- Chimera-users - RBVI Mailing Lists

16,000 molecules slow
by Thomas Goddard 13 Sep '06

13 Sep '06

Email exchange with Brittany Morgan about slow ball and stick display when displaying 16000 molecules. ---- From: "Brittany Morgan" <brmorgan(a)clarku.edu> To: "'Thomas Goddard'" <goddard(a)cgl.ucsf.edu> Subject: RE: [Chimera-users] Memory allocation Date: Tue, 12 Sep 2006 20:52:39 -0400 I am working with molecules, and it has problems redrawing them in ball-and-stick representation, although I expect that at larger system sizes other functions will start slowing down as well. If I look at the memory usage while it is redrawing them, Chimera seems to be using only about 1/4 of the available memory, but creating a paging file nonetheless. It will work, it just takes about 15 minutes to redraw about 64,000 atoms, and I need to go to system sizes much larger. If I need more memory, that is possible, I just wasn't sure if that was the issue because it didn't appear that Chimera was using all of the available memory. I am using Chimera in a non-standard way (I'm not displaying proteins, but rather many small (unrealistic) molecule-type objects). Thank you for your help! Brittany ----- From: Thomas Goddard [mailto:goddard@cgl.ucsf.edu] Sent: Tuesday, September 12, 2006 9:22 PM To: brmorgan(a)clarku.edu Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Memory allocation Hi Brittany, Thanks for the detailed information. I do not think memory is the problem. Display of 58,000 atoms (pdb 1uf2) in ball and stick took 10 seconds on my 4 year old laptop. That is the time to make the intial drawing. Then it update at about 2 frames per second when rotating the model on this rather old machine. Your problem is likely caused by one of two issues. First, if your "molecule-type objects" contain many (tens or hundreds) small rings within a residue then Chimera will bog down trying to compute the chemical atom types (aromaticity...). This is a problem we have recently analyzed when using Chimera with molecules that do not have reasonable chemical structure. We plan on fixing this problem by being able to tag molecules in Chimera as "non-chemical". But we do not have a version of Chimera available with that feature yet. So currently the only solution is to modify your non-molecule model using multiple residues to avoid having many rings in a single residue. The ring computation is not done in wire display style but is invoked when switching to ball and stick style because atom radii are needed and are based on the chemical types. The second possible problem is that you are not using hardware accelerated 3D graphics. On Linux systems you usually need to install a graphics driver to get hardware acceleration. Windows and Mac systems usually already have the appropriate driver. Rendering computations can be 100 times slower if it is done in software instead of by the graphics chip. Ball and stick display style is much more time consuming to render than wire frame. If you are able to rotate the 64,000 atom ball and stick model after it is first displayed (15 minutes) and it updates reasonably fast (> 1 frame per second) then you have hardware acceleration and this is not the problem. Tom ----- From: "Brittany Morgan" <brmorgan(a)clarku.edu> To: "'Thomas Goddard'" <goddard(a)cgl.ucsf.edu> Subject: RE: [Chimera-users] Memory allocation Date: Tue, 12 Sep 2006 21:34:09 -0400 Hi Tom, I can rotate it after it is first displayed with no difficulty, so I would think that the problem is likely the first. My toy model molecules consist of 4 "atoms" in a linear configuration, so these are very small molecules, and I wouldn't have any rings within a residue, if I understand this correctly. However, would the fact that I have so many molecules be an issue (if I have 64,000 atoms, I have 16,000 molecules)? I can tell you more explicitly what I am attempting to display (and how) if that would be of use. Since I guessed, more or less, on how to output the data to get it to display what I want, it is likely that I am doing this in a less than optimal way. Brittany -------- Date: Tue, 12 Sep 2006 18:51:58 -0700 (PDT) From: Thomas Goddard <goddard(a)cgl.ucsf.edu> To: brmorgan(a)clarku.edu Hi Brittany, Ok it's not rings. Very likely something is slow when dealing with your large number of molecules. The typical Chimera use involves only a handful of molecules, twenty or thirty is considered alot, and 16,000 may be a record! Another Chimera developer Eric Pettersen will know more about efficiency with large numbers of molecules. (I work primarily on volume data.) So I've sent this email to him and he may have advice. If it is possible I think you would be better off making your 4 atom chains be a single residue with all chains in a single molecule. Chimera is likely to handle that much better. An immediate problem is that if you are using the PDB file format its residue number field is only 4 digits (max 9999 residues). It is awkward but you could use multiple PDB chain identifiers (single letter a-z, A-Z, 0-9) to handle up to ~600,000 chains. Another approach is to put all the chains in a single residue. But a residue