- Chimera-users - RBVI Mailing Lists

Solvent Accessibility
by Vincent Lynch 12 Oct '05

12 Oct '05

To Whom It May Concern, I am new to Chimera (and molecular modeling in general) and cant figure out if I can color by residue accessibility to solvent and see the raw value of solvent accessibility. Thanks Vinny

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matchmaker alignment
by Boaz Shaanan 11 Oct '05

11 Oct '05

Hi, Is it possible to save as a file (or print) the alignment that is produced by matchmaker between two structures that are read in ? Thanks, Boaz

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DBFILTER_2.2.8 released
by Sheng-Hung Wang 10 Oct '05

10 Oct '05

Dear all: DBFILTER_2.2.8 has been released. This version fixed the bug in counting for H-bond donors & acceptors! Please UPDATE your version to v2.2.8. Download site: CADD toos in Drug R&D http://home.pchome.com.tw/team/gentamicin/mol/mol.htm ------------------------------------------------------------------------- DBFILTER can check the mol2 format database, and pick out any problematic structure which results in "segmentation fault" of DOCK during flexible docking. (for example, salt or structure which contains multi-moleculars built in....) And DBFILTER will output a new database which you want. There are also 12 kinds of filters for spotlighting drug-like properties. Including: Allowed_atoms, Molecular_weight, LogP, H_bond_donors, H_bond_acceptors, Sum_of_N+O, Halogens, Rings, Max_ring_members, Rotatable_bonds, CH3(CH2)n- , CF3(CF2)n-. To enable LogP filter, XLOGP should be run first to calculate your database by: xlogp -m database.mol2>logp.in File 'logp.in' is needed for dbfilter. XLOGP can be download from FTP site of Institute of Physical Chemistry, Peking University. ( ftp://ftp2.ipc.pku.edu.cn/pub/software/xlogp ) ___________________________________________________ ��°� Yahoo!��Ħ��rͨӍ 7.0 beta��M�W·�Ԓ�� http://messenger.yahoo.com.tw/beta.html

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adding chain IDs
by Eric Pettersen 07 Oct '05

07 Oct '05

Hi, Since it's a lot easier to do things in Chimera when a file has chain IDs, Maximilian Andrews wrote a script (below) for adding chain IDs to files that lack them. It does require that TER cards be present at the end of chains, but those are a lot easier to add than chain IDs. Enjoy! Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu #! /usr/bin/env python # Filename: rename_pdb_for_chimera.py ###################################################################### # # # Created: Maximilian N. Andrews, July 18, 2005 # # Ciamician, Bologna University # # # # Function: # # # # This script adds a chain ID to all the subunits (column 22) in # # the PDB file. # # The chains are named 'A','B','C',etc. until all of the subunits # # have been labeled. # # # # For the subunits to be renamed properly the PDB must contain a # # line beginning with TER after each subunit, for example: # # ... # # ATOM 1570 OXT HIE 103 24.590 -9.249 30.054 # # TER # # ATOM 1571 N SER 104 16.936 7.767 30.236 # # ... # # # # Notes: # # # # The original file is first read by the script, then copied to a # # backup file - with the same name, but with "~" added at the end # # of it - and then it is renamed and saved with the original name. # # # # Usage: # # # # rename_pdb.py arg1 arg2 # # arg1 is the the number of chains that have to be renamed; # # arg2 is the name of the input file; # # example: rename_pdb.py 4 MY_PDB.pdb # # # ###################################################################### import sys import os def BAILING_OUT(N_ARG): """ The srcipt needs two arguments: [int] The number of subunits to be renamed; [str] The name of the PDB file to be renamed. The correct use of this script is: rename_pdb.py arg1 arg2 arg1 is the number of chains in the protein; arg2 is the name of the input file; example: rename_pdb.py 4 MY_PDB.pdb """ if N_ARG != 3: print BAILING_OUT.__doc__ sys.exit() else: return BAILING_OUT(len(sys.argv)) NUMBER_CHAINS = sys.argv[1] PDB_IN = sys.argv[2] print 'Number of chains is: ',sys.argv[1] print 'The PDB file to rename is: ',sys.argv[2] PDB_OUT = PDB_IN PDB_BAK = PDB_IN+'~' f = open(PDB_IN,'r') lines = f.readlines() f.close() print 'Making backup file '+PDB_BAK+'...' os.rename(PDB_IN,PDB_BAK) print '...done!' print 'Renaming '+PDB_IN+'...' CHAIN = 65 # this is the integer that corrisponds to the character "A" MAX_CHAIN = int(NUMBER_CHAINS) + CHAIN LETTER = chr(CHAIN) NEW_PDB = [] for i in range(len(lines)): line = lines[i] if line.startswith('TER'): CHAIN = CHAIN + 1 if CHAIN < MAX_CHAIN: LETTER = chr(CHAIN) else: LETTER = ' ' if line.startswith('ATOM'): newline=line[0:21]+LETTER+line[22:] NEW_PDB.append(newline) elif line.startswith('TER') and len(line) > 21: # just in case there's a chain identifier in the "TER" line... (the condition len (line) is added just in case the TER line is a just few characters long... i.e. it would add a blank space at the start of the following line) newline=line[0:21]+' '+line[22:] NEW_PDB.append(newline) else: # if line doesn't start with either ATOM or TER, it will print it as is NEW_PDB.append(line) print '...done!' print 'Writing renamed file '+PDB_OUT+'...' f = open(PDB_OUT,'w') for i in range(len(NEW_PDB)): f.write(NEW_PDB[i]) f.close() print '...done!'

