- Chimera-dev - RBVI Mailing Lists

new Programmer's Example
by Eric Pettersen 15 Jan '13

15 Jan '13

The examples in the Programmer's Guide now include one that discusses the basics of how to measure various atomic-level quantities. http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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How to install? - continued
by pythonchemia Gazeta.pl 14 Jan '13

14 Jan '13

hi, Mr Eric and Greg I would like to thank you for your valuable suggestions. In fact, it would be better to use the Chimera 1.6. 2 or 1.7. Thank you Mr. Greg and Eric. Yours sincerely - Janusz Grabowski

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Re: [chimera-dev] [Chimera-users] How to install ?
by Greg Couch 10 Jan '13

10 Jan '13

And it would help to use a more recent version of Chimera, either version 1.6.2 or the 1.7 release candidate. The newer releases have newer versions of Python and MMTK embedded in them with the associated improvements and bug fixes. -- Greg On 01/10/2013 11:30 AM, pythonchemia Gazeta.pl wrote: > > I have Chimera 1.5 with Python IDLE v 2.7 and Windows XP and MinGW.

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Re: [chimera-dev] [Chimera-users] How to install ?
by Eric Pettersen 10 Jan '13

10 Jan '13

Hi Janusz, Chimera has its own self-contained Python environment, so in order to install these packages so that you can use them from within Chimera you will need to use Chimera's Python whenever the installation procedure for a package calls on you to execute a Python script. For a script with no arguments that would be: chimera --nogui installation-script.py and for scripts with arguments: chimera --nogui --script "installation-script.py argument1 argument2 ..." On non-Mac platforms you can find the chimera executable in: <your chimera installation>/bin On Macs it is in: Chimera.app/Contents/Resources/bin While the 1.5 version of Chimera is nice enough, I would encourage you to upgrade to the 1.7 release candidate, which has many improvements. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jan 10, 2013, at 11:30 AM, pythonchemia Gazeta.pl wrote: > Dear Chimera Team ! > > I intersted in chemistry. I use chimera 1.5 software for personal purposes, non - commercial. > Chimera is a very usefull Tool. I like it :). I know Python language a little. I'm beginner programmer. > I have Chimera 1.5 with Python IDLE v 2.7 and Windows XP and MinGW. My website is pythonchemia.aq.pl > I have some questions: > > 1 - How to install pDynamo library ? from https://sites.google.com/site/pdynamomodeling/home for Chimera 1.5 automatically or manually ? > > 2 - How to install OpenBabel library ? from openbabel.org/wiki/Main_Page for Chimera 1.5 automatically or manually ? > > 3 - How to install Biopython library ? from http://biopython.org/wiki/Main_Page for Chimera 1.5 automatically or manually ? > > Please help me ! - I wait on answer. > Sorry for my english > > Yours sincerely - Janusz Grabowski > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Hello~ how to make a 3D structure for a number of family genes
by tao zhao 03 Dec '12

03 Dec '12

Hello,I am new to chinmera, this tool seems really powerful. Here is my question, I want to build a structure for a number of peptide sequences, all belongs to the AP2 family.It has one homology NMR model, PDB ID: 1gcc. And I don't know what to do next. Could you please give me some instruction?Thank you very much. Tao ZhaoNorthwest A&F University,Yangling, China

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atom.anisoU does update as expected for MD trajectories
by Ryan Harrison 26 Nov '12

