest, Vol 90, Issue 1 > Send Chimera-dev mailing list submissions to > chimera-dev(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev > or, via email, send a message with subject or body 'help' to > chimera-dev-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-dev-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-dev digest..." > > > Today's Topics: > > 1. Residue.uniprotIndex (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Tue, 16 Aug 2011 11:42:15 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: [chimera-dev] Residue.uniprotIndex > To: UCSF Chimera Mailing List <chimera-users(a)cgl.ucsf.edu>, > chimera-dev BB <chimera-dev(a)cgl.ucsf.edu> > Message-ID: <1235B56D-4D54-4ED8-9F5A-BD981304D475(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii" > > I thought some of the script writers out there might want to know > that > in the latest daily builds residues have a "uniprotIndex" attribute > > which gives the position of the residues relative to their UniProt > sequence, if the correspondence can be determined. To determine > the > correspondence the structure must have valid PDB HEADER and SEQRES > records, and the PDB web site must be reachable (to use their > UniProt > mapping service). > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > >

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Residue.uniprotIndex
by Eric Pettersen 16 Aug '11

16 Aug '11

I thought some of the script writers out there might want to know that in the latest daily builds residues have a "uniprotIndex" attribute which gives the position of the residues relative to their UniProt sequence, if the correspondence can be determined. To determine the correspondence the structure must have valid PDB HEADER and SEQRES records, and the PDB web site must be reachable (to use their UniProt mapping service). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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numpy library compiled to run with other libraries inside Chimera
by Terry Lang 15 Jul '11

15 Jul '11

Hey Guys! I use Chimera as a back end library for a bunch of my code. I occasionally run into a function that an external library, scipy for example, has already implemented. I have found the chimera flag that allows me to import python libraries for use. However, because numpy is already distributed with Chimera, importing libraries that depend on numpy is almost _impossible_. We run into a variety of version and compiler issues that are very difficult to work around. Would it be possible to get more transparent documentation on how the numpy library is compiled and when it will be upgraded in a particular release? (NOTE: We actually have this problem right now, so even an email with a description of the current nightly build set up would be SUPER helpful!). Thanks in advance, Terry -- Paula Therese Lang Postdoctoral Scholar Alber Lab UC Berkeley/QB3

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RMSD map, urgent help please
by Jean Didier Pie Marechal 22 Jun '11

