- Chimera-users - RBVI Mailing Lists

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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