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chimera trouble
by flints16 cvd 07 Oct '05

07 Oct '05

Hi Sorry to say this but chimera does not work on win xp, and every computer on campus uses xp, ah so no luck there. Thanks --------------------------------- Yahoo! for Good Click here to donate to the Hurricane Katrina relief effort.

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movie recorder command file help
by Pullan, Lee 05 Oct '05

05 Oct '05

Hi, I am using the movie recorder in Chimera with the command line file, as suggested in the tutorial. What do I enter into the command file in order to switch objects on and off and also how do I change properties like transparencies/colors? Thanks Lee Pullan, PhD Center for Structural Biology Department of Biochemistry and Molecular Biology University of Texas - Houston Medical School Houston TX 77030 Tel: 713 500 6121

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Invitation: Chimera Workshop Announcement - UCSF November 17&18, 2005
by Scooter Morris 05 Oct '05

05 Oct '05

Dear Chimera User: The Resource on Biocomputing, Visualization, and Informatics (RBVI) is going to be holding our Fall UCSF Chimera Workshop on November 17&18, 2005 at the UCSF Mission Bay Campus in San Francisco, CA. More details about the workshop, and a link to the registration form are available at http://www.cgl.ucsf.edu/Outreach/Workshops/. We have also attached a brochure about the workshop which may be distributed amongst any interested colleagues. There are only 30 slots available, so we would recommend that you sign up as soon as possible. Thanks! -- scooter

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Moving molecules independently in chimera
by David Chenoweth 29 Sep '05

29 Sep '05

Hi! I am a new chimera user and was just wondering if someone could tell me how to move a single molecule in chimera when I have two open. I have two separate small molecule pdb files and I want to open both in the same chimera session. I also want to be able to move one independent of the other so I can overlay the two. Once they are overlayed I would also like the option of adjusting either or moving both together. Thanks in advance for the help. David C.