22 Jun '11

Hi guys, Sorry to ask you that but I urgently need to recover the matrix from an RMSD map obtained from a MD movie. Basically, that would be the same as the graphic of the map but in a file with the numbers. I only have 40 structures but doint it by hands is just painful. Could you please tell me how to catch the rmsd map, I guess we can do it from the script section of the MD movie, but can't figure it out. Sorry to bother you, Best JD Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://asklipio.qf.uab.es ----- Missatge original ----- De: chimera-dev-request(a)cgl.ucsf.edu Data: Divendres, Juny 10, 2011 9:00 pm Assumpte: Chimera-dev Digest, Vol 88, Issue 2 > Send Chimera-dev mailing list submissions to > chimera-dev(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev > or, via email, send a message with subject or body 'help' to > chimera-dev-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-dev-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-dev digest..." > > > Today's Topics: > > 1. Re: Protofibril model (Elaine Meng) > 2. Re: Protofibril model (lihong huang) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Thu, 9 Jun 2011 13:30:22 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [chimera-dev] Protofibril model > To: "Russell M. Taylor II" <taylorr(a)cs.unc.edu> > Cc: chimera-dev(a)cgl.ucsf.edu, UCSF Chimera Mailing List > <chimera-users(a)cgl.ucsf.edu>, "Susan T. Lord Ph.D." > <susan(a)sucofa.com>, lihong huang <lihonghuang1980(a)gmail.com> > Message-ID: <865D94CF-7BB4-4C33-952D-5B6178EAFB1A(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=us-ascii > > Dear Lihong and others, > The Multiscale Models tool in Chimera is meant for this purpose --- > it shows low-resolution surfaces, which are often preferred for > large complexes. > > In Chimera I tried opening 1ei3, then started Multiscale Models (in > menu under Tools... Higher-Order Structure), then clicked the "Make > models" button at the bottom of the multiscale dialog. This shows > the structure with low-resolution surfaces and automatically uses > different colors for the different chains. You can adjust the > colors, surface resolution, etc. in the dialog. Click the dialog's > Help button to see its manual page. There is also a copy here: > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemu…> > > I also tried it with 1m1j, which also worked fine on my computer. > > 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 Jun 9, 2011, at 12:13 PM, Russell M. Taylor II wrote: > > > Dear Lihong, > > I am glad to hear that Chimera let you start down this path. > > I'm CCing the Chimera developer mailing list in case they > know of a better solution. > > You can also join the chimera users list at > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users/index.html > and then post a query there. > > > > The following is a somewhat convoluted path to get where you want > to go. Hopefully someone on one of the above mailing lists will > know a better one. If you need to go down this path, we should > probably set a time for us to sit down together and go through this. > > > > Download MGLTools from > http://mgltools.scripps.edu/downloads. I ran the Windows installer. > > This launched the Python Molecule Viewer. > > Select Compute/Coarse Molecular Surface. Kept the default > parameters. This produced a surface that was near the outside of > the molecule. > > Clicked to turn off the red dot under the CPK label so > that we only see the surface. > > Selected File/Save/VRML 2.0 (.wrl) file. Also saved STL > file.> > > I was able to load the resulting .wrl file back into > Chimera. This should provide you with a simplified model. You > should be able to adjust the parameters for the coarse saving to > get different model quality. > > > > I attach the resulting coarse model (inside a Zip file) to > this email. > > Russ > > > > [Things below I tried that didn't work] > > > > (Fine surface) > > Select File/Read Molecule. Opened 1EI3.pdb (when I used > 1M1J.pdb, it crashed trying to make the surface). > > Compute/Molecular Surface/Compute Molecular Surface. Used > the default parameters (other parameters caused it to crash). This > produced a fine molecular surface. This could be used directly or > simplified.> > > VMD uses a program called MSMS, but can't run it. When I go to > the MSMS home page, it eventually redirects me to MGLTools from > Scripps.> > > NOPE: > > > > You can load the PDB file into the VMD program (File/New, > select the file name and click Load on the Molecule File Browser). > Then select Graphics/Representations from the VMD Main menu. Then > pull down Drawing Method and select Surf. Turn off the "Apply > Changes Automatically" control and then set the Probe Radius to 4.0 > and click Apply. > > To turn off the little axes display, select Display/Axes/Off > > To save the resulting geometry, select File/Render from > the main menu. Pull down "Render using" and select Wavefront. > Change the .obj file name to one that is useful to you (I named id > protofibril.obj). Click the "Start Rendering" button. > > > > Open Blender (available from blender.org) Press delete > to get rid of the cube that is created by default. > > Select File/Import/Wavefront to load the model. Pick the > file name and then click "Import a Wavefront OBJ" > > > > At 10:18 AM 6/7/2011, lihong huang wrote: > >> Dear Dr. Taylor, > >> > >> I am postdoc working in Dr. Susan Lord's lab. According to your > suggestion, we set up the protofibril model using UCSF Chimera > program which is very nice. Now we want to move on to make small > fiber model, however, the program run very slowly when we add more > fibrinogen molecules. We are thinking if we could make the > fibrinogen molecule lose more details, maybe the program could run > easily. Do you know which program could do this? We just want to > show the basic shape of fibrinogen, no needs to show very detailed > part, such as alpha, beta and gamma chains. Thanks a lot for your > help.