- Chimera-users - RBVI Mailing Lists

by Ihms, Elihu C 02 May '05

02 May '05

I noted that Apple still has X11 availible for download, just that it's not publicized. http://a1408.g.akamai.net/7/1408/1388/20030317/akamai.info.apple.com/X11/us… Keep up the good work on Chimera! -- Elihu Ihms [ ihms(a)tamu.edu ]

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Chimera Surface Area/Volume
by Elaine Meng 27 Apr '05

27 Apr '05

Hi Dieter, Just a few add-ons to Tom's reply: Another approach to getting the surface area of the receptor buried by the ligand is to run Surface Area/Volume (a) on the complex of ligand and receptor (must delete water and anything else first). Then use Attribute Calculator to sum the surface areas of the receptor atoms only. (b) after deleting ligand, run it again on the receptor. The total is all from the receptor, so it is not necessary to use Attribute Calculator. Subtract the value from (a) from this value. Tom gave a link to the development documentation, which is slightly ahead of the Chimera version you have. It is almost the same, except that the Tools menu has been reorganized. Probably in the version you have, both Attribute Calculator and Surface Area/Volume are in the Utilities submenu of the Tools menu. To get the documentation that goes with your version, use the Help buttons on those dialogs or open the User's Guide from the Help menu. If you have the latest snapshot (1.2105, March) there is an "Attributes" tutorial (Help... Tutorials). Part 2 has one example of using Surface Area/Volume and Attribute Calculator. Finally, if anything is confusing or hard to find in the documentation, please feel free to complain to me! 8-) Elaine ----- 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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buried surface area
by Thomas Goddard 27 Apr '05

27 Apr '05

Hi Dieter, The surface area / volume tool (menu entry Tools -> Utilities -> Surface Area / Volume) could give buried surface areas if you ran it for the unbound receptor, unbound ligand, and then the complex, and then calculated { Area(receptor) + Area(ligand) - Area(receptor+ligand) } / 2 When you use this tool it reports the total area to the Reply Log (menu entry Favorites / Reply Log) and atoms are assigned an attribute saying how much area they contribute. It is a bit of a pain to run it 3 times and do the math yourself. The surface area is calculated by a web server as described in the Chimera User's Guide http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/surfvol.ht… so you will need an internet connection to use it. The Chimera User's Guide is only available in HTML as far as I know. It is written in HTML. Tom > From: "Dieter Blaas" <dieter.blaas(a)meduniwien.ac.at> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Date: Wed, 27 Apr 2005 21:38:46 +0200 > Subject: buried surface area > > Hi Tom, > two quick questions: 1/ can Chimera calculate/display > the surface area buried by e.g. a ligand when bound on > a receptor? 2/ is there a documentation other than htlm > (e.g. pdf file)? > Thanx, Dieter >

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Resize a molecule
by Thomas Goddard 27 Apr '05

27 Apr '05

Here is some code to scale a molecule size by a given factor. That is all atoms have their coordinates multiplied by a factor. Tom ------- Start of forwarded message ------- Date: Wed, 27 Apr 2005 11:05:55 -0700 (PDT) From: Thomas Goddard <goddard(a)cgl.ucsf.edu> Hi Jinghua, By "virus cage pdb file" I guess you mean you placed atoms at icosahedral positions, and want to show them connected up to show some icosahedral pattern. I think the easiest approach is to open your old session, run a command to change the diameter of the cage, then save a new session. Below is some Python code that provides a "scalemol" Chimera command. Make a directory chimera/share/scalemol in your Chimera distribution and put the code below in file chimera/share/scalemol/ChimeraExtension.py. Then start Chimera, open the cage PDB model, use menu entry Favorites/Command line, and type a command: scalemol 0 1.5 to make model number 0 bigger by a factor of 1.5. If you have more than one model open you can see the model numbers using Favorites / Model Panel, the model number is shown in the left hand column. Tom - ---- scalemol/ChimeraExtension.py code follows: # ----------------------------------------------------------------------------- # def scale_molecule(cmdname, args): from Midas.midas_text import error fields = args.split() try: model_num = int(fields[0]) factor = float(fields[1]) except: error('Syntax error: scalemol <model-number> <factor>') return import chimera mlist = chimera.openModels.list(id = model_num) if len(mlist) == 0: error('scalemol: No model number %d' % model_num) return for model in mlist: for a in model.atoms: x, y, z = a.coord().xyz.data() c = chimera.Coord() c.x, c.y, c.z = (factor*x, factor*y, factor*z) a.setCoord(c) # ----------------------------------------------------------------------------- # import Midas.midas_text Midas.midas_text.addCommand('scalemol', scale_molecule) ------- End of forwarded message -------