26 Nov '12

Dear Chimera team, I've encountered a problem with atom.anisoU. Since class Atom is implemented in C++, and I don't have the technical sophistication or nerve to build chimera from scratch after the dire warning, [1<http://www.cgl.ucsf.edu/chimera/sourcecode.html>] I seek council. I'm using PDB ANISOU to store orientation information from a coarse grained model. Using PDB MODEL and PDB ENDMDL I output trajectory information. PDB atom coordinates and aniso change with each frame in the trajectory. When visualizing a coordSet in the trajectory, atom.coord() updates as expected... # m1 is a model with ANISO information >>> m1.activeCoordSet = m1.coordSets[2] >>> m1.atoms[1].coord() chimera.Point(-0.268, 0.002, 0.08) *# <~~~ As expected from PDB file* >>> m1.activeCoordSet = m1.coordSets[10] >>> m1.atoms[1].coord() chimera.Point(0.012, -0.276, -0.043) *# <~~~ Changes as expected from PDB file* However, atom.anisoU does not update as expected [2<http://www.cgl.ucsf.edu/pipermail/chimera-users/2012-February/007246.html>, 3<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-December/003377.html>]. It is always the PDB ANISO information from the last model (last MD trajectory) in the file... >>> m1.activeCoordSet = m1.coordSets[2] >>> m1.atoms[1].anisoU *# <~~~ ANISO for last model in PDB file, not model 2 * array([[ 0.0296, 0.0182, 0.0201], [ 0.0182, 0.0844, -0.0055], [ 0.0201, -0.0055, 0.1258]], dtype=float32) >>> m1.activeCoordSet = m1.coordSets[10] >>> m1.atoms[1].anisoU *# <~~~ Again, ANISO for last model in PDB file, not model 10* array([[ 0.0296, 0.0182, 0.0201], [ 0.0182, 0.0844, -0.0055], [ 0.0201, -0.0055, 0.1258]], dtype=float32) The result is visualizations with proper coordinates (update properly for each frame in trajectory) but inaccurate ellipsoids (ANISO does not update; fixed as last frame / last model). *Work around 1 (Failed):* Since *aniso* takes spec atom-spec as an input, I tried specifying a model and position in trajectory. Unfortunately, this doesn't seem to be possible [4<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> ]. *Work around 2 (Tedious):* Since *aniso* can take submodels, I import (cannot use nifty MD Movie tool) as sub-models instead of as a trajectory. I can then apply aniso to each submodel, which works as expected, and switch submodels on/off sequentially to make a movie (5<http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-April/003800.html>). This is not ideal since I'm missing out on the ease of use of the MD Movie tool, and it's very cumbersome to move through a stack of submodels to emulate a trajectory. Thank you for your time and please help! Best, Ryan -- Ryan M Harrison Wolfson College University of Oxford NIH-Oxford Graduate Partnership Program http://graylab.jhu.edu/~ryan/ http://www.linkedin.com/in/rmharri

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sort a list of residues based on the id.position values
by Jean Didier Pie Marechal 26 Oct '12