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Re: [Chimera-users] color-by-element in v. 2172
by Elaine Meng 22 Sep '05

22 Sep '05

Hi Boaz, It is the same procedure as before. However, it sounds like the coloring target is set to something that does not include atoms and bonds. Look in the Actions... Color menu; the default is "all of the above" which would include "atoms/bonds." However, if the coloring target is set to "ribbons" or "background" (for example) there is nothing to color by element. This is most likely what is happening, since with the "all of the above" setting, the copy of 1.2172 I'm using does color by element as before. I hope this helps, 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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color-by-element in v. 2172
by Boaz Shaanan 22 Sep '05

22 Sep '05

Hi, On the new v. 2172 release candidate, I tried to 'colour by element' a selection of residues in the color panel and got a reply "Nothing applicable to color by element". This is true for both windows and linux. I did this many times before, so has something gone wrong or is there a different path I have to follow to get this type of coloring with the new release ? Thanks for your help. Boaz

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Symmetric copies of molecules
by Thomas Goddard 21 Sep '05

21 Sep '05

Hi Ed, I wrote a Chimera command to show symmetry related copies of a molecule. As you move the original molecule relative to a density map the positions of all the symmetry copies are automatically updated. I tested this with Chimera version 1.2172 just released yesterday. I don't think it will work with earlier versions of Chimera because of some function name changes we made. http://www.cgl.ucsf.edu/home/goddard/temp/symcopies.tar This archive contains a directory SymmetryCopies that you put in your Chimera distribution in chimera/share (or on a Mac in Chimera.app/Contents/Resources/share). Then when you start Chimera you will have two new Chimera commands "sym" and "~sym". The symmetry matrices are read from the REMARK 350 BIOMT records in the PDB file header. Probably you will need to put those matrices in by hand with a text editor. Below is an example. The matrices represent the symmetry of the density map. It would make more sense to put them in the map file header but that is not as easy since it is a binary format file. Once you open your PDB file with the BIOMT matrices in the header and display your density map type sym to the Chimera command-line (menu Favorites / Command Line). This will create copies of the molecule for each symmetry matrix (that is not the identity). If you freeze the density map by turning off the checkbutton in the Active column in Model Panel (menu Favorites / Model Panel) and then move the original molecule with the mouse, all symmetry copies will be moved using the BIOMT positioning matrices in the coordinate frame of the density map. To remove the symmetry copies issue the command: ~sym This is a Chimera convention that tilde in front of a command undoes the command. Here are some more details. If you have multiple molecules opened in Chimera you can specify which one to use in the sym command using the model's id number listed in the Model Panel dialog. For example sym #0 The density map shown in the volume viewer dialog will be used as the reference coordinate system for applying the symmetries. If you want to specify which map to use as the reference coordinate system give a second model id number: sym #0 #1 If you are showing symmetry for multiple models you can remove the symmetry copies for just one molecule by giving its model id number with the ~sym command: ~sym #2 Here is an annoying little problem. If you use the Unshow button on the volume dialog it removes the density map surface model and forgets its orientation. The symmetry copies of the molecule will no longer have their positions updated. Even if you redisplay the map by pressing the Show button, the symmetry repositioning will no longer work. You'll have to use ~sym followed by sym to get it working again. If you want to hide the map you can use the checkbutton in the Model Panel dialog to hide it without actually deleting the surface, so the symmetry copies will continue to have their positions updated. Another problem to look for. Chimera can only handle about 100,000 atoms before it gets slow. Also it uses a few Kbytes of memory per atom. If you specify alot of symmetry matrices you can quickly create a large number of atoms. You may need to limit the symmetry matrices in the PDB header to keep the total number of atoms down. Let me if this command does what you want. I had fun experimenting with it. It should make it into a future Chimera release. We plan on making a production release in early October but have a feature freeze in effect so it will not be in that release. Tom Example BIOMT matrices in PDB file 1fav (3-fold axis of symmetry) REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 35.81900 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 17.90950 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 31.02016 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000

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release candidate
by Eric Pettersen 20 Sep '05