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get to lighting adjustment
by jinghua＠ucsd.edu 26 Apr '05

26 Apr '05

to whom it may concern, How could I get to the adcanced feature of lighting adjustment? Can I add more lights with different directions? Thanks! Jinghua <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>>< Jinghua Tang, Ph.D. Phone: 858-534-5852(o) 4107 Natural Sciences Bldg, MC-0378 858-597-2056(h) Department of Chemistry & Biochemistry Fax: 858-534-5846 University of California, San Diego E-mail: jinghua(a)ucsd.edu La Jolla, CA 92093-0378 http://jinghua.ucsd.edu <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><

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Writing the selection
by Charles Moad 19 Apr '05

19 Apr '05

How can I write the current selection to a file from a script? "write sel filename.pdb" does not work. Thanks, Charlie

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v1.2105 for amd64 (x86_64)
by Sabuj Pattanayek 18 Apr '05

18 Apr '05

Hi, I don't know if this has been asked before (couldn't find anything on searches) but will there be a native amd64/emt64 (x86_64) build of chimera v1.2105? Thanks, Sabuj Pattanayek

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Problem with Large Molecules
by Private 14 Apr '05

14 Apr '05

Dear Chimera Team: I think your work on Chimera has been of very high quality. In fact, I've used it to produce print quality images for an upcoming book of mine. However, I've had some problems with displaying some large molecules, for example, 1AYM and 1P5Y. I use the PDB file for the molecule, but specifically the assumed biological model file, not the the asymmetric unit file. I've been able to open the file in programs like Deepview and Raswin, but I can't open the file in Chimera. I'm running Windows 98 with about 256MB of RAM, and what happens when I attempt to open the assumed biological model file Chimera runs for over an hour trying to open the file and then crashes with a page fault message. I certainly would like to use the image capabilities provided by Chimera, so can you help me with this? Or is this simply a limitation of Chimera?

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Thanks for the movie recorder
by Ann Mullin 08 Apr '05

08 Apr '05

I just tried out the movie recorder and I am very pleased. Thanks very much to the programmers who contributed to the addition of this tool to my favorite molecular graphics program. Ann Ann Mullin Research Scientist Cell and Molecular Biology Dept. Tulane University New Orleans, LA 70118-5698 504-865-6742 (Ph) 504-865-6785 (FAX) amullin(a)tulane.edu

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yet another snapshot
by Eric Pettersen 05 Apr '05

05 Apr '05

A new snapshot release (1.2106) is available for Windows only, which fixes several issues the 1.2105 release had on that platform, namely: Movie Recorder movie encoding now works documentation searching fixed unreadable highlighted text in certain widgets fixed Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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how were the virus images generated?
by Thomas Goddard 05 Apr '05

