- Chimera-users - RBVI Mailing Lists

saving coords from script
by Tetsuro Fujisawa 23 Dec '13

23 Dec '13

The following bug report has been submitted: Platform: windows Chimera Version: 1.8.1 Description Hi, I found some strange behavior in saving pdb file by script file. I tried to modify the orientation of pdb file ‘tst.pdb’ (#1) in reference to axis coordinate (#0), then save the atomic coordinates in pdb file. When I typed in the commands through either command line window or IDLE, transformed coordinates were saved. It worked fine. However, the exact identical commands (inside the brancket) or lines (rc(’..’)) were run by script file shown in below, the untransformed coordinates were saved. This is also the case for “Midas.write method”. I wondered this might be a bug. Regards, Tetsuro Sample.py: ---------------------------------------------- from chimera import runCommand as rc rc('open axis.bild') rc('open tst.pdb') rc('rock y 60 1 center #1 coord #0 models #1') # orientation of tst.pdb was modified rc('focus') rc('write relative #0 #1 tstA.pdb') # write current coordinates to tstA.pdb rc('open tstA.pdb') # opened tstA has original untransformed orientation -----------------------------------------------

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Color by ramachandran probability? Or molprobity overlap?
by Oliver Clarke 19 Dec '13

19 Dec '13

Hi all, Quick question, just wondering if there is any way to color a structure by Ramachandran probability? Or by steric overlap scores for each atom as generated by mol probity? Either of these would be very handy as a way of getting a quick graphical overview of trouble spots in a structure. It seems like Chimera “knows about” Ramachandran plot data, (as one can generate such plots from the model panel) but I can’t find any convenient way to display this data on the structure. Many thanks, Oliver.

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Running Segger from a script
by Tom Goddard 19 Dec '13

19 Dec '13

Hi Rakesh, There is not Chimera command to run Segger, only a dialog. So you would have to use Python to run it and write out map files for each masked region if you wanted to script it. Segger uses several Chimera features such as Gaussian filtering, and watershed calculations that are in written in C++ and compiled against the Chimera Python. While you can get those to run in another Python if it has an identical version (e.g. 2.7.3), setting up the environment variables to find all the needed libraries is a difficult process. So I suggest using the Chimera Python. You can run Chimera scripts without the graphical interface by starting it from a shell "chimera --nogui myscript.py". The Segger Python functions are not documented so you would need to study the (complex and messy) code found in chimera/share/Segger or on Mac in Chimera.app/Contents/Resources/share/Segger Tom On Dec 18, 2013, at 5:54 PM, rakesh ramachandram wrote: > Hi, > > I would like to know if I can run Segger in a script in an automated fashion and then obtain the individual segmented regions as separate density maps. Is there a way to run chimera scripts from command line directly without using the chimera's python interpreter but using the default python interpreter after importing its libraries. > > Regards > Rakesh >

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question
by wanxiaobo＠nibs.ac.cn 17 Dec '13

17 Dec '13

Dear chimera team / users, I was looking for a way to save the content of Axis/plane/centroid information, not only the radii via command line, because I want to analyze the structure movement from MD trajectory. It is not convenient to save the information manually for each frame. Thanks Xiaobo

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Command line export to webgl
by Thomas Hrabe 17 Dec '13

17 Dec '13

Dear Chimera Team, I was curious if there was a functionality to export chimera scenes to webgl through the command line, without having to open the chimera window. Is there a set of python script commands that would do it? Thank you for your support, Thomas

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Attribute Calculator by command line?
by Hurt, Darrell (NIH/NIAID) [E] 16 Dec '13

16 Dec '13

Hi Chimera friends, I'm trying to calculate convexity as demonstrated in the Attributes tutorial: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html I can do it with the graphical tools without a problem, but when I try to do it via the command line, I run into trouble. I cannot find any documentation on running the Attributes Calculator on the command line. I've tried using "setattr": setattr a convexity atom.areaSAS/atom.areaSES This command generates a new atom attribute called "convexity" for every atom, but the value of this attribute for every atom is literally "atom.areaSAS/atom.areaSES" instead of the calculated value. Is there a way to calculate a new attribute value on the command line within Chimera? Sorry to be so demanding… Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Setting selection mode command line
by rswett＠chem.wayne.edu 16 Dec '13

