October 2005 - Chimera-users - RBVI Mailing Lists

new version available
by Eric Pettersen 14 Dec '05

14 Dec '05

Hi all, We've put out a new version (1.2180) which we believe fixes the problems that some people were having on XP platforms. We're hoping that those of you that were having problems will try out the new version at your earliest convenience and let us know how it works. Thanks! Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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chimera and STRAP ?
by Dr. Christoph Gille 01 Nov '05

01 Nov '05

Hi, I contact you because users of the program STRAP for protein structures and sequences asked whether Chimera could be used within STRAP for visualization. Currently Jmol and Pymol are used for visualiziation. For example the results of 3D superpositions and the location of mutations can be viewed. But some users apparently prefere Chimera. My question is whether Chimera could be linked to STRAP as well. The most important point is, what mode of interprocess commmunication exists in Chimera. For example Pymol and STRAP are linked via the stdin/stdout streams. STRAP can send commands to Pymol and is notified when atoms are picked. STRAP uses the scripting language of Pymol to load proteins, create selections and rotate proteins. Could all this be done with Chimera in a similar way ? Best regards Christoph

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how to select multiple residues in multiple chains
by Eric Gillitzer 01 Nov '05

01 Nov '05

I work a lot with symmetrical, multi subunit structures and in order to select say residue 45 in every subunit, I must one at a time go in and in the sequence finder select the residue in each chain and then color it. Is there a way to select all of the same number residues (say number 45, might be an alanine) in the structure displayed and color only those. If you select alanine, it will select every single alanine in the structure. Chimera seems to be a really powerful program, but I am pulling my hair out trying to get it to do something productive in a timely fashion. thanks, eric.

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Re: [Chimera-users] Chimera and secondary structure annotations
by Thomas Goddard 28 Oct '05

28 Oct '05

Hi Julio, The secondary structure calculation requires all peptide backbone atoms. In the Chimera docs it notes: "Ksdssp uses the coordinates of the backbone atoms (N, CA, C, O, and optionally H) of a protein to determine which residues are in alpha helices and beta strands." There is no way in Chimera to determine secondary structure from just CA positions. The error message you sent for pdb2mrc is a bug in the AIRS package which is developed and maintained by Matt Baker (mbaker(a)bcm.tmc.edu) at Baylor College of Medicine, not our group. It is a problem in file C:\Programme\EMAN\chimeraext\Airs\airsIO.py It occurs because you have a model open in Chimera which is neither a density map surface nor a PDB model (maybe a molecular surface or a solid volume rendering?). The airsIO.py code does not handle that correctly. You could try running it with only the PDB model open in Chimera to avoid this problem. Alternatively you could edit the airsIO.py file with a text editor changing near line 32 from: if str(model.__class__)=="VolumeViewer.surface.Surface_Model": path=str(volume_data_set(model).data.path) elif str(model.__class__)=="chimera.Molecule": modelfile=model.openedAs path=str(modelfile[0]) if filecheck.strip()==path: path=os.path.abspath(model.name) to if str(model.__class__)=="VolumeViewer.surface.Surface_Model": path=str(volume_data_set(model).data.path) elif str(model.__class__)=="chimera.Molecule": modelfile=model.openedAs path=str(modelfile[0]) else: path = "" if filecheck.strip()==path: path=os.path.abspath(model.name) Just two lines are added the "else:" and the "path = ""'. Make sure to use this indentation if you make the change since that is important in Python code. I'll send the error message to Matt Baker. Tom > Date: Sat, 29 Oct 2005 01:58:48 +0200 > From: "Dr .Julio Ortiz" <ortiz(a)biochem.mpg.de> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Cc: meng(a)cgl.ucsf.edu > Subject: Re: Chimera and secondary structure annotations > > Dear Thomas and Elaine: > Thank you very much for your answers, I checked the ksdssp command and it works > for some pdbs, but not for those that I mentioned with the ribosomes. I think > that the problem is that some pdbs from ribosomes (like 1GIX and 1GIY) do not > have complete residues (just CAs). In the case of your images, you have use > 1PNS and 1PNU, and only those proteins in the 30S are complete. > I guess I need to contact some of the authors of the structures to see if the > complete coordinates are available. > > Another question: I installed the new version of Chimera and when using pdb2mrc > I received an error message: > ------------------------------ > Traceback (most recent call last): > File "C:\Programme\Chimera\share\__main__.py", line 59, in ? > value = chimeraInit.init(sys.argv) > File "C:\Programme\Chimera\share\chimeraInit.py", line 308, in init > tkgui.eventLoop() > File "C:\Programme\Chimera\share\chimera\tkgui.py", line 2725, in eventLoop > app.mainloop() > File "C:\Programme\Chimera\bin\Lib\lib-tk\Tkinter.py", line 965, in mainloop > self.tk.mainloop(n) > File "C:\Programme\Chimera\bin\Lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", > line 1751, in __call__ > _reporterror(self.func, args) > File "C:\Programme\Chimera\bin\Lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", > line 1814, in _reporterror > displayerror(msg) > File "C:\Programme\Chimera\bin\Lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", > line 1377, in displayerror > _errorReportFile.write(text + '\n') > File "C:\Programme\Chimera\bin\Lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", > line 1747, in __call__ > return apply(self.func, args) > File "C:\Programme\Chimera\share\chimera\baseDialog.py", line 229, in <lambda> > self.__buttonFuncName(txt))() > File "C:\Programme\EMAN\chimeraext\Airs\pdb2mrc.py", line 73, in Apply > targetPath=airsIO.getPath(target) > File "C:\Programme\EMAN\chimeraext\Airs\airsIO.py", line 32, in getPath > if filecheck.strip()==path: > UnboundLocalError: local variable 'path' referenced before assignment > > > ------------------------- > > I have already added the path of the EMAN in the tool menu. Could you tell me > what I am missing? > > > Thanks you very much, > Julio > > > > --------------------------------------------------------------------- > This message was sent using https://webmail.biochem.mpg.de > If you encounter any problems please report to rz-linux(a)biochem.mpg.de >