05 Apr '05

Hi Dieter, To make virus capsid images in Chimera like those on the VIPERdb web site, http://viperdb.scripps.edu/ or like those on our web site http://www.cgl.ucsf.edu/Research/virus/ http://www.cgl.ucsf.edu/chimera/ImageGallery/ you use the Chimera Multiscale tool, menu entry Tools / Multiscale / Multiscale Models. I'm guessing you tried making solvent excluded molecular surfaces with menu entry Actions / Surface / Show. That makes much higher resolution surfaces and tends to crash for large molecules or complexes. (We are working on replacing that third party code.) If your virus capsid PDB file header contains sixty REMARK 350 BIOMT matrices then you can just press the "Make Models" button at the bottom of the Multiscale dialog. This uses the matrices to make sixty copies of the asymmetric unit. You don't need a file containing coordinates for the full capsid with this tool. If your virus capsid PDB doesn't have the BIOMT matrices, but uses the coordinate system defined by the VIPER site (eg a PDB downloaded from VIPER), then you can instead choose Multimer Type: Icosahedral Symmetry, VIPER Z(2)35X(2) from the menu at the bottom of the Multiscale dialog, and then press the "Make Models" button. Once you have displayed the capsid model, you can color, hide, or display capsomeres at atomic resolution or with ribbons using the other buttons in the Multiscale dialog. For the full details look at the Tools section of the Chimera User's guide for Multiscale. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemu… You can show this documentation in a web browser by just pressing the Help button at the bottom of the Multiscale dialog. Let me know if you have additional questions, Tom > From: "Dieter Blaas" > To: goddard(a)cgl.ucsf.edu > Date: Tue, 05 Apr 2005 12:38:20 +0200 > Subject: how were the virus images generated? > > Dear Tom, > Vijay referred my question to you: As far as I > understand were the virus images in VIPER generated > with Chimera. I have tried hard to generate similar > surface renderings with this software on a win2k 2 GB > machine but Chimera always crashes upon trying to > make the surface! Are there any particular parameters > which must be set? What is the limit of atoms, > coordinates, surface resolution, RAM? Many thanks for > any hints. > > Regards, Dieter Blaas > ------------------------------------------------------------------------ > Dieter Blaas, > Medical University of Vienna, > Inst. Med. Biochem., Vienna Biocenter (VBC), > Dr. Bohr Gasse 9/3, > A-1030 Vienna, Austria, > ------------------------------------------------------------------------ >

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HAVING TROUBLE W/ PROGRAM!
by Desmond McMahon 05 Apr '05

05 Apr '05

I downloaded Chimera and I tried to understand the help section. I'm a high school student and i'm using this for a report. CAN YOU PLEASE PLEASE PLEASE tell me how to START a DNA/Double helix structure and I can't find out. Can you help me??? Desmond __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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by Andreas Linden 31 Mar '05

31 Mar '05

Hi, maybe you can incorporate drag and drop into chimera? It's a bit of a hassle having to go through file>open> and then go through directories to get at the pdb file! Otherwise an excellent program, thanks for making it available! Cheers Andy (University of Sheffield, UK)

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new snapshot
by Eric Pettersen 29 Mar '05

29 Mar '05

We've put out a new snapshot (version 1.2105) which is basically the same as the 1.2104 snapshot but has the zone-selection crash bug fixed. --Eric

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Mac OS X stereo
by David Belnap 27 Mar '05

27 Mar '05

As a follow-up to the discussion about stereo by Virginia and Sabuj, will Chimera currently, or in the future, work in stereo on a Mac running OS X? David ============================================ David M. Belnap Department of Chemistry and Biochemistry Brigham Young University Provo, Utah 84602 USA Phone: 801-422-9163 FAX: 801-422-0153 David_Belnap(a)byu.edu ============================================

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Fwd: [Chimera-users] Zones to create inspector list of "contacts"
by Elaine Meng 23 Mar '05