16 Dec '13

Hi all, I'm interested in putting together a script that will open several large pdb files, select some very specific pieces of those files and save the output to another file. The problem is that they are large files and unwieldy in a graphics window. I have no problem generating the commands to select the regions I'm interested in, but I still need to be able to switch selection modes in between commands. Is there a way to change the selection mode at the command line without navigating the selection menu? Rebecca

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Export options for x3d2stl
by Hurt, Darrell (NIH/NIAID) [E] 16 Dec '13

16 Dec '13

Hi Chimera friends, Here's the second question of the day. Thanks for your patience with me. When I export the scene as an STL (for 3D printing), I think what happens is that Chimera outputs first an X3D file and then runs the utility program "x3d2stl" to create the STL. The X3D file is about 5 MB, but the STL is about 100 MB. I understand that much of this size inflation is because the "primitives" in X3D have to be converted to mesh objects for STL. However, when I look at the STL file, the meshes derived from the primitives are finer than I really need. I find that I can "get away with" a coarser meshification by using x3d2stl on the command line: x3d2stl -c -r 2 -o sticks.stl < sticks.x3d If I want to export the scene via the command line within Blender, is there any way to issue options to x3d2stl? Or should I just run x3d2stl outside of Blender? Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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import binary format .raw file
by Carol J Hirschmugl 16 Dec '13

16 Dec '13

Hello, I am new to chimera, but have seen its capabilities for rendering 3D images of complex data sets, and think that this will be an appropriate program for excellent image analysis for my 3D tomography data sets. My data sets are in general binary format, (.raw file), 32 float, big endian, x fastest order for an x,y,z data set of 128 x 128 x 128 voxels of grey scale information. I am using AVIZO and FIJI at present. Avizo is expensive, and fiji is slow and reduces the data to 8 bit before rendering it, which I find unacceptable. TO move to Chimera - I found the web page in the Users Manual that suggested ADDING A FILE TYPE But I am lost by the description of how to proceed since I do not have prior knowledge of python and how to do the mapping to CHIMERA (x,y,z) that is suggested. I gather I need to write a python code - or numpy code maybe. Can you help or provide more context or a self-tutorial link so I can fill in the details? Thank you, Carol

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Local execution of pdb2pqr and APBS
by Hurt, Darrell (NIH/NIAID) [E] 16 Dec '13

16 Dec '13

Hi Chimera friends, Sorry to bother you again with so many questions. I'm trying to use PDB2PQR and APBS in a script to calculate an EP map. I know how to specify a local executable location for these external applications if I use the graphics interface, but the documentation that I can find does not indicate how to do this via the command line. Is it possible? How do I do it? Thanks! Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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changing the rgb for stereo images
by Bala subramanian 13 Dec '13

13 Dec '13

Friends, I have a glass with a red-cyan color. When i use the Chimera stereo mode (red-cyan) under view controls. I still see some ghost images. I would like to know if there is any possibility to add a features something like a box where i can give the rgb (the light frequencies) values of the images to match my glass. Thank you, Bala -- C. Balasubramanian

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Dynamic scolor custom cmap?
by Hurt, Darrell (NIH/NIAID) [E] 13 Dec '13

13 Dec '13

Hi Chimera friends, I have a volumetric potential file loaded that I want to map onto a molecular surface. For my application, I want the color mapping to use a custom palette of at least three colors that spans the full range of surface values. I know that I can do this by simply specifying the custom colors in the Surface Color panel and then clicking "Set full range of surface values". That works for me. However, I want to do this via command line. The following line works for me (I've omitted "cmapRange full" because that is the default setting): scolor #0 volume #1 offset 1.4 cmap cyanmaroon My problem become if I want to set a custom palette: scolor #0 volume #1 offset 1.4 cmap -10,yellow:0,white:10,green This line also works, but for values lower or higher than –10 or +10, the color ramp "plateaus". And this line only works because the extents of this particular mapping happen to go from –29 to +17. Is it possible to obtain the values for the full range and specify them for a custom palette? Or is it possible to assign a custom palette and call it like the default palettes? I'm happy to clarify if needed. Thanks! Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Modeling with cryo-EM
by Aurore Vaitinadapoule 13 Dec '13

