- Chimera-users - RBVI Mailing Lists

Changes after 1.3
by Jon Rumbley 12 Jan '09

12 Jan '09

I noticed you were going to remove the DelPhi interface after Chimera ver 1.3. I have used this interface to generate electrostatic surfaces in Chimera for both teaching and research, will there be something replacing it? Thank you, Jon Rumbley Dr. Jon N. Rumbley Assistant Professor Dept. of Chemistry and Biochemistry/ Dept. of Pharmaceutical Sciences University of Minnesota-Duluth 253C SSB 1035 Kirby Dr. Duluth, MN 55812 Phone: 218-726-7423 email: jrumbley(a)d.umn.edu

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Higher Order
by hsosa＠aecom.yu.edu 11 Jan '09

11 Jan '09

I have another related question: If I were to deposit a PDB coordinates file of a helical structure, what would be the best place to put helical symmetry information (the file includes the full coordinates for only one asymmetric unit) so that chimera can generate a model with more than one asymmetric unit ?. The idea being to be able to see the contacts between asymmetric units and the symmetry of the complex. Should I use the the SMTRY, or the MTRIX entries ?. Does it make any difference in chimera ?. Thanks Hernando . -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

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Higher order
by hsosa＠aecom.yu.edu 11 Jan '09

11 Jan '09

Hi, Is it possible to use the tools in: Higher Order Structures > Multiscale Models to generate full atomic models (with atoms and all the display capabilities of chimera) from the symmetry entries in the PDB file (SMTRY entries) ? So far I been able to produce only a rough surface representation of the symmetry related molecules. Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

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Re: [Chimera-users] delphi
by Elaine Meng 08 Jan '09

08 Jan '09

Hi everybody, I'm happy to report that Chimera (version 1.4 builds Jan 8, 2009 and later) can now read electrostatic potential maps from the Intel Mac version of DelPhi provided by the Honig lab as of mid-2008: <http://wiki.c2b2.columbia.edu/honiglab_public/index.php/ Software:DelPhi_System_Requirements> The problem was that part of the potential file was written in double precision. Their group may be updating that executable so that it does not write double precision, but either way, the newer builds of Chimera will be able to read the maps. This does not solve the problem Darren was having, I assume using a PPC Mac rather than an Intel Mac. The PPC Mac version of DelPhi from the Honig lab still requires certain library files that I don't think are freely available. The Honig web site (URL above) does mention this issue. Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 30, 2008, at 4:55 PM, Elaine Meng wrote: > Hi Darren, > Unfortunately it is an unsolved problem getting a pre-made delphi > executable for Mac OSX that gives results that can be shown in > Chimera. Just to clarify for everybody, DelPhi is a program freely > provided by another group, but without official support. > > I went through several weeks of trying to get an older executable from > the Honig site to work, installing various files myself just as you > have. Here is the chimera-users message where I describe running up > against this wall: > <http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-November/ > 001113.html >> > > I reported these problems to the Honig group, and some months later > (July 2008) they updated their Mac OSX Intel executable so it does not > require these additional libraries. Maybe you downloaded an > executable before that time or have a PPC Mac rather than Intel. > Honig group DelPhi download page: > <http://wiki.c2b2.columbia.edu/honiglab_public/index.php/ > Software:DelPhi_System_Requirements >> > > However, although the Intel executable runs nicely and can be > controlled by DelPhiController, something about the map format changed > and Chimera cannot read the result. We were unable to get information > from the Honig lab on how the format changed, or even reverse-engineer > the changes given our example maps. There is nothing else we can do - > it is a limitation recorded in our database as problem report #6228.

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question about measuring volume via command line and the nogui option
by Bruno Villoutreix 07 Jan '09

07 Jan '09

Dear Chimera Users i am new to chimera, is it possible using something like: chimera --nogui open myfile.mol2 and then i would like to measure the area and volume...but i am not sure which command to use. I can get the surface with this command but to get the volume, i have to use the graphic interface, i do not see either the name of the command in the command history list... thanks if you can give me some advices Bruno

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problem with new release
by Lionel Nauton 06 Jan '09