23 Mar '05

Begin forwarded message: > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Date: Wed Mar 23, 2005 9:39:41 AM US/Pacific > To: Grant Jacobs <gjacobs(a)bioinfotools.com> > Subject: Re: [Chimera-users] Zones to create inspector list of > "contacts" > > Hi Grant, > You can write out the contents of the current selection with > Actions... Write. More details can be viewed at: > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#writespec > > However, the resulting text file will simply list all selection > contents (i.e., not in pairs of what is contacting what). I don't > know if that is sufficient for your purposes. > > If you are specifically looking at H-bond interactions, however, > FindHBond includes an option to write out all the H-bonded atom pairs > and the distances between them. Man pages: > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/ > findhbond.html > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html > Best, > Elaine > ----- > 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 > > On Wednesday, March 23, 2005, at 02:55 AM, Grant Jacobs wrote: >> >> I am trying to achieve something with this effect: >> >> Generate a list of all the atoms in other molecules of a >> multi-protein complex that are within a specific "contact" distance >> of atoms a molecule of interest in the complex, with them presented >> in the same way that H-honds or distances are illustrated. >> >> You can use Select:Zones to get the atoms that lie within a set >> distance of a molecule. All that seems to be needed is for the >> Select:Zones operation to optionally generate a list of atom pairs >> that the inspection things present. >> >> So far I can't seem a simple way of doing this without hacking code >> or doing it manually. Is there a way of doing this currently, or >> should this be looked at as future possible feature? >> >> Obviously, there are other useful "neighbour" operations you can do >> also, e.g. neighbours within the current selected molecule, >> neighbours by atom/residue type. >> >> Grant >

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1.2104 snapshot release available
by Eric Pettersen 17 Mar '05

17 Mar '05

Hi all, A new Chimera snapshot release (1.2104) is available. As usual, we recommend you download a snapshot release only if you need features not found in the preceding production release (in this case version 1.2065) since snapshot releases don't get the same level of testing as production releases. Also, in this snapshot the Collaboratory feature doesn't work on Windows. That said, here's the major things that are new: GENERAL: local documentation searching added (Help... Search Documentation) nucleic acid ambiguity codes (R = A/G, Y = C/T/U, N = A/C/G/T/U) can be used in subsequence searching (Select...Sequence... and Sequence Panel) new residue attribute "isHet" (whether the residue is in HETATM records in the input PDB file) NEW TOOLS: Attribute Calculator (Utilities) - generate new numerical attributes from existing ones; calculate totals or averages of a given numerical attribute Demo Editor (Demos) - graphical interface for creating demos Movie Recorder (Utilities) - capture image frames from Chimera and assemble them into a movie file Surface Capper (Graphics) - cap surfaces where they intersect a clipping plane (the cap is maintained interactively) Surface Color (Volumes) - color surfaces according to volume data 2D Labels (Graphics) - create arbitrary text labels and place them in 2D [really a preliminary version; will be improved in the production release] TOOL CHANGES: Demos - changes in demo dialog buttons/menu; demo source file format changed to XML (see new Demo Editor); older format can still be played MD Movie (formerly Movie) - added step size option for playing the movie; RMSD map calculation faster; added option to automatically recolor the RMSD map for contrast; new prefix for metafiles ("md:") Multalign Viewer - Region Browser acts upon chosen region(s) (not necessarily the active region) and includes checkboxes to control which is active and which are shown in the sequence window ViewDock - H-bond statistics can be included in the sortable columns of ligand descriptors Volume Viewer - support added for UHBD electrostatic potential (binary only) NEW COMMANDS: movie - capture image frames and assemble them into a movie file; command-line implementation of Movie Recorder writesel - write a parsable text file containing specifications of the currently selected (or unselected) items; command-line implementation of Actions... Write Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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how save cyclooxygenase demo
by J. David Rawn 16 Mar '05

16 Mar '05

Sir: I would like to save the cyclooxygenase demo to show my class in a classroom without a unix based system. How is that done? J. David Rawn

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hardware stereo question
by Virginia B. Pett 16 Mar '05