>> > >> Lihong Huang, > >> Postdco > >> Pathology and lab medicine > > > > --- > > Russell M. Taylor II, Ph.D. > taylorr(a)cs.unc.edu> CB #3175, Sitterson Hall > www.cs.unc.edu/~taylorr> University of North Carolina, > Voice: (919) 962-1701 > > Chapel Hill, NC 27599-3175 FAX: (919) > 962-1799 > <protofibril.zip>_______________________________________________> > Chimera-dev mailing list > > Chimera-dev(a)cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev > > > > > ------------------------------ > > Message: 2 > Date: Fri, 10 Jun 2011 09:32:02 -0400 > From: lihong huang <lihonghuang1980(a)gmail.com> > Subject: Re: [chimera-dev] Protofibril model > To: "Russell M. Taylor II" <taylorr(a)cs.unc.edu> > Cc: meng(a)cgl.ucsf.edu, chimera-dev(a)cgl.ucsf.edu, susan(a)sucofa.com > Message-ID: <BANLkTinJsiLgAiE9ghyTyP-0TUZT_YP_Nw(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Russ, Elaine and Tom, > > Thank you very much for your help. We will try what you suggested > and let > you know how it works. > > Best, > Lihong > > On Thu, Jun 9, 2011 at 3:13 PM, Russell M. Taylor II > <taylorr(a)cs.unc.edu>wrote: > > Dear Lihong, > > I am glad to hear that Chimera let you start down this path. > > I'm CCing the Chimera developer mailing list in case they > know of a > > better solution. > > You can also join the chimera users list at > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera- > users/index.html and > > then post a query there. > > > > The following is a somewhat convoluted path to get where you want > to go. > > Hopefully someone on one of the above mailing lists will know a > better one. > > If you need to go down this path, we should probably set a time > for us to > > sit down together and go through this. > > > > Download MGLTools from > http://mgltools.scripps.edu/downloads. I > > ran the Windows installer. > > This launched the Python Molecule Viewer. > > Select Compute/Coarse Molecular Surface. Kept the default > > parameters. This produced a surface that was near the outside of > the> molecule. > > Clicked to turn off the red dot under the CPK label so > that we only > > see the surface. > > Selected File/Save/VRML 2.0 (.wrl) file. Also saved STL > file.> > > I was able to load the resulting .wrl file back into > Chimera. This > > should provide you with a simplified model. You should be able > to adjust > > the parameters for the coarse saving to get different model quality. > > > > I attach the resulting coarse model (inside a Zip file) to > this> email. > > Russ > > > > [Things below I tried that didn't work] > > > > (Fine surface) > > Select File/Read Molecule. Opened 1EI3.pdb (when I used > 1M1J.pdb,> it crashed trying to make the surface). > > Compute/Molecular Surface/Compute Molecular Surface. Used > the> default parameters (other parameters caused it to crash). > This produced a > > fine molecular surface. This could be used directly or simplified. > > > > VMD uses a program called MSMS, but can't run it. When I go to > the MSMS > > home page, it eventually redirects me to MGLTools from Scripps. > > > > NOPE: > > > > You can load the PDB file into the VMD program (File/New, > select the > > file name and click Load on the Molecule File Browser). Then select > > Graphics/Representations from the VMD Main menu. Then pull down > Drawing> Method and select Surf. Turn off the "Apply Changes > Automatically" control > > and then set the Probe Radius to 4.0 and click Apply. > > To turn off the little axes display, select Display/Axes/Off > > To save the resulting geometry, select File/Render from > the main > > menu. Pull down "Render using" and select Wavefront. Change the > .obj file > > name to one that is useful to you (I named id protofibril.obj). > Click the > > "Start Rendering" button. > > > > Open Blender (available from blender.org) Press delete > to get rid > > of the cube that is created by default. > > Select File/Import/Wavefront to load the model. Pick the > file name > > and then click "Import a Wavefront OBJ" > > > > > > At 10:18 AM 6/7/2011, lihong huang wrote: > > > >> Dear Dr. Taylor, > >> > >> I am postdoc working in Dr. Susan Lord's lab. According to your > >> suggestion, we set up the protofibril model using UCSF Chimera > program which > >> is very nice. Now we want to move on to make small fiber model, > however, the > >> program run very slowly when we add more fibrinogen molecules. > We are > >> thinking if we could make the fibrinogen molecule lose more > details, maybe > >> the program could run easily. Do you know which program could do > this? We > >> just want to show the basic shape of fibrinogen, no needs to > show very > >> detailed part, such as alpha, beta and gamma chains. Thanks a > lot for your > >> help. > >> > >> Lihong Huang, > >> Postdco > >> Pathology and lab medicine > >> > > > > --- > > Russell M. Taylor II, Ph.D. > taylorr(a)cs.unc.edu> CB #3175, Sitterson Hall > www.cs.unc.edu/~taylorr<http://www.cs.unc.edu/%7Etaylorr>> > University of North Carolina, Voice: (919) 962- > 1701> Chapel Hill, NC 27599-3175 FAX: > (919) 962-1799 >