with 64,000 atoms may also cause poor Chimera performance. I'll also warn you that Chimera is not at good as other molecular graphics programs (PyMol, and VMD) at handling systems larger than 100,000 atoms. Chimera uses much more memory (about 3 Kbytes per atom). PyMol and VMD I am told are 5-10 times more memory efficient on a per-atom basis. Chimera may be better for doing custom types of analysis though. Tom Is it OK if I forward your last email to the chimera-users mailing list? That may help others with similar problems. ----- From: "Brittany Morgan" <brmorgan(a)clarku.edu> To: "'Thomas Goddard'" <goddard(a)cgl.ucsf.edu> Subject: RE: [Chimera-users] Memory allocation Date: Wed, 13 Sep 2006 13:57:36 -0400 Hi Tom, Feel free to forward anything that you think would be of use to others. Unfortunately, 16,000 is only a moderately large system for me. I'm looking to be able to get up to around 112,500 atoms and a little under 30,000 molecules. I only need the visualization aspects of Chimera, all analysis I do on my own. Do you think PyMol would be able to handle something like that? I can try making them all a single molecule, but I also suspect that having a chain with 112,500 atoms would cause problems. Thanks again, Brittany ---- Date: Wed, 13 Sep 2006 11:07:59 -0700 (PDT) From: Thomas Goddard <goddard(a)cgl.ucsf.edu> To: brmorgan(a)clarku.edu Hi Brittany, There are two difficulties you are likely to run into: PDB file format limits on number of atoms (100,000) and number of residues (10,000), and poor software performance for such large systems. If you are primarily concerned with visualization rather than analysis than PyMOL I believe will give better performance. But you may have a hard time with the file format issues. I think you will get better support solving the file format problems with Chimera since we have 5 developers while PyMOL has just one. Having 100,000 atoms in a single PDB chain is not a problem. I believe also that Chimera can handle a modification of PDB file format where the atom number starts in column 6 instead of column 7 allowing up to 1,000,000 atoms. Eric would know. Tom ---- From: Eric Pettersen <pett(a)cgl.ucsf.edu> To: brmorgan(a)clarku.edu Date: Wed, 13 Sep 2006 12:26:30 -0700 Hi Brittany, I confess I find your problem somewhat mysterious. I wrote a Chimera Python script (attached) that can either generate a single molecule with 16000 4-atom residues or 16000 4-atom molecules (depending on whether the 'singleMol' variable is True or False). While Chimera is better with the single-molecule system (on my mac, taking about 5 seconds each to run the script and to change to ball- and-stick), it isn't that much worse using the 16000-molecule system (about 20 seconds each -- not nearly 15 minutes!). It also took about twice as much memory (~1GB vs ~480 MB; this was using the 1.2255 snapshot). You can try it out yourself by using File..Open to open the script and changing the "singleMol = False" line in the script beforehand to choose modes. You should check that Chimera is using your graphics card rather than software rendering. One way to do that is to use Help->Report A Bug.. and click the Next button in the resulting dialog. The ensuing panel will have a "Bug Description" field that reports your OpenGL vendor and renderer. What does it say? If it says something involving "Mesa" then you are using software rendering and should try to update the driver for you card by visiting your card manufacturer's web site. You can click "Cancel" in the bug dialog to dismiss it. As Tom mentioned, we allow a modified PDB format where the sixth column of an ATOM record can be a digit, effectively allowing 1 million atoms. There are several gotchas in your situation. Whereas most such large systems are composed of standard residues with known connectivity, you may well need to specify your connectivity -- and CONECT records are strictly limited to 5-digit atom serial numbers. If your molecules do have typical bonding distances, you can let Chimera figure out the connectivity, but you would need to put each molecule in its own residue to prevent the N-squared intra-residue connectivity search from getting out of hand (so you would likely need to use chain IDs once you're past 9999 residues), and you would need to insert TER cards between residues to prevent the implied connectivity between residues (may not actually be necessary in the 1.2255 snapshot). --Eric File manyMols.py follows import chimera singleMol = False if singleMol: m = chimera.Molecule() m.name = "test" mols = [m] for ri in range(16000): r = m.newResidue("UNK", " ", ri+1, " ") prev = None for ai in range(4): a = m.newAtom("C%d" % (ai+1), chimera.Element("C")) r.addAtom(a) if prev: m.newBond(a, prev) crd = chimera.Coord(ri, ai, 0.0) a.setCoord(crd) prev = a else: mols = [] for mi in range(16000): m = chimera.Molecule() m.name = "test%d" % mi mols.append(m) r = m.newResidue("UNK", " ", 1, " ") prev = None for ai in range(4): a = m.newAtom("C%d" % (ai+1), chimera.Element("C")) r.addAtom(a) if prev: m.newBond(a, prev) crd = chimera.Coord(mi, ai, 0.0) a.setCoord(crd) prev = a chimera.openModels.add(mols)