16 Mar '05

I am interested in computer visualization, computer modeling, and crystallographic software for teaching and research at The College of Wooster. We are going to replace our five-year old cluster of Silicon Graphics machines in the near future. We are considering a cluster of PCs with either Windows or Linux, or Macs with OS X. The big stumbling block for us has been figuring out what is the best hardware platform for three-dimensional stereo viewing. Our current Silicon Graphics machines have the Stereographics Crystal Eyes viewing system. Is there something newer, better, or less expensive than the Stereograhics Crystal Eyes viewing system that is compatible with PC or Mac? Or is the Crystal Eyes still the best system for Chimera and other molecular modeling and computer visualization software? Stereographics sells a CrystalEyes Workstation (either Windows/Linux or Mac) that looks attractive. I would appreciate any advice you can offer. ________________________________________ Virginia B. Pett Professor of Chemistry Department of Chemistry, The College of Wooster 943 College Mall, Wooster, OH 44691 Telephone: 330-263-2114 Fax: 330-263-2386

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Re: [Chimera-users] Intersurf, protein interface display
by Thomas Goddard 14 Mar '05

14 Mar '05

Miguel suggests another coloring for protein interface surfaces based on surface complementarity judged by looking at surface normals. Tom ------- Start of forwarded message ------- Date: Sat, 12 Mar 2005 17:25:29 +0000 From: =?ISO-8859-15?Q?Miguel_Ortiz_Lombard=EDa?= <mol1(a)york.ac.uk> To: Thomas Goddard <goddard(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Intersurf, protein interface display - -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Tom, With regard to your very interesting message, I would like to add another useful way of studying the surfaces of protein-protein (or protein-whatever) interactions. This way involves the concept of "surface complementarity", where the buried surfaces are scanned to see how parallel are the normals to them at every point (in a grid). It is shown that specific or high-affinity interactions have usually higher complementarity. There is a paper by Lawrence and Colman (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=A…) and a program by the same authors in the CCP4 suite called "sc" that performs such calculation. The "sc" program is also able to add the "surface complementarity value" to the vertexes of the interacting surfaces calculated in GRASP. I currently have a little program (modified by me from a Raster3D jiffy) to colour such a modified surface according to those values and render it with the render program from Raster3D. But I don't like GRASP and would like to have this analysis as a possibility in chimera. Such analysis have been very useful for me in the past, especially to study protein-protein interactions. If this is also interesting for you I would be glad to be of help. Cheers, Miguel Thomas Goddard wrote: > Hi Conrad, > > I read the paper > > Intersurf: dynamic interface between proteins > Nicolas Ray, Xavier Cavin, Jean-Claude Paul, Bernard Maigret > Journal of Molecular Graphics and Modelling, 23 (205) 347-354 > > It addresses 3 problems: how to find a surface interface between 2 proteins, > ways to color such a surface, and how to flatten that surface into two > dimensions. > > The surface calculation was a neat algorithm -- take the > Delauney tetrahedralization of all atom positions from both proteins, > then find tetrehedra with vertices from both proteins and cut those > tetrahedra in half. The tetrahedra are cut in half with one or 2 > triangles using vertices on tetrahedron edges that connect an atom > in one protein to an atom in the other protein. The vertices are > placed midway between the atoms moved in by their vdw radii. > > They proposed 2 ways of coloring the surface. One colored vertices > by how far apart the atoms were in the two proteins that were used to > create that vertex. Red to blue shows short to long distances. The > other coloring shows types of possible interactions between the two > residues associated with the two atoms for the tetrahedron edge that > the surface vertex splits. They gave different colors for predicted > hydrogen bonding, hydrophobic packing, pi ... X, pi ... pi, same charges, > opposite charges. Not sure what the pi bonding notation means. > > They also described how to flatten the 3-dimensional to a 2-dimensional > surface with one to one correspondence between vertices and edges. > Their method tried to come as close as possible to a conformal map. > Conformal means the angles of the triangles stay the same to the extent > possible. > > These calculations took a few seconds on 2000-5000 atom proteins. > > Here's my assessment. I think the concept of showing a protein interaction > interface and coloring it to show interactions sounds useful for protein- > protein interaction people. I think the flattening into 2 dimensions > is probably not useful. Conformal maps greatly distort the area of > the surface if it has curvature (you've seen the maps where Greenland > is bigger than Africa, Americas, Asia and Europe combined). So the flattened > surface is going to be hard to recognize as the interface, unless it > is already pretty flat. If it is already pretty flat you might as > weill just look at the 3-d surface. > > If we wanted to do something with interface surfaces I would suggest > talking to Tanya Korteme. We already have all the infra-structure to > create the surfaces. I would not use the Delauney surfaces, instead > just use MSMS surfaces on both proteins showing only the parts associated > with atoms in one protein that are within 5 angstroms of atoms in the > other protein. The zone calculation code I wrote for multiscale could > do that fast. We could offer a range of atom colorings that map onto > the surface (hydrogen bonds, distance to nearest atom in other protein, > charge complementarity, etc...). > > I don't have time or enough interest to work on this project. But > perhaps someone else will. We have talked about collaborating with > Tanya Korteme in the past and this would be a good opportunity. > > Tom > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users - - -- correo-e: mol1(a)york.ac.uk http://www.ysbl.york.ac.uk/~mol - - ----------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées - -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.0 (MingW32) Comment: Using GnuPG with Thunderbird - http://enigmail.mozdev.org iD8DBQFCMyYJF6oOrDvhbQIRAttkAJ0frREWIEA7IYDE2LY38jdcyfuRoACgkHLn M9VEY8TEz8HnR3F763pws0A= =zoYa - -----END PGP SIGNATURE----- ------- End of forwarded message -------