13 Dec '13

Dear all, I'm would like tu use this following script to model with cryo-EM: from modeller import * log.verbose() env = environ() struct='./M60_9.pdb' map='new_map.mrc' resolution=10.2 box_size=48 # how to define the box size ?? apix=1.88 x=90; y=63; z=23 #origin steps=20 # Read in cryo-EM density map den = density(env, file=map, em_density_format='MRC', voxel_size=apix, resolution=resolution, em_map_size=box_size, density_type='GAUSS', px=x,py=y,pz=z) # Fit the PDB file into the map by MC simulated annealing den.grid_search(em_density_format='MRC', num_structures=1, em_pdb_name=struct, chains_num=[1], start_type='CENTER', number_of_steps=steps, angular_step_size=30., temperature=100., best_docked_models=1, translate_type='RANDOM', em_fit_output_file='modem.log') But i got this error message: _modeller.ModellerError: read_mrc_h_E> Density map must be cubic, and of dimension em_map_size (48): actual dimensions (40, 40, 36) What is exactly the box size? And how to define it? Thank's Aurore -- Aurore G. VAÏTINADAPOULÉ aurore <a.vaitinadapoule(a)inserm.fr>.vaitinadapoule(a)inserm.fr<a.vaitinadapoule(a)inserm.fr> a.vaitinadapoule(a)gmail.com PhD Student in Bioinformatics INSERM UMR-S665, DSIMB Team, Dynamique des Structures et des Interactions des Macromolécules Biologiques Mobile phone: +33(0) 778 18 52 07

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chimera slow
by Daniel Murin 12 Dec '13

12 Dec '13

Hi, I have been trying to use the Unit Cell function on Chimera. It works, but the graphic is so large that moving it around is nearly impossible because the program is running so slowly. It is rendered in ribbon. Is there a way to lower the quality in order to manipulate the graphic faster? Thanks! Charles Daniel Murin Ph.D. Candidate - Ward/Ollmann Saphire Labs Integrative Structural and Computational Biology Immunology and Microbial Science Kellogg School of Science and Technology The Scripps Research Institute 10550 North Torrey Pines Road, CimBio 105 La Jolla, CA 92037 Office: 858.784.3326 Lab: 858.784.7170 Fax: 858.784.8218 email: cmurin(a)scripps.edu

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(no subject)
by Danilo Di Maio 12 Dec '13

12 Dec '13

danilo.dimaio(a)gmail.com

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Launch external program from Chimera python script?
by Hurt, Darrell (NIH/NIAID) [E] 11 Dec '13

11 Dec '13

Hi Chimera friends, I am thinking of writing a script for Chimera that allows the user to map lipophilicity to the surface of protein. There are a few algorithms out there, but the easiest that I've found to use is "pyMLP": http://code.google.com/p/pymlp/ I see two ways to do this: (1) Write a wrapper script (shell, Python, etc.) to first run pyMLP to generate a DX file and then launch Chimera with its own script to generate the surface and do the mapping. (2) Write a Chimera Python script to launch pyMLP to get the DX file, generate the surface, and do the mapping. For my purposes, it might be easier in the long run to choose option 2, but that seems a little trickier starting out. Can you advise me on the best way to proceed? Also, I know that you aren't looking to add new functionality to Chimera v1, but the generation of a lipophilicity map might be a nice feature to add to Chimera at some point and pyMLP seems relatively easy to package with Chimera… Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Journal of Organic and Biomolecular Simulations: Full page charge waiver
by CompChem News 11 Dec '13

11 Dec '13

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select all side chains
by Zhou, Ming (NIH/NCI) [C] 09 Dec '13

09 Dec '13

Dear Elaine: I have a quick question for you. How should I select all the amino acid side chains in a protein but not the backbone (without CA/C1/N/O). How should I write this command? Thanks Ming Zhou