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Memory allocation
by brmorgan＠clarku.edu 13 Sep '06

13 Sep '06

Does Chimera have a fixed amount of memory allocated to it, and if so, is it possible to increase this amount? I am working with very large system sizes and am trying to reduce the amount of time it takes to perform certain operations.

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Re: [Chimera-users] Memory allocation
by Thomas Goddard 12 Sep '06

12 Sep '06

Hi Brittany, Thanks for the detailed information. I do not think memory is the problem. Display of 58,000 atoms (pdb 1uf2) in ball and stick took 10 seconds on my 4 year old laptop. That is the time to make the intial drawing. Then it update at about 2 frames per second when rotating the model on this rather old machine. Your problem is likely caused by one of two issues. First, if your "molecule-type objects" contain many (tens or hundreds) small rings within a residue then Chimera will bog down trying to compute the chemical atom types (aromaticity...). This is a problem we have recently analyzed when using Chimera with molecules that do not have reasonable chemical structure. We plan on fixing this problem by being able to tag molecules in Chimera as "non-chemical". But we do not have a version of Chimera available with that feature yet. So currently the only solution is to modify your non-molecule model using multiple residues to avoid having many rings in a single residue. The ring computation is not done in wire display style but is invoked when switching to ball and stick style because atom radii are needed and are based on the chemical types. The second possible problem is that you are not using hardware accelerated 3D graphics. On Linux systems you usually need to install a graphics driver to get hardware acceleration. Windows and Mac systems usually already have the appropriate driver. Rendering computations can be 100 times slower if it is done in software instead of by the graphics chip. Ball and stick display style is much more time consuming to render than wire frame. If you are able to rotate the 64,000 atom ball and stick model after it is first displayed (15 minutes) and it updates reasonably fast (> 1 frame per second) then you have hardware acceleration and this is not the problem. Tom > From: "Brittany Morgan" <brmorgan(a)clarku.edu> > To: "'Thomas Goddard'" <goddard(a)cgl.ucsf.edu> > Subject: RE: [Chimera-users] Memory allocation > Date: Tue, 12 Sep 2006 20:52:39 -0400 > > I am working with molecules, and it has problems redrawing them in > ball-and-stick representation, although I expect that at larger system sizes > other functions will start slowing down as well. If I look at the memory > usage while it is redrawing them, Chimera seems to be using only about 1/4 > of the available memory, but creating a paging file nonetheless. It will > work, it just takes about 15 minutes to redraw about 64,000 atoms, and I > need to go to system sizes much larger. If I need more memory, that is > possible, I just wasn't sure if that was the issue because it didn't appear > that Chimera was using all of the available memory. I am using Chimera in a > non-standard way (I'm not displaying proteins, but rather many small > (unrealistic) molecule-type objects). > > Thank you for your help! > Brittany

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Re: [Chimera-users] Can I use "Chimera" to measure length of a VRML file?
by Thomas Goddard 12 Sep '06

12 Sep '06

Hi Masako, Chimera does not read IMOD files but perhaps I can add a file reader for you. Have you already defined a path in IMOD along the structure you want to measure? Or have you just segmented out the structures. If you have segmentations but no explicitly defined 1 dimensional path then it is not clear how to define the length. Is the IMOD format you are using the following? http://bio3d.colorado.edu/imod/doc/binspec.html Could you send me an example file? Tom > Date: Mon, 11 Sep 2006 17:41:20 -0700 > From: Masako Terada <mterada(a)ncmir.ucsd.edu> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Can I use "Chimera" to measure length of a VRML > file? > > Hi. Thank you for your e-mail. I have tried using volume path tracer > as you instructed. Even though it looks very promising, it is > time-consuming since we have 90 different objects to measure. So I > would like to try your another suggestion, importing trace file into > Chimera and measure lengths. Are you familiar with IMOD segmentation > file format? I tried to import this IMOD file into Chimera, but > unsuccessful, so I am guessing that I have to convert it to something > else... Any more suggestion? > > Masako >