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Intersurf, protein interface display
by Thomas Goddard 09 Mar '05

09 Mar '05

Hi Conrad, I read the paper Intersurf: dynamic interface between proteins Nicolas Ray, Xavier Cavin, Jean-Claude Paul, Bernard Maigret Journal of Molecular Graphics and Modelling, 23 (205) 347-354 It addresses 3 problems: how to find a surface interface between 2 proteins, ways to color such a surface, and how to flatten that surface into two dimensions. The surface calculation was a neat algorithm -- take the Delauney tetrahedralization of all atom positions from both proteins, then find tetrehedra with vertices from both proteins and cut those tetrahedra in half. The tetrahedra are cut in half with one or 2 triangles using vertices on tetrahedron edges that connect an atom in one protein to an atom in the other protein. The vertices are placed midway between the atoms moved in by their vdw radii. They proposed 2 ways of coloring the surface. One colored vertices by how far apart the atoms were in the two proteins that were used to create that vertex. Red to blue shows short to long distances. The other coloring shows types of possible interactions between the two residues associated with the two atoms for the tetrahedron edge that the surface vertex splits. They gave different colors for predicted hydrogen bonding, hydrophobic packing, pi ... X, pi ... pi, same charges, opposite charges. Not sure what the pi bonding notation means. They also described how to flatten the 3-dimensional to a 2-dimensional surface with one to one correspondence between vertices and edges. Their method tried to come as close as possible to a conformal map. Conformal means the angles of the triangles stay the same to the extent possible. These calculations took a few seconds on 2000-5000 atom proteins. Here's my assessment. I think the concept of showing a protein interaction interface and coloring it to show interactions sounds useful for protein- protein interaction people. I think the flattening into 2 dimensions is probably not useful. Conformal maps greatly distort the area of the surface if it has curvature (you've seen the maps where Greenland is bigger than Africa, Americas, Asia and Europe combined). So the flattened surface is going to be hard to recognize as the interface, unless it is already pretty flat. If it is already pretty flat you might as weill just look at the 3-d surface. If we wanted to do something with interface surfaces I would suggest talking to Tanya Korteme. We already have all the infra-structure to create the surfaces. I would not use the Delauney surfaces, instead just use MSMS surfaces on both proteins showing only the parts associated with atoms in one protein that are within 5 angstroms of atoms in the other protein. The zone calculation code I wrote for multiscale could do that fast. We could offer a range of atom colorings that map onto the surface (hydrogen bonds, distance to nearest atom in other protein, charge complementarity, etc...). I don't have time or enough interest to work on this project. But perhaps someone else will. We have talked about collaborating with Tanya Korteme in the past and this would be a good opportunity. Tom