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Silhouette toggle
by Luca Pellegrini 05 Dec '13

05 Dec '13

Hi, I have set Silhouette ON in the Effects tab of the Viewing panel, and now I would like to toggle it off for one specific object. However, the Attributes window from Model Panel does not show the Silhouette option (it should feature between 'ribbon spline' and 'stick scale'). Can anyone please advice? I am using Chimera 1.9 (build 39137) for Mac . 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

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calculate buried surface area
by Bala subramanian 05 Dec '13

05 Dec '13

Friends, I have a dimer protein (say monomers 1,2). I have calculated the electrostatic potential of monomer 1 using apbs. I used volume viewer to display the electrostatic surface. I see that the elect. surface of one monomer 1, touches the vdw surface of monomer 2 at a contour level of 1. I want to calculate the total surface area of monomer 2 that is exposed/buried within the elec. surface of monomer 1. Is there any simple. If not suggestion how i can do it with a python script perhaps. Thanks, Bala -- C. Balasubramanian

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Problem of Launching Chimera Remotely on a Mac
by Anindito Sen 05 Dec '13

05 Dec '13

Dear All, I am having difficulty to launch Chimera remotely with the following Error message on my Mac. I understand that the current OS X (version 10.8.5) and the latest Xcode has some issues and cannot handle the process ?! Is there a way out of this ? Thanks and Best Wishes Andy [andy@****** ~]$ chimera Xlib: extension "NV-GLX" missing on display "localhost:15.0". Xlib: extension "NV-GLX" missing on display "localhost:15.0". X Error of failed request: GLXBadCurrentWindow Major opcode of failed request: 149 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1354 Current serial number in output stream: 1354 Dr. Anindito Sen (Ph.D) >Department of Cell Biology & Anatomy >Graduate School of Medicine >University of Tokyo >Tel & fax: +81-3-5841-3339

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Electrostatic potential values at each residue
by Tatsuhito Matsuo 04 Dec '13

04 Dec '13

Dear All, I'd like to get the electrostatic potential (ESP) values at each residue in a protein. I implemented the "Coulombic Surface Coloring", then get the distribution of ESP values at each residue by "Render/Select by Attribute" (Attributes of [residues], Select -> Attribute [value_Coulombic_ESP]). However, The surface plot and the ESP values obtained by "Render/Select by Attribute" do not coincide with each other. For example, there are some residues where the surface plot reports positive ESP values, while "Render/Select by Attribute" gives negative ones (e.g. VAL70 CG2 in the Chimera session file attached.). Could you teach me how to solve this discrepancy? Thank you very much in advance, T.M.

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Re: [Chimera-users] Surface area with positive electrostatic potential
by Tom Goddard 04 Dec '13