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Can I use "Chimera" to measure length of a VRML file?
by Masako Terada 11 Sep '06

11 Sep '06

Hi. I have a VRML file, which was created with different softwares. Is there anyway I can use Chimera to measure length of this tube-like structure? Thanks, in advance! ---------------------------------------------------- Masako Terada National Center for Microscopy and Imaging Research Center for Research in Biological Systems University of California, San Diego (858)534-7968 mterada(a)ncmir.ucsd.edu ----------------------------------------------------

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display multiple bonds
by Dave Roe 05 Sep '06

05 Sep '06

Is there a way to display multiple bonds so bond types (single, double, triple) can be distinguished? -- Dave Roe roex0050(a)umn.edu

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color a residue
by Xuehong Liu 05 Sep '06

05 Sep '06

Hi, I chose the target as "selected residues", then selected the residue I want to put certain color on, but only a bond color was changed when I did that. However, if I did not select a residue, then the color option will change the color for the whole helix selected. thank Xuehong Xuehong Liu, Ph.D Research Assistant Professor Department of Physiology/Pharmacology Oregon Health & Science University 3181 SW Sam Jackson Park Rd. L334 Portland, OR 97239 phone: (503) 494-3230 fax: (503) 494-4352

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PDB Coordinates
by Albion Baucom 01 Sep '06

01 Sep '06

I have docked several models into density manually using Chimera. I saved the session, reopened it, and when I write out the docked PDB files, and read them back in, they are not oriented the same way as the model I wrote them from. Is there something I have to do to "fix" their new orientation so when they are written out they retain this orientation? I am using beta version 1 build 2199 01/24/2006 on a linux platform. Thanks Albion

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how to save a copy of the reply log via command line
by Cathy Lawson 01 Sep '06

01 Sep '06

Hi, I'd like to issue a command-line command within a python script read into chimera to save a copy of the reply log. I tried googling the chimera site but didn't find the answer--what would be the command to do this? thanks, Cathy

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question about annealing residues in pdb file
by Shah, Sanket S 31 Aug '06

31 Aug '06

Hello, I have been using chimera extensively for pdb rendering and manipulation. I needed some information that i couldn't find in the archives. I am aware that chimera displays the pdb file according to the co-ordinates mentioned in the pdb file. However in my situation I have changed co-ordinates of some of the secondary structure elements like helices to do a better fit. and I have saved the new coordinates in the same pdb file. So now when i render this pdb file it shows me the structure with the modified orientation, however chimera displays a continuous model. In the sense, the breaks that I had introduced by changing the angles of some of the helices and thus making the linkage discontinuous are somehow annealed by chimera. So my question is what sort of algorithm chimera employs to seal breaks in the pdb structure. The same pdb strucutre when viewed in swiss model deepview software contains gaps/breaks at the junctions where the coordinates of the helices have been modified from the original ones. however no such breaks are seen when displayed through chimera. First I thought chimera does energy minimization to find out the best way to arrange the loops between the helices so as to create the best continuous structure. However it seems that chimera doesn't do energy minimization, yet it's able to display a complete structure. Could you please inform me about how this is accomplished. Thanks Sanket

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change chain id
by Yunierkis Perez Castillo 28 Aug '06

28 Aug '06

Hi all, I need to change the chain ID for a protein, that is, change the chain A to chain B. Can I do that with chimera? Thanks in advance Yunierkis

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addH/removeH for charged a.a.
by Dave Roe 26 Aug '06

26 Aug '06

Is there functionality that will - add a hydrogen (if needed) to all Lysines and Arginines to give the protonated form - remove a hydrogen (if needed) from Aspartic and Glutamic acids to give the deprotonated form? -- Dave Roe roex0050(a)umn.edu

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Volume color zones
by hsosa＠aecom.yu.edu 21 Aug '06

21 Aug '06

Is is possible to use different colors for different Volume zones ?. I have a volume (MRC format) and have defined two marker sets using the Volume-Path-Tracer. Then I select one of the path and colored the surface volume around using the Volume Color Zone utility. This work fine but then if I selected the other markers and do the same the volume close to the new markers get colored but anything else get uncolored, including the areas previously colored. Am I doing something wrong ?. Can I color several Volume zones independently ? Thanks Hernando --

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RealD (Stereographics) E2SGI emitter on Quadro 3450?
by Sabuj Pattanayek 18 Aug '06