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Re: [Chimera-users] Chimera and secondary structure annotations
by Thomas Goddard 28 Oct '05

28 Oct '05

Hi Julio, The "ksdssp" command in Chimera will compute secondary structure for proteins. This uses the Kabsch and Sander algorithm. As far as I know you do not need any secondary structure info for the ribosomal RNA to make a nice ribbon. To use this command use Chimera menu entry Favorites / Command Line and then type ksdssp in the command entry at the bottom of the Chimera window. More details are in the Chimera manual: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html Here are some ribosome pictures I made with Chimera a few months ago. http://www.cgl.ucsf.edu/chimera/complexes05/bakeoff-talk.html Tom > Date: Fri, 28 Oct 2005 21:21:44 +0200 > From: "Dr .Julio Ortiz" <ortiz(a)biochem.mpg.de> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Chimera and secondary structure annotations > > Hi Thomas: > It is time for a couple of new questions about Chimera. > I am trying to generate some nice representations of the 70S ribosome showing > its proteins as ribbons, but the PDBs do not have annotations of secondary > structure. In many papers that I have seen the people use the program "Ribbons" > and a collegue suggested me also "DSSP" to generate the annotations and > visualize the results in "PyMOL". I am still fighting with some installation > problems, so I have not succeed yet in my original goal. > > The question for you is if Chimera, or some assotiated tool can generate the > annotations for secondary structure from a PDB file. In particular, do you have > some suggestions for the ribosome structures (large file with also RNA?). > > Thanks, > Julio > > > > -- > Max-Planck Institut für Biochemie > Abteilung Molekulare Strukturbiologie > Am Klopferspitz 18 > D-82152 Martinsried > Germany > Tel: +49 (89) 8578 2032 > fax: +49 (89) 8578 2641 > > --------------------------------------------------------------------- > This message was sent using https://webmail.biochem.mpg.de > If you encounter any problems please report to rz-linux(a)biochem.mpg.de

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list index out of range
by Paula Petrone 25 Oct '05

25 Oct '05

Hi, I am trying to load in an MD-ensemble, using a pdb and an X-plor file .dcd. For some reason, it gives me "IndexError: list index out of range". I generated the .dcd file myself (with Fortran). VMD program seems to have no problem with it. Is it a format problem? Is it a bug? Any suggestion? Thanks a lot! (I attach the files) paula

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Error when making Covalent bonds
by David Chenoweth 25 Oct '05

25 Oct '05

Hi! I am trying to pull up two molecules in chimera and link them by forming a covalent bond between a N and C atom. I am selecting only the N of one molecule and the C of the other. When I go to command line and use the bond sel command I get the following error message. Type error: Cannot form covalent bond joining two molecules. Does anyone know how to get around this. Thanks, David C.