26 Oct '12

Hi guys, how could I sort a list of residues based on their id.position value? thanks a lot jd Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://asklipio.qf.uab.es ----- Missatge original ----- De: chimera-dev-request(a)cgl.ucsf.edu Data: Dijous, Octubre 18, 2012 9:00 pm Assumpte: Chimera-dev Digest, Vol 102, Issue 5 > Send Chimera-dev mailing list submissions to > chimera-dev(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev > or, via email, send a message with subject or body 'help' to > chimera-dev-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-dev-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-dev digest..." > > > Today's Topics: > > 1. Re: Moving a residue and an VRML object (Tom Goddard) > 2. Re: Moving a residue and an VRML object (Greg Couch) > 3. Re: Moving a residue and an VRML object (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Wed, 17 Oct 2012 13:25:18 -0700 > From: Tom Goddard <goddard(a)sonic.net> > To: ladam <ladam(a)smbh.univ-paris13.fr> > Cc: chimera-dev(a)cgl.ucsf.edu > Subject: Re: [chimera-dev] Moving a residue and an VRML object > Message-ID: <507F142E.4080906(a)sonic.net> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > The arrow you drew has no idea that the atoms have moved, so of > course > it doesn't move with them. If you just want to rigidly rotate the > whole > molecule in Python you can change the matrix that places it in space > > mol.openState.xform = xf > > instead of changing the coordinates of atoms. Then you could > rigidly > move the VRML model in the same way so that the arrow stays in the > same > position relative to the molecule. > > vrml.openState.xform = xf > > If you are not moving the molecule rigidly then you really do need > to > move individual atoms and then you will have to delete the old > arrow and > make a new arrow if it is intended to have its ends follow certain > atoms. > Tom > > > -------- Original Message -------- > Subject: [chimera-dev] Moving a residue and an VRML object > From: ladam > To: chimera-dev(a)cgl.ucsf.edu > Date: 10/17/12 4:45 AM > > Hi all, > > I have a problem associating a vrml object an a molecule : > > Let's say I have an arrow created using the bild format to which > I gave > > 0.0 0.0 0.0 coordinates. > > This arrow and the molecule translate/rotate together using the > mouse.> Now if I translate / rotate my molecule using the setcoord > command on > > the atoms in a python script, the arrow won't follow up the > molecule.> I tried the addAssociatedModel command to link the arrow > and the > > molecule but still the same result. > > How can I handle this? > > Thanks for your attention > > > > > > ------------------------------ > > Message: 2 > Date: Wed, 17 Oct 2012 15:21:35 -0700 > From: Greg Couch <gregc(a)cgl.ucsf.edu> > To: Tom Goddard <goddard(a)sonic.net> > Cc: chimera-dev(a)cgl.ucsf.edu, ladam <ladam(a)smbh.univ-paris13.fr> > Subject: Re: [chimera-dev] Moving a residue and an VRML object > Message-ID: <507F2F6F.30800(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Salut, > > The other trick is to give the VRML model the same model id and > submodel > id as its associated model. Then the openState is identical, so > there > would be no need to copy the transformation matrix. Again, this > only > works for rigid rotations. > > -- Greg > > On 10/17/2012 01:25 PM, Tom Goddard wrote: > > The arrow you drew has no idea that the atoms have moved, so of > course > > it doesn't move with them. If you just want to rigidly rotate > the > > whole molecule in Python you can change the matrix that places it > in > > space > > > > mol.openState.xform = xf > > > > instead of changing the coordinates of atoms. Then you could > rigidly > > move the VRML model in the same way so that the arrow stays in > the > > same position relative to the molecule. > > > > vrml.openState.xform = xf > > > > If you are not moving the molecule rigidly then you really do > need to > > move individual atoms and then you will have to delete the old > arrow > > and make a new arrow if it is intended to have its ends follow > certain > > atoms. > > > > Tom > > > > > > -------- Original Message -------- > > Subject: [chimera-dev] Moving a residue and an VRML object > > From: ladam > > To: chimera-dev(a)cgl.ucsf.edu > > Date: 10/17/12 4:45 AM > >> Hi all, > >> I have a problem associating a vrml object an a molecule : > >> Let's say I have an arrow created using the bild format to which > I gave > >> 0.0 0.0 0.0 coordinates. > >> This arrow and the molecule translate/rotate together using the > mouse.>> Now if I translate / rotate my molecule using the setcoord > command on > >> the atoms in a python script, the arrow won't follow up the > molecule.>> I tried the addAssociatedModel command to link the > arrow and the > >> molecule but still the same result. > >> How can I handle this? > >> Thanks for your attention > >> > > > > _______________________________________________ > > Chimera-dev mailing list > > Chimera-dev(a)cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev > > > > ------------------------------ > > Message: 3 > Date: Wed, 17 Oct 2012 15:26:03 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > To: ladam <ladam(a)smbh.univ-paris13.fr> > Cc: chimera-dev BB <chimera-dev(a)cgl.ucsf.edu> > Subject: Re: [chimera-dev] Moving a residue and an VRML object > Message-ID: <C66C5891-76C8-4D20-B82E-572E6F919DF2(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii" > > On Oct 17, 2012, at 3:21 PM, Greg Couch wrote: > > > Salut, > > > > The other trick is to give the VRML model the same model id and > submodel id as its associated model. Then the openState is > identical, so there would be no need to copy the transformation > matrix. Again, this only works for rigid rotations. > > ...and the simplest way to do this is to supply the "sameAs" > keyword, with the associated model as the argument, to the > openModels.add() or openModels.open() call that you use. > > --Eric > > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > >

