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October 2009

43 participants
52 discussions

segmentation fault
by Francesco Pietra 01 Oct '09

01 Oct '09

Hi: On Debian Linux i386 squeeze I had the X system broken while attempting to install the gnome cd burner "brasero". I purged everything about that bad code, installed and reconfigured the X system, however something is still broken. Attempts at launching CHIMERA returned "segmentation fault". That also sitting in the directory where chimera is installed ( /usr/local/chimera/bin). As I had an old version, I reinstalled chimera-1.3-linux.exe, while that did not solve the above problem. I do not remember where to put the hands in such cases. Thankful for reminding me about that. francesco@deb32:~$ gcc --version gcc (Debian 4.3.4-2) 4.3.4 francesco pietra

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Re: [Chimera-users] Solvent Accessible Surface Area
by Elaine Meng 01 Oct '09

01 Oct '09

On Sep 28, 2009, at 10:46 AM, Thiruvarangan Ramaraj wrote: > Hi Elaine, > I am using Chimera for identifying the surface residues. > > I select areaSAS > 0.05 square angstroms, is this same as saying > areaSAS > 5%, I am getting confused with the numbers 5% and 0.05 sq > angstroms have these been switched some how or are they curiously > the same in the following statement? > > I just need some help in understanding. > Thank You > Sincerely > -Thiru Ramaraj Hi Thiru, In Chimera there is no percentage (%) measurement, it is only the area value in square angstroms. Some other programs give % exposed for a residue, which is a ratio of the area of that residue in your structure to the area of the same type of residue in some theoretical unfolded state. See for example the GetArea server, which gives "Ratio(%)": <http://curie.utmb.edu/area_man.html> However, what Chimera reports is just the surface area of the atom or residue in your structure. To choose surface residues, I'd probably use a bigger cutoff, say select :/areaSAS>10 but it depends on what you are going to do with the results. You can try different values and see what looks reasonable. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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