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Re: [chimera-dev] Protofibril model
by Russell M. Taylor II 10 Jun '11

10 Jun '11

Dear Lihong, I am glad to hear that Chimera let you start down this path. I'm CCing the Chimera developer mailing list in case they know of a better solution. You can also join the chimera users list at http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users/index.html and then post a query there. The following is a somewhat convoluted path to get where you want to go. Hopefully someone on one of the above mailing lists will know a better one. If you need to go down this path, we should probably set a time for us to sit down together and go through this. Download MGLTools from http://mgltools.scripps.edu/downloads. I ran the Windows installer. This launched the Python Molecule Viewer. Select Compute/Coarse Molecular Surface. Kept the default parameters. This produced a surface that was near the outside of the molecule. Clicked to turn off the red dot under the CPK label so that we only see the surface. Selected File/Save/VRML 2.0 (.wrl) file. Also saved STL file. I was able to load the resulting .wrl file back into Chimera. This should provide you with a simplified model. You should be able to adjust the parameters for the coarse saving to get different model quality. I attach the resulting coarse model (inside a Zip file) to this email. Russ [Things below I tried that didn't work] (Fine surface) Select File/Read Molecule. Opened 1EI3.pdb (when I used 1M1J.pdb, it crashed trying to make the surface). Compute/Molecular Surface/Compute Molecular Surface. Used the default parameters (other parameters caused it to crash). This produced a fine molecular surface. This could be used directly or simplified. VMD uses a program called MSMS, but can't run it. When I go to the MSMS home page, it eventually redirects me to MGLTools from Scripps. NOPE: You can load the PDB file into the VMD program (File/New, select the file name and click Load on the Molecule File Browser). Then select Graphics/Representations from the VMD Main menu. Then pull down Drawing Method and select Surf. Turn off the "Apply Changes Automatically" control and then set the Probe Radius to 4.0 and click Apply. To turn off the little axes display, select Display/Axes/Off To save the resulting geometry, select File/Render from the main menu. Pull down "Render using" and select Wavefront. Change the .obj file name to one that is useful to you (I named id protofibril.obj). Click the "Start Rendering" button. Open Blender (available from blender.org) Press delete to get rid of the cube that is created by default. Select File/Import/Wavefront to load the model. Pick the file name and then click "Import a Wavefront OBJ" At 10:18 AM 6/7/2011, lihong huang wrote: >Dear Dr. Taylor, > >I am postdoc working in Dr. Susan Lord's lab. According to your >suggestion, we set up the protofibril model using UCSF Chimera >program which is very nice. Now we want to move on to make small >fiber model, however, the program run very slowly when we add more >fibrinogen molecules. We are thinking if we could make the >fibrinogen molecule lose more details, maybe the program could run >easily. Do you know which program could do this? We just want to >show the basic shape of fibrinogen, no needs to show very detailed >part, such as alpha, beta and gamma chains. Thanks a lot for your help. > >Lihong Huang, >Postdco >Pathology and lab medicine --- Russell M. Taylor II, Ph.D. taylorr(a)cs.unc.edu CB #3175, Sitterson Hall www.cs.unc.edu/~taylorr University of North Carolina, Voice: (919) 962-1701 Chapel Hill, NC 27599-3175 FAX: (919) 962-1799

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Biopython paths
by Mateusz Dobrychłop 19 May '11

19 May '11

Hi, I've got another problem, that also revolves around "paths". In my extension I use BioPython libraries. Unfortunately, in every file I have to determine the path to my Python installation (sys.path.append("C:\Python27\Lib\site-packages"), because otherwise, Chimera isn't able to import Biopython. Is there any way to fix that? Mateusz

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Extensions - problem with paths
by Mateusz Dobrychłop 10 May '11