20 Sep '05

So we've put a release candidate on the download page (http:// www.cgl.ucsf.edu/chimera/download.html) We're hoping that if you have the time, you'll download it and bang on it and let us know about any bugs you find before it turns into a production release. It's been a _long_ time since the previous production release (December of last year). Here are the major highlights: General ----------- -> selections can be inverted (Select menu, "select" command, arrow keys) -> additional arrow key functions: left: undo selection shift-left: clear selection right: invert selection in models with selections shift-right: invert selection in all models -> PDB file writing can be restricted to displayed and/or selected atoms -> Chimera scene can be exported (formats: X3D, POV-Ray, Renderman, VRML [latter surfaces only]) -> Actions...Set Pivot sets center of rotation w/o zooming -> Help...Search Documentation searches local documentation -> Tools menu reorganized -> balloon help over bonds/pseudobonds includes length -> residue labels now positioned at centroid of displayed atoms -> new residue attribute "isHet" (whether residue is in HETATM PDB records) -> nucleic-acid ambiguity codes can be used in subsequence searching (R=A/G, Y=C/T/U, N=A/C/G/T/U) -> switched to Python 2.4 New Tools --------------- -> Attribute Calculator (Structure Analysis): generate new numerical attributes from existing ones; calculate totals or averages of an attribute -> Color Zone (Volume Data): color surface patches near selected atoms with those atoms' colors [for GRASP surfaces and Volume Viewer/ Multiscale surfaces rather than standard molecular surfaces] -> Demo Editor (Demos): graphical interface for creating demos -> Movie Recorder (Utilities): capture image frames from Chimera and assemble them into a movie file -> Surface Capping (Depiction): cap surfaces where they intersect a clipping plane (giving the illusion of the surface as a solid object rather than a hollow object) -> Surface Color (Volume Data): color surfaces according to volume data or geometry (distance from a point, plane, or axis) -> Electrostatic Surface Coloring (Surface/Binding Analysis): specialization of preceding tool to facilitate coloring with electrostatic volume data; also replaces DelphiViewer -> Surface Zone (Surface/Binding Analysis): restrict GRASP or Multiscale Models surface display to zone around selected atoms -> Values at Atom Positions (Volume Data): map volume data to atom positions; create atom attributes with the values -> 2D Labels (Utilities): create arbitrary text labels and place them in 2D Tool Changes -------------------- -> Benchmark (Utilities): now also benchmarks molecule display performance -> Demos (Demos): new Hormone-Receptor Complex demo -> Lighting (Viewing Controls): new simplified interface available -> MatchMaker (Structure Comparison): can include secondary- structure term in the alignment score and can iterate the fit -> MD Movie (formerly Movie; Utilities): new "md:" prefix for metafiles; add step size option for playback; RMSD map calculation speeded up; can automatically recolor RMSD map for contrast; ability to collect atom occupancy data and display it with Volume Viewer; user-friendly interface to Movie Recorder for generating movie from trajectory -> MultAlign Viewer (Structure Comparison): all-gap positions can be omitted from saved files; all headers available as residue attributes in associated structures; more sophisticated conservation measures available (calculated with AL2CO program); headers can be saved to a file or loaded from a file; structure association info can be saved to a file -> Multiscale Models (Higher-Order Structure): separate surfacing threshold for CA-only chains -> Nucleotides (Depiction): now assigns a pucker value to all sugar atoms (plane/envelope/endo/exo) -> Per-Model Clipping (Depiction): new slab mode to show just a slice of a model -> ViewDock (Surface/Binding Analysis): saves in sessions; H-bond statistics can included in the columns of ligand descriptors (and used for sorting) -> Volume Viewer (Volume Data): major interface reorganization; added support for UHBD electrostatic potential (binary only), gOpenMol, and PROFEC grid formats; support added for non-orthogonal crystal data New Commands ------------------------ -> 2dlabels: command-line version of 2D Labels tool -> movie: command-line version of Movie Recorder tool -> writesel: command-line version of Actions...Write List Command Changes ----------------------------- -> color: can now also color ribbons -> British spellings added for gray, color, and center -> match: added "iterate" keyword to allow pruning bad pairs until worst pair is below a threshold -> matchmaker (mmaker): added keywords corresponding to new MatchMaker tool abilities -> select: new keyword for inverting selections -> write: keywords for restricting to displayed/selected atoms Documentation ---------------------- -> new Attributes tutorial: covers Render by Attribute, Surface Area/ Volume, Attribute Calculator, and advanced command-line usage full release notes are at: http://www.cgl.ucsf.edu/chimera/docs/ relnotes/1.2172.html Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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OS X Native
by William Sofer 20 Sep '05