18 Aug '06

Hi all, Anyone know if it's possible to use a RealD (Stereographics) E2SGI emitter on Quadro hardware? Thanks, Sabuj Pattanayek

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addH utility and PDB files
by Nihshanka Debroy 15 Aug '06

15 Aug '06

Hi, I have a couple of questions about the addH utility built into Chimera, and about PDB files in general. I used addH to protonate (add hydrogens) to PDB files. Does it use a force field of some kind in the process, like Amber or Charmm? It seems that depending on the force field used to protonate a PDB, the values for the partial charges and the van der waals radii are different. Specifically, I am using these charges and radii in the DelphiController. Another thing I've noticed is that when adding hydrogens, for the same amino acid, the hydrogens are sometimes different in name or number. For example if I have a Cysteine, in some cases, an HG (gamma hydrogen) is added for the gamma sulphur, balancing out charges completely. In other cases, the HG is not added, and so the amino acid ends up with a net negative charge. I was just wondering if this is supposed to happen. Here's another example. For Alanine, I was getting 1H, 2H and 3H attached to the nitrogen in some cases. In other cases, I just got "H" attached to the nitrogen. Does this mean those particular instances of ALA in the PDB had one only hydrogen attached to the nitrogen, instead of 3 ? Wouldn't the missing 2 hydrogens lead to a net negative charge on the ALA? Thanks for all the help and for this mailing list. It is a wonderful resource. Sincerely, Nihshanka Debroy

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Surfactant
by Annalisa Mercuri 14 Aug '06

14 Aug '06

Hallo everybody, I'm working with surfactants and emulsions. I'd like to use Chimera to reconstruct a micelle with my components, but I have no clue how to do that. Further my emulsion is made by a mixture of two surfactants. I would like to have a emulsion droplet image like the virus one. What do you suggest? Thank you for your help and advices Annalisa Mercuri MSc PhD Student School of Chemical Sciences and Pharmacy University of East Anglia Norwich Norfolk NR4 7TJ UK

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structure slice
by Raquel Hernandez 14 Aug '06

14 Aug '06

Hello chimera e-mail, I have received from a colleague data set from a virus reconstruction. I am a novice in the use of your program but have managed to make an image of my virus. I would like to add an image of a slice of the virus through the center perpendicular to the three fold axis. Can you please advise me on what I need to do to make a slice? I can get the tech people here to help if you tell me the tools, etc that I need to use. Thanks. Raquel Raquel Hernandez Research Associate Professor Department of Molecular and Structural Biochemistry 128 Polk Hall North Carolina State University Raleigh, NC 27695 office:919-515-5765 lab: 919-515-5786 Fax: 919-515-2047

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Fwd: Chimera and Macs
by Elaine Meng 14 Aug '06

14 Aug '06

Hello Mac users! When the Chimera window gets obscured by other windows on a Mac, clicking the X11 icon will bring it to the front (assuming you are using the recommended Mac/X11 version of Chimera). Begin forwarded message: > From: Kevin Dalby <dalby(a)mail.utexas.edu> > Date: August 13, 2006 11:54:43 PM PDT > To: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: Chimera and Macs > > Hi Elaine > > I think we spoke briefly at the enzymes GRC. > > I am not a sophisticated chimera user. I use it on my mac while > working with another 10 programs . Usually i cant see the chimera > screen when i need it. Normally, when I want to get back to a > program that is hidden i go to the doc and just click on the > program icon and it comes to the front. This does not happen for > chimera. I know other spoilt mac users would enjoy a remedy. > > > best wishes > > Kevin > > > Kevin Dalby > Associate Professor of Medicinal Chemistry > University of Texas at Austin > tel 512-4719267 > fax 512-2322606 > > > > ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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spaceball
by Mario Halic 09 Aug '06

09 Aug '06

hi!, can I use spaceball 5000 as input device in chimera? thanks, Mario

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Re: [Chimera-users] Electrostatic Potentials
by Thomas Goddard 08 Aug '06