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Re: mdmovie/1508: instantaneous segmentation fault after clicking OK to multiple PDB molecular dynamics movie
by Sabuj Pattanayek 09 Mar '05

09 Mar '05

Hi, Thanks for looking into the problem. It would be nice to be able to read trr/xtc trajectories, but then would you also need to add functionality to read the gro file as well? Perhaps other Chimera users would also find these features useful. Thanks, Sabuj Pattanayek Eric Pettersen wrote: > Hi Sabuj, > I understand the problem now. My code is not expecting the > individual PDB files to have MODEL/ENDMDL records in them (the code is > placing these records around each file as it collates them). The > result is a mess. I will work on making my code more robust in this > regard. > There is a fairly easy workaround for you though: don't give the > -sep flag to trjconv. You will get a single file containing the > frames bracketed by MODEL/ENDMDL records (which is what Chimera would > have had to assemble anyhow), which you can read by using the "single > file" option of the PDB format trajectory reader. One caveat is that > the MD code expects the model numbers to start at 1, not 0, so you > will either have to renumber the MODEL records somehow, or delete > MODEL 0 from the file. I will also work on handling files where the > numbering starts at zero. > Do you work with Gromacs trajectories a lot? If you do, I could > put reading Gromacs trajectories directly on my to-do list. > > --Eric >

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Registration and VRML output for molecules
by Thomas Goddard 09 Mar '05

09 Mar '05

Julio Ortiz asks about registration behind a fire wall, and VRML output for molecules (ribbons, sticks, spheres). Tom ------- Start of forwarded message ------- Date: Wed, 09 Mar 2005 09:09:04 +0100 From: Julio Otiz <ortiz(a)biochem.mpg.de> To: Thomas Goddard <goddard(a)cgl.ucsf.edu> Subject: Registration-VRML-Chimera Hi Thomas: A couple of question: 1) Chimera registration: When I try to register from our institute, behind a firewall, I can not register, I received an error message as there were not internet connection. For my personal computer is not a problem. I can do it from home, but for other computers at the institute, it could be a problem. I would like to update all our versions from chimera, so..how to deal with the registration problem afterwards? 2) VRML export of pdb file representations: As far as I know Chimera can export surfaces of density maps to VRML format. It is possible to export some representation of a pdb files, like ribbons, sphere or sticks also to VRML?. There are some programs that do it, so maybe could be a nice feature to introduce in Chimera (if is not already possible). Greetings, Julio ------- End of forwarded message -------

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Combining ribbons and ball-n-stick using neon
by Todd Weaver 09 Mar '05

09 Mar '05

Dear Chimera- Wondering if there is a way to combine ball-n-stick rendered with neon and displaying distances as dashed lines with ribbons for other parts of the protein. I have attached an image captured with save, all looks good except the distances are not displayed as black lines because it has not gone through neon. If I run neon the ribbons do not show up. I would like to have both in the final image. Warmest regards, TOdd -- Todd M. Weaver, Ph.D. UW-La Crosse 1725 State Street Chemistry Department 4020 Cowley Hall La Crosse, WI 54601 Ph. (608)785-8269 Fax (608)785-8281

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suggestion
by Esther Garcia-Rodriguez 07 Mar '05

07 Mar '05

Hi, I am working with structure superposition and I have noticed that labelling relevant residues when two structures or more are superimposed is a bit of a nightmare. As the labels go to C-alpha in all cases it is very difficult to see anything. I would suggest to allow the user to change the default and be able to establish particular positions for labels, as well as the distance from the relevant atom. For example, label all selected residues in one chain at 0.1 angstroms from the CG atom and all of the second chain at 0.2 (in X or Y). Or maybe just been able to change the minimum distance between labels in all directions. Thanks, Esther Esther Garcia Rodriguez Henry Wellcome Building for Biocatalysis University of Exeter Stocker Road Exeter EX4 4QD United Kingdom

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