20 Sep '05

Hi, We're using Chimera for educational purposes for a university program aimed at high school teachers and students. I love the program, but am a bit frustrated by the lack of an aqua version for OS X. Do you plan on developing a native version for OS X 10.4? Bill Sofer Professor Dept. Genetics Waksman Institute Rutgers University Piscataway, NJ 08854

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creating a symmetric tetramer from a PDB file for a monomer?
by gtseng＠mail2.vcu.edu 14 Sep '05

14 Sep '05

Dear Chimera creators: Could you please let me know whether it is possible to create a tetramer structure with 4-fold symmetry from a PDB file for a monomer? Specifically, I want to create a structure of a voltage-gated K channel which has 4 monomers surrounding a central pore symmetrically, beginning with the PDB file for a monomer. There is no 'transformation matrix' in the PDB file to allow me to create the tetramer easily. Thank you very much for your help! Gea-Ny Tseng

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Re: [Chimera-users] Re: stereo viewing on Windows
by Kishor Kulawade 12 Sep '05

12 Sep '05

Hello, Thank you very much for your reply. We have the required hardware here. We have NVidia Quadro FX 3400/4400 video card. I am trying to figure out how to start stereo mode on Windows XP machine. Documentation states that append the desired options and inputs to the command in the target field. What command should I type in Target field to start stereo mode. If you can provide any kind of help with that, would be wonderful Thanks >>> Greg Couch <gregc(a)cgl.ucsf.edu> 9/9/2005 4:50 PM >>> For the --stereo option to work you need a graphics card that supports "stereo in a window" (consumer/gaming cards only do full screen stereo) and the associated special glasses that alternate which eye can see the screen at any moment. Those graphics cards are the workstation graphics cards -- the 3DLabs Wildcat series, the ATI FireGL series and the NVidia Quadro series. See <http://www.3dlabs.com/>, <http://www.ati.com/products/workstation.html>, or <http://www.nvidia.com/page/workstation.html> -- stay away from the versions designed for 2D applications and make sure the card you buy has a stereo connector. High-quality glasses (and the emittors that control them) can be purchased from StereoGraphics Corporation, <http://www.stereographics.com/>. Cheaper alternatives exist, but we don't have any experience with them (google for "stereo glasses"). Make sure that the emittor that controls the glasses works with the graphics card you get (there are different connectors out there). Hope this helps, Greg Couch UCSF Computer Graphics Lab gregc(a)cgl.ucsf.edu On Fri, 9 Sep 2005, Virginia B. Pett wrote: > Date: Fri, 9 Sep 2005 16:26:16 -0400 > From: Virginia B. Pett <pett(a)wooster.edu> > To: chimera-users(a)cgl.ucsf.edu > Cc: Kishor Kulawade <kkulawade(a)wooster.edu> > Subject: [Chimera-users] Re: stereo viewing on Windows > > We have windows XP machine in one of our labs. The machine is running > chimera. We want to run chimera in stereo mode on this machine. as per the > documentation, create a shortcut of chimera on the desktop and then append > "--stereo" options in target mode. But target mode does not recognize this. > Which file helps start the stereo mode on windows machine, so that i can put > that file path in target? > > > ________________________________________ > 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] Re: stereo viewing on Windows
by Eric Pettersen 12 Sep '05

12 Sep '05

Hi Virginia, Another thing to note is that in the target field, the path to the Chimera executable is embedded in double quotes (e.g. it is something like: "C:\....\chimera.exe"). To add the --stereo option, you need to add it outside the ending double quote and separated by a space, like this: "C:\...\chimera.exe" --stereo . Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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phi psi angles
by Zenon Grabarek 12 Sep '05

