- Chimera-users - RBVI Mailing Lists

superimpose --matchmaker.
by Vinay Kumar 19 Dec '07

19 Dec '07

Hi all, There have been a few posts previously regarding superimposing of molecules. using matchmaker would work for a pdb file. I was curious if small molecules (ligands) could be matched. I did check out the documentation and the command match. But what i am not sure abt is, in wht format should the input file for a small molecule be?? could someone suggest!! regards, Vinay

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Question regarding multiple mutant in the same chimera session
by Jean-Didier Maréchal 18 Dec '07

18 Dec '07

Hi, Is there a way to copy, in the same instance of chimera, a model X time? I'd like to generate different mutant of the same prot and have them stocked in the same session of chimera. Cheers, JD -- Dr. Jean-Didier Maréchal Assistant Professor Computational Bioorganic and Bioinorganic Chemistry @Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona 08193 Bellaterra, Spain Tel: +34.(0)1935814936 Fax: +34.(0)1935812920 e-mail:jeandidier.marechal@uab.es

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rmsd cluster analysis
by Francesco Pietra 18 Dec '07

18 Dec '07

Is it feasible to command a cluster analysis from rmsd? I would like to group for likeliness snapshots from MD with respect to, say, the structure from which MD was started. Thanks francesco pietra ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

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Problem with Chimera under Windows XP
by Peter Girard 18 Dec '07

18 Dec '07

I am running release 2304 of Chimera under Windows XP with service pack 2 on a Dell Inspiron 9300 laptop. The image disappears from the screen for no apparent reason. With the structures I am currently working on, this has become frequent and often occurs after just a few seconds when I click anywhere in the Chimera window. I have found that if I use Model Panel, I can get the picture back by clicking the 'Shown' box to remove the tick mark, then clicking it again to re-insert the tick. But the picture soon disappears again. Occasionally, it doesn't disappear completely, but part of it collapses, or spurious long lines appear. I had the same problem with a previous release, 2184, and was disappointed that upgrading didn't fix it. I can find no mention of anything similar in the documentation or email archive. Can anyone suggest a possible cause? Peter Girard (University of Nottingham, UK)

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Regarding getSequence
by Jean-Didier Maréchal 18 Dec '07

18 Dec '07

Hi again, I'd like to return the sequence of the protein I opened in chimera in the python shell. >From what I read through, I thought that chimera.getSequence could be used to do so. I was thinking in a simple script beginning with : import chimera s=chimera.getSequence(0,0) .. However the chimera.getSequence(0,0) comes back with: Traceback (most recent call last): File "<pyshell#50>", line 1, in ? chimera.getSequence(0, 0) File "CHIMERA/share/chimera/Sequence.py", line 614, in getSequence File "CHIMERA/share/chimera/Sequence.py", line 656, in getSequences AttributeError: 'int' object has no attribute 'residues' and chimera.getSequence(0,A) with Traceback (most recent call last): File "<pyshell#48>", line 1, in ? chimera.getSequence(0,A) NameError: name 'A' is not defined Did I understand correctly the role of getSequence? if yes, what would be the correct syntax please? Thanks a lot! All the best, JD -- Dr. Jean-Didier Maréchal Assistant Professor Computational Bioorganic and Bioinorganic Chemistry @Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona 08193 Bellaterra, Spain Tel: +34.(0)1935814936 Fax: +34.(0)1935812920 e-mail:jeandidier.marechal@uab.es

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Re: [Chimera-users] Chimera-users Digest, Vol 56, Issue 14
by Jonathan Hilmer 17 Dec '07