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Problem with m.openState.xform.getCoordFrame() ?
by ladam 24 Oct '12

24 Oct '12

Hi all, I noticed this : >>> >>> print m.openState.xform 0.23153 -0.972828 0 0 0.972828 0.23153 0 0 0 0 1 0 >>> print m.openState.xform.getCoordFrame()[0] 0.23153 0.972828 0 >>> print m.openState.xform.getCoordFrame()[1] -0.972828 0.23153 0 >>> print m.openState.xform.getCoordFrame()[2] 0 0 1 >>> Looks like there is a problme with signs here between first two elements [0] and [1] with respect to m.openState.xform or am I missing something? Bye -- -------------------------------- Patrick Ladam Maître de Conférence Université Paris 13 - UFR SMBH CSPBAT - Service RMN 74, rue Marcel Cachin 93017 Bobigny Cedex Tel: 01 48 38 73 25 Fax: 01 48 38 77 77 mail: ladam(a)smbh.univ-paris13.fr -------------------------------

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Re: [chimera-dev] [Chimera-users] Amber Force Field
by Tom Goddard 17 Oct '12

17 Oct '12

Hi Forbes, I think Eric and Conrad may no more about your problem than I do. But I can tell you my best guess why your calculation is abysmally slow. I think the basic trouble is that useRotamer() decides to replace the existing residue rather than simply update its coordinates. In other words it deletes the old side chain atoms and bonds and makes new ones. Then the new ones don't have charges assigned for energy calculation. So the minimize "prep" option adds hydrogens and computes charges. It does this for the entire molecule because it doesn't know how to prep just one atom. So for each residue and each rotamer tried you end up adding hydrogens and recomputing charges for the whole molecule. Turning prep off in the minimize() call will just cause an error because the charges are missing. The "cache" option in the minimize() call also won't work because the molecule has changed. In fact the minimize code is not smart enough to realize the molecule has new atoms and will try to use the cached MMTK copy of the former molecule and this will probably lead to errors (as you describe). So my 30 minute look at the various parts of the Chimera code without any testing suggests the slowness is because hydrogens/charges are recomputed for every rotamer. The new MMTK molecule object is just the one residue you are calculating the energy of. You realize your code does not take account of any interactions of that residue with any other residues. The other residues are completely ignored. That is what exclres means. So you may as well be asking for the energy of a one residue molecule starting in the rotamer configuration with the actual residue backbone atom positions. I bet this would be very much faster if using a rotamer simply changed existing atom coordinates, then you add hydrogens and charges just one time for all the calculations, and you can cache the MMTK molecule object for each single residue energy calculation which will speed up calculating the different rotamer energies for that residue. Eric is the one who would know why the useRotamer() code deletes atoms and adds new ones instead of just changing the coordinates. It would probably be pretty easy to make a new routine to use instead of useRotamer() that simply copied atom coordinates from the rotamer molecules returned by getRotamer() to the original molecule. Or what about just calculating the energy of the rotamer molecules directly without trying to put them into the protein (with all its other residues ignored)? I see when I use the Rotamer dialog and hide the original molecule that the returned rotamers include CA and N backbone atoms but not C, O. Tom > Hi Tom: > > Thanks for your email of May 4. After some experimenting I got the code > to work but the execution times are deplorable! As I indicated earlier I > want to use the Amber energy calculations to compare various confirmations > involving different rotamers. My problem seems to be that I cannot get a > fast execution because I am unable to cache the results of various > computations and I believe the calculations are starting from scratch for > each rotamer combination. Here is a simplified version of the code that I > am using (in this case working with only one rotamer and essentaily > computing its intrinsic energy (I hope)): > > import chimera > import Rotamers > from Rotamers import getRotamers, useRotamer, NoResidueRotamersError > from MMMD import base > > > def evaluateAmberEnergy(res_L, prot): > > fixedAtoms = set() > molecules = list([prot]) > usingResidues = set(res_L) > > exclres = set(sum((m.residues for m in molecules), [])) > exclres.difference_update(usingResidues) > > def run(minimizer): > minimizer.run() > > minimizer = base.Minimizer(molecules, nsteps=0, stepsize=0.02, > cgsteps=0, cgstepsize=0.02, interval = 10, > fixedAtoms=fixedAtoms, nogui=True, > addhyd=True, callback=run, > exclres=exclres, cache=False, prep=True) > > energy = minimizer._mi.universe.energy() > print "energy value: ", energy > return energy > > #========================================================================== > > # Global variable: > prot = chimera.openModels.open("1CRN", type="PDB")[0] > > for rc in prot.residues: > rotCur_L = getRotamers(rc)[1] > for rotC in rotCur_L: > useRotamer(rc, [rotC]) > energyAmber = evaluateAmberEnergy([rc], prot) > print rc.type, rc.id.position, energyAmber > > > > This is producing a lot of text in the Python Shell and when the program > is run with a large protein it will go for hours... > > Any suggestions for speeding this up would be greatly appreciated. I > tried different settings of cache and prep but got Chimera errors such as > missing C++ atom objects. > > Depressing.... > > Best regards, > Forbes > > > > > > On Fri, 4 May 2012, Tom Goddard wrote: > >> Hi Forbes, >> >> If you want to get the minimized energy within your Python script >> then you need to run the minimization using a Python function call >> rather than a Chimera text command. To figure out how to do that I look >> at the Python code that is called by the Chimera text command in your >> Chimera distribution >> >> chimera/share/MMMD/cmdline.py >> >> or also available online >> >> >> http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/MMMD/cmdline.py >> >> The minimize() Python function is called using the text command >> arguments. I see it basically does >> >> from MMMD import base >> minimizer = base.Minimizer(molecules, nsteps, stepsize, cgsteps, >> cgstepsize, interval, >> fixedAtoms, memorize, nogui, addhyd, lambda m: >> m.run(), exclres, cache, prep) >> >> Looking at base.py in the same directory and tracking back from where >> "Initial energy..." is printed in file MMTKinter.py I see the energy is >> obtained using >> >> minimizer._mi.universe.energy() >> >> I have not tested this out but perhaps it will move you in the direction >> you want to go. >> >> Tom >> >> >>> Hi: >>> >>> Thanks for the response. The code that you suggested seems to work. I am >>> getting the initial energy reported in the Python Shell along with other >>> lines that are reporting on the activities of the command. >>> >>> Since I am embedding this command in a runCommand statement, I would like >>> to get the initial energy value put into a variable within the Python >>> script instead of the Python Shell window. Is there any way to accomplish >>> this? >>> >>> Cheers, >>> Forbes >>> >>> >>> On Fri, 13 Apr 2012, Elaine Meng wrote: >>> >>>> Hi Forbes, >>>> The minimization tool reports the total energy, not any breakdown into components (electrostatic, VDW, strain) or interactions between sets of atoms. However, the "minimize" command has a "fragment" option for ignoring all but the specified residues, so you could at least limit what is considered the total system. That also makes the calculation faster, although single-point energy calculation (0 steps minimization) should already be pretty fast. >>>> Best, >>>> Elaine >>>> >>>> Example (and see also "nogui true"): >>>> >>>> minimize spec :13.a,17.a fragment true cgsteps 0 nsteps 0 >>>> >>>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html> >>>> >>>> On Apr 13, 2012, at 10:38 AM, Conrad Huang wrote: >>>> >>>>> Chimera's "Structure Editing -> Minimize Structure" tool (or the "minimize" command) may be used to do this. The tool reports the initial energy of the system in the Reply Log. If you give zero as the number of steps for both steepest descent and conjugate gradient minimization, then Chimera should return immediately. >>>>> >>>>> Conrad >>>>> >>>>> On 4/13/12 7:09 AM, Forbes J. Burkowski wrote: >>>>>> Hi: >>>>>> >>>>>> I have noticed that scripts can start with: >>>>>> >>>>>> import MMTK >>>>>> import MMTK.ForceFields >>>>>> from MMTK.ForceFields import Amber94ForceField >>>>>> >>>>>> We are doing some side chain packing studies that would benefit from the >>>>>> availablity of "easy" force field calculations. Currently, the algorithm >>>>>> works with useRotamers() to set two neighbouring rotamers and this is >>>>>> followed by a simple energy calculation to evaluate the interaction energy >>>>>> between the two rotamers. Right now, the energy calculation is only a bit >>>>>> more sophisticated than a steric collision detector. >>>>>> >>>>>> Question: Can we use some functions in the MMTK.ForceFields module to get >>>>>> an improved energy calculation? >>>>>> >>>>>> Any suggestions would be appreciated. >>>>>> >>>>>> Cheers, >>>>>> Forbes >>>>>> _______________________________________________ >>>>>> Chimera-users mailing list >>>>>> Chimera-users(a)cgl.ucsf.edu >>>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>>> _______________________________________________ >>>>> Chimera-users mailing list >>>>> Chimera-users(a)cgl.ucsf.edu >>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >>