12 Sep '05

Hello, I am looking for a script that would allow me to change the phi psi angles in a selected residue (allowing the C-terminal part of the chain to move) and output the coordinates. Chimera has a very nice interactive tool to do that, but I need to do it systematically in small increments over a specified range of angles. I would be grateful for any help in this matter. Zenon Grabarek Ph.D. Boston Biomedical Research Institute 64 Grove St. Watertown MA 02472 tel: 617-658-7805 email: Grabarek(a)BBRI.org

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Re: stereo viewing on Windows
by Virginia B. Pett 09 Sep '05

09 Sep '05

We have windows XP machine in one of our labs. The machine is running chimera. We want to run chimera in stereo mode on this machine. as per the documentation, create a shortcut of chimera on the desktop and then append "--stereo" options in target mode. But target mode does not recognize this. Which file helps start the stereo mode on windows machine, so that i can put that file path in target? ________________________________________ 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 On Sep 7, 2005, at 3:00 PM, chimera-users-request(a)cgl.ucsf.edu wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. creating a symmetric tetramer from a PDB file for a monomer? > (gtseng(a)mail2.vcu.edu) > 2. Re: creating a symmetric tetramer from a PDB file for a > monomer? (Elaine Meng) > 3. Visualizing Electrostatic Potential of *.grd format? > (Anna Feldman-Salit) > 4. Re: Visualizing Electrostatic Potential of *.grd format? > (Elaine Meng) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 06 Sep 2005 15:53:41 -0400 > From: <gtseng(a)mail2.vcu.edu> > Subject: [Chimera-users] creating a symmetric tetramer from a PDB file > for a monomer? > To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Message-ID: <200509061953.PAA18668(a)despina.vcu.edu> > Content-Type: text/plain; charset=iso-8859-1 > > Dear Chimera creators: > Could you please let me know whether it is possible to create a > tetramer structure with 4-fold symmetry from a PDB file for a monomer? > Specifically, I want to create a structure of a voltage-gated K > channel which has 4 monomers surrounding a central pore symmetrically, > beginning with the PDB file for a monomer. There is no 'transformation > matrix' in the PDB file to allow me to create the tetramer easily. > Thank you very much for your help! > > Gea-Ny Tseng > > ------------------------------ > > Message: 2 > Date: Tue, 6 Sep 2005 13:48:50 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] creating a symmetric tetramer from a PDB > file for a monomer? > To: <gtseng(a)mail2.vcu.edu> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <7485CA73-9B1A-492C-9F71-FB36FBF5B103(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > Hello Gea-Ny, > The Chimera features that generate multimers (the tools Unit Cell > and Multiscale Models) all use matrix information in the PDB file. > Multiscale Models uses BIOMT, MTRIX, SMTRY, and/or CRYST1 records, > and Unit Cell uses MTRIX, SMTRY, and/or CRYST1. > > It sounds like you don't have any of those in your PDB file. > > You could either > (A) figure out what information should be in such a matrix line > and edit it into your file before using one of the Chimera tools, > or > (B) open four copies of your monomer and try to position them > by hand. If you know what the axis of rotation should be, you > can use Constrained Move (Tools... Movement... Constrained Move > in recent versions) to define and use an axis of rotation. > http://www.cgl.ucsf.edu/chimera/1.2065/docs/ContributedSoftware/ > constrained/constrained.html > > Neither of these is very easy, but I don't know of any way to > automatically position the monomers without the matrix information. > It sounds like BIOMT (REMARK 350) records would be the most > appropriate. Even with an appropriate example, you would still > have to change the values. > > REMARK 350 is described at the PDB web site (you have to scroll > down to get to the description of REMARK 350): > http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_31.html > > Here is an example from 1fav (threefold): > REMARK 350 > REMARK 350 BIOMOLECULE: 1 > REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C > REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 > REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 > REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 > REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 35.81900 > REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 > REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 > REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 17.90950 > REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 31.02016 > REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 > > I hope this helps, > 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 Sep 6, 2005, at 12:53 PM, <gtseng(a)mail2.vcu.edu> wrote: > >> Dear Chimera creators: >> Could you please let me know whether it is possible to create a >> tetramer structure with 4-fold symmetry from a PDB file for a monomer? >> Specifically, I want to create a structure of a voltage-gated K >> channel which has 4 monomers surrounding a central pore symmetrically, >> beginning with the PDB file for a monomer. There is no 'transformation >> matrix' in the PDB file to allow me to create the tetramer easily. >> Thank you very much for your help! >> >> Gea-Ny Tseng >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > > ------------------------------ > > Message: 3 > Date: Wed, 07 Sep 2005 13:14:05 +0200 > From: Anna Feldman-Salit <anna.feldman-salit(a)eml-r.villa-bosch.de> > Subject: [Chimera-users] Visualizing Electrostatic Potential of *.grd > format? > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <431ECB7D.8090203(a)eml-r.villa-bosch.de> > Content-Type: text/plain; charset=us-ascii; format=flowed > > Dear All, > > I would like to ask you a question regarding the visualization of > electrostatic potential on msms. For this purpose, of course, I need a > readable format for Potential Map. > In the past I used to work with DelPhi for potential calculations and > then visualize the outputted *.14 file by Chimera. > Today I calculate potentials by using UHBD program, while output files > are saved in /phi/ format with .grd extension (could be written either > in binary or ascii form). > Unfortunately, the Chimera doesn't recognize this format. > > Dear Chimera users, do you know the way to convert the *.grd files to > the *.phi ones readable by Chimera, or any other trick? > I can't recalculate the potentials by DelPhiController, because I have > only one dat-file for both radii sizes and charges (it also doesn't > work > in the simple way). > > I'd very appreciate any help of yours! > > Yours sincerely, > > Anna. > > ------------------------------ > > Message: 4 > Date: Wed, 7 Sep 2005 09:16:40 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Visualizing Electrostatic Potential of > *.grd format? > To: Anna Feldman-Salit <anna.feldman-salit(a)eml-r.villa-bosch.de> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <6902E794-4AAB-438D-A8D8-FB8E8849D7D6(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > Hi Anna, > Actually, Chimera does read UHBD grids, the binary version. The older > approach to displaying potential on a surface, DelPhiViewer, is being > phased out in favor of the newer and more general tool, Surface Color > (Tools... Surface/Binding Analysis... Electrostatic Surface Coloring > or Tools... Volume Data... Surface Color both open this tool). > > Surface Color can color surfaces based on any of the volume data (3D > grid) formats that can be read by Volume Viewer (which include UHBD > binary): > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/ > volumeviewer.html#formats > > Surface Color is relatively new. It is available in the snapshots > 1.2154 (linux, mac) and 1.2143 (windows). It is also available in > 1.2105, but I don't recommend using that one because we have made it > easier to use in the more recent snapshots. Here is the man page for > Surface Color in version 1.2154: > http://www.cgl.ucsf.edu/chimera/1.2154/docs/ContributedSoftware/ > surfcolor/surfcolor.html > > I hope this helps, > 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 Sep 7, 2005, at 4:14 AM, Anna Feldman-Salit wrote: > >> Dear All, >> >> I would like to ask you a question regarding the visualization of >> electrostatic potential on msms. For this purpose, of course, I >> need a readable format for Potential Map. >> In the past I used to work with DelPhi for potential calculations >> and then visualize the outputted *.14 file by Chimera. >> Today I calculate potentials by using UHBD program, while output >> files are saved in /phi/ format with .grd extension (could be >> written either in binary or ascii form). >> Unfortunately, the Chimera doesn't recognize this format. >> >> Dear Chimera users, do you know the way to convert the *.grd files >> to the *.phi ones readable by Chimera, or any other trick? >> I can't recalculate the potentials by DelPhiController, because I >> have only one dat-file for both radii sizes and charges (it also >> doesn't work in the simple way). >> >> I'd very appreciate any help of yours! >> >> Yours sincerely, >> >> Anna. >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 29, Issue 5 > ********************************************

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Rotation Angle
by Huang, Zhong 07 Sep '05

