September 2008 - Chimera-dev - RBVI Mailing Lists

add h
by Virginie Lafont 01 May '09

01 May '09

Hi, I am a new user of chimera and I already have a question. I have an protonated aspartic acid in my protein and I was wondering, is it possible to add hydrogen atom to aspartic acid with chimera? Thanks Virginie

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Hydrophobicity
by Leo O'Young 18 Sep '08

18 Sep '08

Hi I am new to the list, I am wondering if it is possible to increase the geometry of the Hydrophobicity-Surface models. Thanks, Leo

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reference guide: long walk off a short pier
by Eric Pettersen 16 Sep '08

16 Sep '08

To reduce the developer's maintenance load, we're looking to shave off parts that don't get much use. One item getting the hairy eyeball is the auto-generated Programmer's Reference Manual pages. Is anyone getting any value from these? If not, we will give them the heave ho. It will also save some on Chimera's download size (800K compressed for download; 21MB on disk). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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chimera import from unmodified python 2.5
by Ondrej Marsalek 12 Sep '08

12 Sep '08

hello everyone, first of all, i would like to say thank you for using vanilla python 2.5, i think this could be quite useful. unfortunately, there is one problem that keeps me from using chimera from a session of my regular python 2.5 installation (on ubuntu 8.04). after setting paths properly, an attempt to import chimera (or the binary module _chimera) produces the following exception: In [1]: import chimera --------------------------------------------------------------------------- <type 'exceptions.ImportError'> Traceback (most recent call last) /home/andy/<ipython console> in <module>() /home/andy/CHIMERA/share/chimera/__init__.py in <module>() <type 'exceptions.ImportError'>: /opt/chimera/lib/libwrappy2.so: undefined symbol: PyUnicodeUCS2_AsUTF8String In [2]: import _chimera --------------------------------------------------------------------------- <type 'exceptions.ImportError'> Traceback (most recent call last) /home/andy/<ipython console> in <module>() <type 'exceptions.ImportError'>: /opt/chimera/lib/libwrappy2.so: undefined symbol: PyUnicodeUCS2_AsUTF8String it seems that the python 2.5 provided with chimera is compiled with different unicode settings than the one in ubuntu. the shared chimera objects are compiled against that version of python and therefore can't be used from my normal python. the only way i see around this at the moment is to recompile chimera, but i wanted to leave that as the very last option. i would appreciate any suggestions, as a straightforward way to use chimera from my normal python would be really neat. i'll be glad to provide details if anyone is interested. regards, ondrej marsalek

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structure analysis feature in UCSF Chimera
by Serge Gorelsky 08 Sep '08

08 Sep '08

Hello, would it be possible to add the two following features to the "Tools/Structure Analysis" menu of UCSF Chimera: the distance between atom A and a plane of other 3 atoms B,C,D ("the height of a trigonal pyramid with atoms B, C, D at the base ") and the angle between an axis (defined by atoms A and B) and the plane B-C-D ? Thank you very much in advance. -- Best regards, Serge Gorelsky (a Chimera user since 2005)

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