17 Dec '07

Ryan, Try this as a way to figure out what you can do with an object: dir(chimera.selection.currentResidues()[0]) In the above command I've indexed the list of selections to return just one object, and the dir() function will return a list of names defined by the currentResidues module. It should contain something like the following: ... 'addAtom', 'atomNames', 'atoms', 'atomsMap', 'bondedTo', 'count', 'findAtom', 'findRangeAtoms', 'getDefaultRibbonStyle', 'hasRibbon', 'id', 'isHelix', 'isHet', 'isSheet', 'isStrand', 'isTurn', 'kdHydrophobicity', 'label', 'labelColor', 'labelOffset', 'molecule', 'numAtoms', 'oslChildren', 'oslIdent', 'oslLevel', 'oslParents', 'oslTestAbbr', 'removeAtom', 'ribbonBinormals', 'ribbonCenters', 'ribbonColor', 'ribbonData', 'ribbonDisplay', 'ribbonDrawMode', 'ribbonFindStyle', 'ribbonFindStyleType', 'ribbonFindXSection', 'ribbonNormals', 'ribbonResidueClass', 'ribbonStyle', 'ribbonXSection', 'selLevel', 'type' If you try: chimera.selection.currentResidues()[0].type it will return a string with the 3-letter aa code, and the other options displayed by dir() will output useful things such as more strings, lists, or other objects that can be likewise explored. Try this combination: mySel = chimera.selection.currentResidues()[0] print "%s, %s" % (mySel.oslIdent(), mySel.type) On my test structure it returns '#0:127.A, ARG'. The second line is equivalent to 'print str(mySel.oslIdent() + ", " + mySel.type)', but the formatting I used in the above example helps to keep things clean if you have a complicated output that needs to have a specific format. There are some more advanced features of that approach detailed here: http://www.python.org/doc/1.5/tut/node45.html Jonathan > Date: Fri, 14 Dec 2007 19:55:39 -0500 > From: Ryan <pavlovicz.7(a)osu.edu> > Subject: Re: [Chimera-users] printing "zone" search > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <17bf4817f850.17f85017bf48(a)osu.edu> > Content-Type: text/plain; charset=us-ascii > > Hi Eric, thanks for your help. I'm getting closer to achieving the results i'd like. > > So i've been able to properly select the residues within a specified radius of my ligand, but am a little confused as to how Chimera handles the selection list. If i try: > > print chimera.selection.currentResidues() > > i get a list like this: > > > [<_chimera.Residue object at 0x578d2020>, <_chimera.Residue object at 0x578cbfb0>, ... ] > > but if i try: > > for x in chimera.selection.currentResidues(): > print x > > i get output that is much closer to what i'm looking for: > > > #0:499 > > #0:496 > > ... > > What is the reason for the difference between these two forms of output that seem to be accessing the same list? Also, is there a way i can get more detailed output with residue names and numbers, such as ['#0:TYR499','#0:TRP496',...]? > > Sorry if these questions are answered elsewhere, but i could not find the answers online. Is there a document out there that can teach me how to better master the Chimera Python modules for scripting? I'm no Python expert -- i've so far only been learning things as i need them. Thanks again, > > ryan

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Re: [Chimera-users] other/5067 (error adding hydrogens)
by Eric Pettersen 17 Dec '07

17 Dec '07

Hi Jean-Francois, I have seen this error reported, but only very rarely (maybe once a year at most). Is there any chance you can tell me how to reproduce it? --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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setting pdb path for local mirror
by Moo Cow 17 Dec '07

17 Dec '07

Sorry for an easy question. Chimera has a hook to use a local mirror of the PDB (preferences-PDB) I am too thick to see what path to give it. If you have the PDB, you have the top level /blah/blah/pdb the structure directory /blah/blah/pdb/data/structures/all and the divided directory /blah/blah/pdb/data/structures/divided/pdb When a non-python reader looks at the code (__init__.py), it seems to be trying out the divided directory IDcode = IDcode.lower() subpath = IDcode[1:3] + os.sep + "pdb" + IDcode + ".ent" pdbDir = systemPDBdir() if pdbDir is not None: ..... but this does not look correct. The PDB divided path would want subpath IDcode[1:2] to get the subdirectory "pt" from a file like "5pti" Many thanks and sorry for a seemingly daft question. -- Got No Time? Shop Online for Great Gift Ideas! http://mail.shopping.com/?linkin_id=8033174

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Loading .dx maps to chimera
by maya shcushan 17 Dec '07

17 Dec '07

Dear sir, I am trying to load a .dx file (electrostatic potential) onto a molecule in chimera. I successfully loaded the map onto a the molecule's surface. The problem is the potentials I get look differently than the original map. That is, the potentials appear different in the visualization tool of PMV, the program which generated the .dx file I tried to e-load on chimera. Thanks, Maya Schushan, Tel-Aviv university, Israel.

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crystallographic symmops and lattice translations in Chimera
by Boaz Shaanan 16 Dec '07

16 Dec '07

Hi, Since the question was raised before, I think I know the answer to my first question about lattice translations but let me verify: 1) Chimera can apply crystallographic symmetry operations to the model as they're listed in the pdb file but it won't apply lattice translations, or in other words, won't display molecules in neighbouring unit cells. Am I correct ? maybe you can surprize me me on this and prove me wrong ? 2) Is it possible to draw the unit cell boundaries after reading in the pdb or should I read in a dummy pdb with coordinates of the unit cell vertices ? Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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