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Benchmarks
by Mingfeng Yang 24 Oct '05

24 Oct '05

Just realized there must be some benchmarks on chimera's webpages, and I found them. :) Glad to provide the benchmarks from my systems. Benchmark 1: Computer: IBM T41 Graphics Card: ATI Radeon mobility M7 (32M?, not 100% sure) CPU: pentium-m 1.4GHz System Memory: 512M OS: Ubuntu GNU/LINUX 5.10 Driver for video card: the built-in open-source radeon driver from Xorg-x11 6.8.2 Chimera: version 1 build 2176 Benchmark scores: surface 147 mesh 127 contour 133 solid 128 recolor 68 Benchmark 2: Computer: HP XW5500 workstation Graphics Card: ATI FireGL 8800 (128M memory) CPU: pentium-4 2.4GHz System Memory: 512M OS: Gentoo GNU/LINUX Driver for video card: ATI fglrx driver 8.14.30 Chimera: version 1 build 2176 Benchmark score: surface 234 mesh 227 contour 142 solid 256 recolor 107 Something is confusing me. As you see that scores from benchmark 2 are higher than scores from benchmark 1. But in case that I want to save a protein structure as a png file, the rendering in system 1 is nearly two times faster. How can this happen? Best, Mingfeng Yang

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preferences file
by Boaz Shaanan 22 Oct '05

22 Oct '05

Hi, After upgrading to a new version, is it advisable to use a preferences file from the previous version (which is set up to turn on all sorts of things tuned to my liking) with the new one or are there possible issues of versions incompatibility which should rather be avoided ? I'd appreciate your advice. Thanks, Boaz Boaz Shaanan, Ph.D. Associate Professor Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone:972-8-647-2220 Fax: 972-8-647-2992 972-8-646-1710 E-mail:bshaanan@bgu.ac.il

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1.2180 on Windows
by Eric Pettersen 20 Oct '05

20 Oct '05

We are now aware that the 1.2180 release still doesn't work on some people's XP installations -- so don't rush out to try it! Seems fine on non-Windows platforms. I'll post something when I think we have a fixed version. Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Bug?
by Mingfeng Yang 19 Oct '05

19 Oct '05

Chimera version 1 build 2176, 1. start chimera, load in a protein 2. from help-->user guide, open firefox webbrowser to read help information 3. chimera main window becomes dead (black screen, not respond to mouse click and keyboard.) 4. close firefox browser, chimera goes back to normal OS: Gentoo linux, kernel-2.6.10 Firefox: version 1.07, build from gcc-3.4.4

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exporting ribbon models to vrml
by Doug Huff 18 Oct '05

18 Oct '05

Hello I work at Arkitek studios. We create rendered 3D for the science and technology crowd. I am a animator and have been charged with creating a rendering of a ribbon model in 3DS max (our software package). Your Chimera program displays the type of geometry I need and I can import vrml into my application. I can't seem to find the method to export ribbon models to vrml. When I use the multiscale models tools I always wind up with a surface model. Please remember I am not a scientist :) Thanks in advance for your help. Doug Huff 206 286 0337 http://www.arkitek.com

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ATI-Driver & Chimera hangs OS
by Mingfeng Yang 16 Oct '05

16 Oct '05

I am using Chimera build version 1 build 2176 on my Gentoo Linux platform, with ati firegl 8700 graphic card. After I upgraded the ati-drivers from 8.14.13 to 8.16.20, chimera will hang the whole system, everything dead, including the keyboard. I can only see the chimera window frame (the border), nothing else. What could be the problem? Thanks. Yang

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image use
by Rosalba.O'Brien＠informa.com 12 Oct '05

12 Oct '05

Dear Chimera I work for a small circulation trade publication, Animal Pharm. We are doing a story on small interfering RNAs for animal health and would like to use one of the images in the USCF Chimera image library to illustrate (the bluetongue one). Is this allowed? I'm afraid we don't have a budget to pay a fee but we are happy to credit whoever needs crediting. Thanks Rosalba O'Brien Latin America & Southern Europe Reporter Animal Pharm, World Animal Health & Nutrition News Informa Group 69-77 Paul Street London, UK EC2A 4LQ Tel. +44 (0)20 7017 5040 Email rosalba.obrien(a)informa.com Website www.animalpharmnews.com ******************************************************************************** The information contained in this email message may be confidential. If you are not the intended recipient, any use, interference with, disclosure or copying of this material is unauthorised and prohibited. Although this message and any attachments are believed to be free of viruses, no responsibility is accepted by T&F Informa for any loss or damage arising in any way from receipt or use thereof. Messages to and from the company are monitored for operational reasons and in accordance with lawful business practices. If you have received this message in error, please notify us by return and delete the message and any attachments. Further enquiries/returns can be sent to postmaster(a)tfinforma.com

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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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