March 2005 - 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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C++ headers
by Eric Pettersen 28 Mar '05

28 Mar '05

Hi, We've made Chimera's C++ header files available for download from the Programmer's Guide main page: http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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[chimera-dev] Re: [Chimera-users] Zones to create inspector list of "contacts"
by Eric Pettersen 23 Mar '05

23 Mar '05

Tom, Wanted to alert you to a couple of functions in chimera.misc that will be in the next _production_ release: getAtoms(atomContainer) returns a list of atoms from various things (or lists of things) that can contain atoms, such as residues, sequences, molecules atomSearchTree(atomContainer, sepVal=5.0) returns a adaptive search tree of the atoms in the atomContainer (ala arg to getAtoms()). CGLutil.AdaptiveTree has docs for these trees. Typically searched with the 'searchTree' method. --Eric On Mar 23, 2005, at 11:37 AM, Thomas Goddard wrote: > Hi Grant, > > Below is some Python code that will create pseudobonds between all > pairs of selected atoms from different molecules that are within 3 > angstroms. > It is quite slow for large sets of selected atoms. It could be made > much > faster but I chose to keep it simple. > > Tom > > # > ----------------------------------------------------------------------- > ----- > # Check all pairwise distances between selected atoms and connect those > # atom pairs that are close by a pseudobond if the atoms belong to > different > # molecules. > # > # To run this use Tools / Programming / Idle to show the Python shell > and > # type > # > # >>> execfile('path-to-this-file.py') > # > # For large selected sets of atoms this will be slow. > # > > # > ----------------------------------------------------------------------- > ----- > # > def connect_close(dist): > > from chimera import selection, distance > atoms = selection.currentAtoms() > atom_pairs = [] > n = len(atoms) > for i1 in range(n): > a1 = atoms[i1] > for i2 in range(i1+1, n): > a2 = atoms[i2] > if a1.molecule != a2.molecule: > if distance(a1.xformCoord().xyz, a2.xformCoord().xyz) > <= dist: > atom_pairs.append((a1,a2)) > print len(atom_pairs), 'atom pairs' > > from chimera import PseudoBondGroup, PseudoBondMgr_mgr, PseudoBond > pg = PseudoBondMgr_mgr().newPseudoBondGroup('close contacts') > bonds = [] > for a1, a2 in atom_pairs: > bonds.append(pg.newPseudoBond(a1, a2)) > > import chimera > chimera.openModels.add([pg]) > > selection.setCurrent(bonds) > > # > ----------------------------------------------------------------------- > ----- > # > connect_close(3) > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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mrc file format difference in win-linux ??
by shrikant gutta 17 Mar '05

17 Mar '05

Hi all, I was working on the mrc file format difference between that of windows and linux. I couldnt figure out the difference between these file formats. (My job is to modify prog code to read linux_mrc`s on a windows software which can already read win_mrc`s in C++) I had got one site saying abt MRC specs: http://ami.scripps.edu/prtl_data/mrc_specification.htm i guess this site says abt win_mrc format no abt lin_mrc`s. I couldnt find anymore clues for my problem. Thanks & Regards Gutta __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Chimera-dev March 2005