06 Jan '09

hi all, I don't know if everyone else have this problem, but i 'm not able to use the last release of chimera (chimera-1.3.2577-linux.exe <https://www.cgl.ucsf.edu/cgi-bin/chimera-get.py?file=linux/chimera-1.3.2577…>) installation script works well, but when I try to start the program, i have a black screen , and my session shutdown and restart, it seems that chimera fall down my Xorg. I'm working on PC linux ( X86_64), but i used the 32 bits version of chimera, ( test with X86_64 version give the same result), my pc linux work with fedora 10 , i have no problem with chimera-1.3.2540-linux.exe thanks per advance for your answer ================================================= NAUTON Lionel Ingénieur d'études. Laboratoire de Synthèse Et Etude de Systèmes à Intérêt Biologique UMR6504 : université Blaise Pascal – CNRS 24, avenue des Landais – Campus des Cézeaux 63177 AUBIERE Cedex France Tel : 04 73 40 55 06 mèl : lionel.nauton(a)univ-bpclermont.fr <mailto:lionel.nauton@univ-bpclermont.fr> site web : http://seesib.univ-bpclermont.fr/site_web/pageaccueil.htm <http://seesib.univ-bpclermont.fr/site_web/pageaccueil.html> =================================================

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delphi
by Darren Thompson 05 Jan '09

05 Jan '09

I installed the ibm compiler libraries on Mac OSX tiger, but delphi still does not see them Applications System Folder mach.sym Applications (Mac OS 9) TheVolumeSettingsFolder mach_kernel Desktop (Mac OS 9) Trash opt Desktop DB Users private Desktop DF Volumes sbin Desktop Folder automount sw Developer bin tmp Documents cores usr Library dev var Network etc System mach the opt folder (ibm) is there. I did a symbolic link to the Mac OSX executable in the /usr/local/ release1.1/exe directory to /usr/bin/delphi, downloaded the example files from delphi's website, [psb-232-45:release1.1/examples/example_1] darren% delphi param_1 dyld: Library not loaded: /opt/ibmcmp/lib/libxlf90.dylib Referenced from: /usr/bin/delphi Reason: image not found Trace/BPT trap when I try directly [psb-232-45:local/release1.1/exe] darren% ./delphiMacOSX dyld: Library not loaded: /opt/ibmcmp/lib/libxlf90.dylib Referenced from: /usr/local/release1.1/exe/./delphiMacOSX Reason: image not found Trace/BPT trap Does it matter that it's looking for /libxlf90.dylib and I have / libxlf90.A.dylib? Have some xmas charity Help a newb Darren Thompson Graduate Student UCSC 1156 High St. Santa Cruz, CA 95064 831-459-3390 voice 831-459-2395 fax http://people.ucsc.edu/~ministry

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Motivational Posters, Demotivators
by Breann Crenshaw 02 Jan '09

02 Jan '09

Rofl Motivational Posters http://www.roflposters.com

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Re: [Chimera-users] Chimera - calculating surface area?
by Elaine Meng 29 Dec '08

29 Dec '08

On Dec 29, 2008, at 8:54 AM, Uli Strych wrote: > Hi Dr. Meng, > I would like to calculate the surface exposed area of only the > hydrophobic amino acid residues for my protein of interest. > I saw your email (at > http://www.ccl.net/cgi-bin/ccl/message-new?2008+03+07+013+raw ) where > you explain how to do so using Chimera. > My problem is the "Attribute Calculator" step, where I don't seem to > be able to find the correct format of entering the formula to > calculate the surface area of the residues that I have previously > selected in the Render/Select menu. Hi Uli, Another necessary step is to show the surface (which creates the surface area values): command "surface" or menu "Actions... Surface... show". You could do that for the whole protein before selecting the residues, or just for the selected residues, either way is fine. That will assign values for the residue attributes named areaSES (solvent-excluded surface area) and areaSAS (solvent- accessible surface area). Then in "Attribute Calculator" you would Calculate attribute [some name, doesn't matter] for [models] Formula: sum(residue.areaSES) with these options checked on: "Restrict formula domain to current selection, if any" (only sum over the selected residues, not all residues) "Open Render/Select by Attribute" (because this dialog will show the answer, the sum value) You want a "models" attribute because you want only one number, the sum over the selected residues. Click Apply (or OK, which would also dismiss the calculator dialog) to calculate the value and show it in the Render/Select by Attribute dialog. Of course, you could use areaSAS instead of areaSES as you prefer. The SES is probe contact and re-entrant surface, and is shown in Chimera. The SAS is where the probe center goes, about 1.4 Angstrom farther out from the molecule, not shown in Chimera. Attribute Calculator manual page: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calcula… > This tool is also used in the Attributes tutorial, part 2: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html#p… > I hope this helps! Best regards, 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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transparent background error
by odonnell＠chem.fsu.edu 23 Dec '08

23 Dec '08

Hi, I can't find a previous entry in the archives for an error message i receive when i impose a transparent background. As soon as i read in a map i receive this: Runtime error! ProgramC:\Program Files (x86)\Chimera\bin\pythonw.ese R6025 -pure virutal function call Hitting OK I receive... Chimera failed abnormally; the exit code was:255. Thanks in advance for any advice!!!! -Jason ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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