04 Dec '13

Hi T.M., To find the surface area with positive electrostatic potential would require computing the potential at surface points. Chimera does not compute solvent accessible surface (SAS) points (although it does compute total area). So there is no simple way to get the SAS area for positive potential points. Chimera does compute the solvent excluded surface (SES) using menu Actions / Surface or command "surface". For an SES surface a little Python code can give the fraction of the surface area colored red. I've attached that Python code red_area.py. You color the surface using the normal red-blue electrostatic coloring. The red_area.py code adds a command called "redarea" that computes the area of the surface that is more red than blue. Here's an example from the header of the red_area.py file. # Example use. # # menu File / Open..., red_area.py, Creates the new redarea command. # # open 1a0m # surface # coulombic -10 red 0 white 10 blue #0 # redarea #0 # # menu Favorites / Reply Log # -> "Surface MSMS main surface of 1a0m, red area 1400, total area 1888, ratio 0.7414" This script and other odd Python code for doing computations is on the Chimera developer web site: http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts Tom On Dec 3, 2013, at 9:05 PM, Tatsuhito Matsuo wrote: > Dear Tom, > > Thank you very much for the reply and I'm sorry for inadequate information on what I've done (your guess is completely right). What I'd like to know is the ratio of the solvent accessible surface (SAS) with positive (or negative) potential values to the total SAS. The total SAS value is automatically calculated by the surface plot, and I need the value of SAS having positive/negative potential values. > At first, I thought the ESP value of "Attributes of Residues" is relevant to the one at the corresponding protein surface area. I now understand that this was wrong. Could you teach me how to get the SAS having positive/negative potential values? > > Best regards, > > T.M. > > On 2013/12/04, at 12:19, Tom Goddard wrote: > >> Hi T.M., >> >> I think you've left out details about what you have done -- how did you get this value_Coulombic_ESP attribute? Did you use values at atom positions? Did you use the "compute grid" option in the Coulombic Surface Coloring dialog? I guess you did that. And you say you use Attributes of Residues -- is that an average of the atom attribute obtained from the values at atom positions dialog? I can't be sure what you've done, but here's a guess at what your problem is. The Chimera Coulombic Surface Coloring dialog computes the potential at points 1.4 Angstroms out from the solvent excluded molecular surface and colors the surface points using that value. If you instead use a potential value interpolated at the center of an atom, that will give a much different value -- in fact it should tend to give an extremely large value because if the atom is charged the potential at the atom center is infinite using the simple Coulomb calculation. But because you are (I think) using a value interpolated from a grid you don't get an infinite value, just a very large value. So I think your problem is you are not considering that the electrostatic potential varies rapidly in space and you are comparing colors using potential values at different positions in space. >> >> Tom >> >> >> >> On Dec 2, 2013, at 6:31 PM, Tatsuhito Matsuo wrote: >> >>> Dear All, >>> >>> I'd like to get the electrostatic potential (ESP) values at each residue in a protein. I implemented the "Coulombic Surface Coloring", then get the distribution of ESP values at each residue by "Render/Select by Attribute" (Attributes of [residues], Select -> Attribute [value_Coulombic_ESP]). However, The surface plot and the ESP values obtained by "Render/Select by Attribute" do not coincide with each other. For example, there are some residues where the surface plot reports positive ESP values, while "Render/Select by Attribute" gives negative ones (e.g. VAL70 CG2 in the Chimera session file attached.). Could you teach me how to solve this discrepancy? >>> >>> Thank you very much in advance, >>> >>> T.M. >>> >>> <ubiquitin.py><ubiquitin.pyc>_______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > >

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request for removal from mailing list
by Aani Homeira 03 Dec '13

03 Dec '13

Thanks . . . . . . . . . . . . . . . . . . . A n i . H o m e i r a . A m i r k h a n i .

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Re: [Chimera-users] reading PDB-format alignment files
by Tom Duncan 03 Dec '13

03 Dec '13

Eric, It's not the structural info I want to extract - just the sequence alignment info. See the remarks in the file header. Thanks, Tom ----------------------------------------------------- Thomas M. Duncan, Ph.D. Associate Professor Dept Biochemistry & Molecular Biology SUNY Upstate Medical University Syracuse, NY On Dec 3, 2013, at 3:00 PM, chimera-users-request(a)cgl.ucsf.edu wrote: > Date: Tue, 3 Dec 2013 11:27:02 -0800 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > To: Tom Duncan <duncant(a)upstate.edu> > Cc: chimera-users BB <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] reading PDB-format alignment files > Message-ID: <9EF6E8D1-3C93-4C30-AD51-2B110CF5C813(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii" > > On Dec 3, 2013, at 7:47 AM, Tom Duncan <duncant(a)upstate.edu> wrote: > >> Can Chimera read sequence alignments from PDB-format alignment files, such as those generated by the I-Tasser modeling server? Or are there scripts to convert them? I have attached an example file. > > Hi Tom, > Well, this "PDB" file doesn't conform to the PDB standard in a variety of ways, but the one you care about is the extra two columns on the ATOM records. The presence of those columns causes Chimera to skip those records. If you simply edit them out then Chimera displays the structure. I've attached an edited version of your file. I will open an enhancement-request ticket in our bug-tracking database for having Chimera ignore non-standard columns past the coordinate records (there are some standard columns that are supposed to be there!) and put you on the notification list for that ticket. > > --Eric

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