July 2006 - Chimera-users - RBVI Mailing Lists

about installation of Chimera in SUSE Linux 10.0 plateform
by Ching-Yi Hsieh 31 Jul '06

31 Jul '06

Hi, I have trouble to install Chimera in in SUSE Linux 10.0 plateform. Can you e-mail me the detail instruction about how to install soon??? Best, Dr. ChingYi Hsieh UCDavis Cancer Center

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Chimera and DelphiController
by Nihshanka Debroy 31 Jul '06

31 Jul '06

Hi, My name is Nihshanka Debroy, and I am a graduate student at Duke University. I recently joined this mailing list. I was wondering if I could ask a couple of questions about the software. The first one is more related to Delphi. I have been using the Delphi Controller tool in Chimera, and I have been getting warnings that certain radii records are missing from my .siz file, and some residues have a net positive charge. I used the default files provided when installing Delphi. I was wondering if anyone has faced this problem before. Is there an online database where I could get the missing radii and charge values for atoms and residues ? Secondly, I am trying to generate the Connolly surface for certain proteins. What I have been doing so far is running Delphi Controller and assigning a probe radius of 1.4 Angstroms in the Parameter section. I just wanted to make sure that this is different from the molecular surface (MS) that is generated when simply choosing Actions->Surface->Show. Thank you for your time. Sincerely, Nihshanka

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Segmentation Fault
by Donglu Xie 24 Jul '06

24 Jul '06

Hi All, Anybody has met this issue. When running chimera, it only shows "Segmentaion Fault", or " Segmentaion Fault (core dump)". No interface is shown. If you need more information about the system, please let me know. Any help is appreciated. Donglu Xie

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Surface color key
by Alexander Rusnak 19 Jul '06

19 Jul '06

Hey Folks, I'm using Chimera to create a surface colored representation of a virus based on radius. That was not the hard part, my question is how do you make a key to show the scale of coloring. I cannot find that in the documentation, faq nor the server list. If it's there and I missed it sorry but you point it out to me and if it's not an option any suggestions on how to create one. Thanks. Alex

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write out adjusted EM map?
by jbrown 19 Jul '06

19 Jul '06

Hi, I've recently used Chimera to manually fit several PDB subunits into my EM map. I am trying to figure out a way to write out the EM map in CCP4 format with the adjusted rotation/translations that I performed during my fit. Is there anyway to do this in Chimera (or are there any other programs you would suggest)? Also, any plans to include a means for writing out EM maps from Chimera in future versions? Thanks a lot, Jesse --------------------------- Jesse Brown Research Technician TSRI, Dept. of Cell Biology 858.784.8598 jbrown(a)scripps.edu

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chimera on linux ia64 (sgi prism)
by Sabuj Pattanayek 14 Jul '06

14 Jul '06

Hi, I was wondering if there is a port for chimera to run on Linux IA64 (sgi prism)? The x86 version runs in emulation mode on the system, thus the graphics defaults to Mesa indirect glx (really slow). Would a dev be willing to port it for this system if given access to the system? I'm also working on getting pymol compiled for it. vmd already has a native port with good performance. Thanks, Sabuj Pattanayek

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matchmaker command
by Haas, Ryan Matthew 10 Jul '06

10 Jul '06

Dear Chimera Users, How does the matchmaker command perform its superposition? Is it a C-alpha superposition, or just backbone atoms, or all atoms? Is it appropriate to use these RMSD values obtained from "mmaker" in a manuscript? Help is greatly appreciated. Matthew Haas

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Re: [Chimera-users] script for residues w\in zone
by Eric Pettersen 06 Jul '06

06 Jul '06

On Jul 6, 2006, at 1:54 PM, Sorani, Marco wrote: > Thanks. I'm running Chimera and Python\IDLE on Windows XP. > > a) Can I still use the "script.com" you suggested? You could, by getting a UNIX-shell-like environment such as Cygwin (www.cygwin.com) or possibly just from the DOS prompt. If you don't care if Chimera's interface shows as the script runs, you could just run Chimera and then use File...Open to run the script. > b) When I try "script.py", I can't find the module "chimera" or > "chimera.py". Where should I look? script.py will only work if Chimera is the interpreter, rather than a stand-alone Python interpreter. So you need to either run "chimera -- nogui script.py" using methods like in the previous answer, or open the script using Chimera's main File...Open dialog. --Eric

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script for residues w\in zone
by Sorani, Marco 06 Jul '06

06 Jul '06

Hi, A question: For a given PDB structure (say, 1J4N) and a given point mutation (say, C104K), I want to find all residues within 5 angstroms. Manually, this is easy to do with 'Select' --> 'Zone...', but if I have 1000 mutations, is there a way to automate the process and send results to a file? ****************** soranim(a)pharmacy.ucsf.edu Marco Sorani Program in Biological & Medical Informatics University of California, San Francisco

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