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set bond to wire and specific width
by Jean Didier Pie Marechal 11 Oct '12

11 Oct '12

Sorry to bug again, I'd like to change the aspect of the bonds I selected using a python code. I'd like a wide wire representation. I am not sure how to handle the Wire attribute. With the drawMode I can switch the representation from ball and stick to wire. However, I do not manage to change the width. I thought that radius would work out but it sounds that is does not work for this mode. Any help? Cheers JD for b in chimera.selection.currentBonds(): b.drawMode=0 b.radius=1 Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://asklipio.qf.uab.es ----- Missatge original ----- De: Jean Didier Pie Marechal <JeanDidier.Marechal(a)uab.cat> Data: Dijous, Octubre 11, 2012 2:19 pm Assumpte: Re: attribute for selection? > Sorry, > > just to clarify my previous request: > > this is a script that does what I want though a selection attribute > would be faster I think. > > for a in chimera.openModels.list()[0].atoms: > if a in chimera.selection.currentAtoms(): > print "this atom of the molecule is selected" #to say > somethingelse: print "this one isn't" > > cheers > > > Dr. Jean-Didier Maréchal > Lecturer > The Computational Biotechnological Chemistry Team > Unitat de Química Física > Departament de Química > Universitat Autònoma de Barcelona > Edifici C.n. > 08193 Cerdanyola (Barcelona) > Tel: +34.935814936 > e-mail: JeanDidier.Marechal(a)uab.es > www: http://asklipio.qf.uab.es > > ----- Missatge original ----- > De: Jean Didier Pie Marechal <JeanDidier.Marechal(a)uab.cat> > Data: Dijous, Octubre 11, 2012 12:39 pm > Assumpte: attribute for selection? > > > HI, > > > > I want to add attributes to atoms that are selected and those > that > > aren't. I thought that atoms had a selection attribute already > > defined in chimera (something like a boolean) but I don't find > it. > > I am wrong with that? > > > > best, > > JD > > > > > > Dr. Jean-Didier Maréchal > > Lecturer > > The Computational Biotechnological Chemistry Team > > Unitat de Química Física > > Departament de Química > > Universitat Autònoma de Barcelona > > Edifici C.n. > > 08193 Cerdanyola (Barcelona) > > Tel: +34.935814936 > > e-mail: JeanDidier.Marechal(a)uab.es > > www: http://asklipio.qf.uab.es > > >

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