10 May '11

Hello, I'm trying to write my own Chimera extension. First of all, I'd like to thank you for providing so much useful information and so many examples on your site, it's extremely helpful. But there's one problem that might be a serious issue once I try to share this extension with other people. I don't know why, every time I need the extension to write a file, I have to determine an exact path to the localisation where I want the file to be placed. Otherwise it always creates the file on the desktop (I use Windows 7). Is there any way to make Chimera create new files in the extension's directory without giving it an accurate path? Thank you in advance for your help, Mateusz

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Monitor lines
by moneal＠notes.cc.sunysb.edu 19 Apr '11

19 Apr '11

Hello, We just purchased a Zcorp 650, http://www.zcorp.com/en/Products/3D-Printers/ZPrinter-650/spage.aspx and would like to begin building models of proteins. As you probably know, when you print a physical model of a protein @ 100,000x scale on one of these printers, it is very fragile. To help support the model, one must place "Struts" in key locations. We currently use Jmol because it has a strut algorithm built into the software. The algorithm is open source, written originally by George Phillips and adapted by Bob Hanson (see email below). But Stony Brook faculty are begging us to train our students on Chimera and not JMol because (not surprisingly) most faculty at SBU use Chimera and not JMol. My question: would you be willing to incorporate this algorithm into Chimera (or does it already exist)? This would allow Chimera to output pdb files that are ready for rapid prototyping, a blossoming field: http://www.economist.com/node/18114327?story_id=18114327&CFID=162504503&CFT… I look forward to your response, Marvin Marvin H. O'Neal III, Ph.D. Undergraduate Biology 108 CMM/BLL Stony Brook University Stony Brook, NY 11794-5110 Phone: (631) 632-1326 Fax: (631) 632-1680 Sure, why not! It's not my algorithm, though. See http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/modelse… 125 // 126 // Struts calculation (for rapid prototyping) 127 // 128 /////////////////////////////////////////////////////////// 129 /** 130 * 131 * Algorithm of George Phillips phillips(a)biochem.wisc.edu 132 * 133 * originally a contribution to pyMol as struts.py; 134 * adapted here by Bob Hanson for Jmol 1/2010 135 * 136 * Return a vector of support posts for rapid prototyping models 137 * along the lines of George Phillips for Pymol except on actual molecular 138 * segments (biopolymers), not PDB chains (which may or may not be 139 * continuous). Bob On Thu, Apr 14, 2011 at 9:57 AM, <moneal(a)notes.cc.sunysb.edu> wrote: Bob, I teach introductory biology labs at Stony Brook and use physical models to introduce students to research. I have used Ras-Mol but recently switched to Chimera. I would like to share your strut algorithm with the Chimera group in hopes that they will incorporate it into the software. Would you be willing to work with me on this? Marvin Marvin H. O'Neal III, Ph.D. Undergraduate Biology G-05 CMM/BLL Stony Brook University Stony Brook, NY 11794-5110 Phone: (631) 632-1326 Fax: (631) 632-1680 -----Forwarded by Marvin O'Neal/CAS on 04/14/2011 10:45AM ----- To: "moneal(a)notes.cc.sunysb.edu" <moneal(a)notes.cc.sunysb.edu> From: "Franzen, Margaret" <franzen(a)msoe.edu> Date: 04/13/2011 01:56PM Subject: RE: strut algorithm (See attached file: Bob Hansen.vcf) Hi, Marvin! Your earlier question now makes sense! Bob Hansen is the Jmol guru who teaches Chemistry at St. Olaf – and breathes life into all things Jmol. His contact is below: Margaret From: moneal(a)notes.cc.sunysb.edu [mailto:moneal@notes.cc.sunysb.edu] Sent: Wednesday, April 13, 2011 12:51 PM To: Franzen, Margaret Subject: RE: strut algorithm Hey Margaret, My question about the Strut command in Jmol was specific to the math of the algorithm. I was looking for the equation that runs in the background when a student types this command. I couldn't find it in the documentation guide. Do you have Bob's email? There seem to be several Bob Hanson's on the internet. Marvin Marvin H. O'Neal III, Ph.D. Undergraduate Biology G-05 CMM/BLL Stony Brook University Stony Brook, NY 11794-5110 Phone: (631) 632-1326 Fax: (631) 632-1680

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