07 Sep '05

Hi, dear chimera developers' I am a Chimera user of UT Medical school at Houston . Here I want to know how chimera rotates the loading structure. I wish to know what the rotation parameters mean? Which coordinate sysmtem they refere to? I check the on-line tutorial. Unfortunately, I didn't get the answer. Best Zhong Huantg

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[Chimera-users] Visualizing Electrostatic Potential of *.grd format?
by Anna Feldman-Salit 07 Sep '05

07 Sep '05

Dear All, I would like to ask you a question regarding the visualization of electrostatic potential on msms. For this purpose, of course, I need a readable format for Potential Map. In the past I used to work with DelPhi for potential calculations and then visualize the outputted *.14 file by Chimera. Today I calculate potentials by using UHBD program, while output files are saved in /phi/ format with .grd extension (could be written either in binary or ascii form). Unfortunately, the Chimera doesn't recognize this format. Dear Chimera users, do you know the way to convert the *.grd files to the *.phi ones readable by Chimera, or any other trick? I can't recalculate the potentials by DelPhiController, because I have only one dat-file for both radii sizes and charges (it also doesn't work in the simple way). I'd very appreciate any help of yours! Yours sincerely, Anna.

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Suggestion re Docking Results
by Philip Crawford 06 Sep '05

06 Sep '05

Hi. I like Chimera and hit a limit yesterday. (Windows version.) We are running DOCK using the ZINC databases, which produces very large output_scored.mol2 files. I tried using Chimera to open and sort one of these. After an hour, I killed Chimera. John Irwin suggested (via the Dock-fans list) that I recommend you set a limit on the size of output file to be opened. An alternative may be to set a limit on the number of records which will be read, regardless of file size. Thanks for a useful product. Cheers, Philip Crawford __________________________________________________ Philip Crawford, B. Comp. Sc., MIEEE Structural BioInformatics and Drug Design Group http://www.sbio.med.unsw.edu.au/sbio School of Medical Sciences The University of NSW Phone: +61-2-9385 2564 Mobile: +61-419-294 698 Fax: +61-2-9385 1059 Email: <mailto:p.crawford@unsw.edu.au> p.crawford(a)unsw.edu.au __________________________________________________

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changing the rendering of distanced dotted lines
by Boaz Shaanan 06 Sep '05

06 Sep '05

Hi, Distances between pairs of atoms are marked as dotted lines by the 'distances' panel. Is it possible to make those dots bigger by scaling them up somehow so that they are seen more clearly ? They obviously get larger when I zoom in but sometimes I'd rather stay in the zoom-out view but make the dots more visible. Please let me know. Thanks, Boaz

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[Chimera-users] Save pdb files only have 5 subunits at 5-fold at virus?
by Jason 04 Sep '05

04 Sep '05

Hi all Is it possible to save pdb files that only have 5 subunits at 5-fold after using mulitscale tools buliding virus paritle. And this pdb file can open at other programs too, ex: DeepView, PyMOL. When I use File/Save PDB chimera can save pdb file, but this file(model) only can show correctly at chinera. If I opened this file at PyMOL or DeepViewit only show the origional 3(A, B, C)chain model thanks Jason

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Using the Chimera Tutorial
by Gea-Ny Tseng 31 Aug '05

31 Aug '05

Dear Chimera creators: I am trying to learn how to use Chimera by using your on-line Tutorial. Is there a printable version of the Tutorial and User's Guide? I am not sure how to read the Tutorial and then try out the commands using one single monitor (that is all I have). Or did I miss something obvious? Your help is highly appreciated? Gea-Ny Tseng, PhD Physiology Virginia Commonwealth University

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helices display in latest snapshots
by Boaz Shaanan 30 Aug '05

30 Aug '05

Hello, I the latest snapshots (Windows 2143 and linux 2154) helices show up as thin worms when I ask for 'ribbons' under action (they used to look like nice ribbons in previous releases). I found the tools/depiction/ribbons display and managed somehow to change the look of the ribbons (still, they looked nicer before) but failed to change the look of the helices. Where can I do this now ? Thanks, Boaz

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