08 Aug '06

Hi Nihshanka, Oops! My previous descriptions of how to determine electrostatic potential values at specific surface points assumed you were using the Surface Color tool to display the potential (menu entry Tools / Structure&Binding Analysis / Electrostatic Surface Coloring, or menu entry Tools / Volume Data / Surface Color). But you are using DelphiController and it has its own code for displaying potential values for which my previously described techniques will not work. To print the potential values at every surface point when the potential display was done with Delphi Controller you could put a print statement in chimera/share/DelphiViewer/MSMSTexturer.py at line 155, after the following lines of code else: # Point is outside of phi map. phivalue = 0 add the line print v_rs, phivalue Make sure the "print" line is indented the same as the "else:". This is going to print many thousands of lines in the Reply Log so be prepared to wait a bit. You could also use my previously described methods for showing potential values by using the Electrostatic Surface Coloring tool. Show a surface for your PDB model using Actions / Suface / show. Then in the Electrostatic Surface Coloring dialog press the "Open map data..." button and select the *.phi file generated by DelPhi (the one computed when running Delphi Controller). Then press the Color button on the surface color dialog. My previous code modification or the marker probe method could them be used. Tom

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Electrostatic Potentials
by Nihshanka Debroy 07 Aug '06

07 Aug '06

Hi everyone, I have a couple of questions about the electrostatic potentials generated in Chimera using the Delphi Controller. If I have a protein with 5 chains A,B,C,D,E, and I choose to show the surfaces of all chains except C (but keep the wireframe of chain C's atoms) and then run Delphi using the DelphiController, does that mean that the potential surface generated is in the absence of chain C (which is what I want)? I'm trying to generate the potential surface without taking into account chain C, but would like to see C's wire frame for analysis purposes. Also, is there a way to get the actual potential values at each surface coordinate? Thanks a lot for the help. Sincerely, Nihshanka

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coloring carbon and deleting hydrogens
by Narender Singh Maan 04 Aug '06

04 Aug '06

Dear all, I am trying to show two residues of a protein structure with 50% surface transparency along with a stick model (rest of the protein is 0% surface transparent). Now in this i am having trouble in showing those stick residues in a different color (for e.g. the default for C atom is gray, which i want to show in green). Is there anyway in which i can do it?. also for those two residues i want to delete the hydrogens (only in stick, and not in surface representation)? any suggestions would be of great help. Thank you

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Coloring binding modes according to an energy term with ViewDock
by Vincent Zoete 04 Aug '06

04 Aug '06

Hi, Does it exist a way to color the different ligand positions obtained during a docking run, and displayed by the Viewdock module of chimera, as a function of a given energy term present in the columns of the viewdock table? If not, I think this could be an useful option to add to chimera. Also, it could be interesting to have the possibility to display the color scale as a function of the energy term together with the structures. If it cannot be done in the chimera display, it could be in the generated figures. Otherwise, congratulation for the great job the UCSF computer graphics lab is making with Chimera! Thank you for your time. Sincerely, Vincent

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Re: [Chimera-users] X3D to VRML conversion
by Thomas Goddard 01 Aug '06

01 Aug '06

> Date: Tue, 01 Aug 2006 12:27:52 -0700 > From: Ben Morris > > Hey Tom, > > Were you using the chimera VRML viewer when you tested the new x3d2vrml > output? I had the same exact problem in my testing of the code before > submitting it, and Conrad told me that the Chimera vrml viewer is less > than perfect when it comes to complex geometry (surfaces and ribbons). I > don't know if you were using Chimera, or even if it is the only problem, > but when I tested the code using a third party viewer, ribbons and > surfaces worked fine! > > ~Ben Hi Ben, Yeah, I tested Chimera VRML output by reading it back into Chimera. I agree that the fact that ribbons did not display properly could very well be a problem with the Chimera VRML renderer rather than the output. I just displayed a Chimera round ribbon (1a0m) using FreeWRL 1.15 on Linux and it displayed correctly. It gave about 30 warnings like the following which may or may not be important: WARNING -- node Normal may not be ok as a field of type normal (...called from VRML::Field::SFNode, 1363) It sounds like you are the one who have worked on the Chimera VRML output rather than Greg. Thanks for working on this. I think it will be useful to many people. Tom

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X3D to VRML conversion
by Nihshanka Debroy 01 Aug '06

01 Aug '06

Hi Dr. Meng, Thank you for your informative reply. That was very helpful. I was wondering if I could ask another quick question. I don't think that in Chimera, using the VRML format one can save non-surface information, like the backbone structure of a peptide (but one can display it). So I saved the information in X3D. And now, I'm trying to convert back to VRML format to be able to display it. I got completely lost when looking for some software to do this conversion. I tried using something called X3D to VRML97, but got a "segmentation fault" when I tried to open up the created VRML file. Has anyone faced this sort of an issue ? Thanks a lot, Nihshanka

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