- Chimera-users - RBVI Mailing Lists

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?

2 3

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

1 0

yet another snapshot
by Eric Pettersen 06 Apr '05

06 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

1 0

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, > ------------------------------------------------------------------------ >

1 0

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

2 1

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)

2 1

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

1 0

Mac OS X stereo
by David Belnap 28 Mar '05

28 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 ============================================

5 5

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 >

1 0

1.2104 snapshot release available
by Eric Pettersen 18 Mar '05

18 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

1 0