October 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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examples of 2-D plotting in plugins?
by Randy Heiland 14 Jan '09

14 Jan '09

Hi gang, For one of the Chimera plugins that I now maintain, I'm considering eliminating the use of matplotlib and wondering if Chimera's innards are capable of doing what I want. For starters, are there any example plugins, etc that demonstrate how one could do simple plotting and simple (image) contours? In addition, I'd need to handle mouse events, e.g. to retrieve x,y positions on the contour image. thanks, Randy

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python for finding clashes
by Jean Didier Pie Marechal 29 Oct '08

29 Oct '08

Hi everyone, I am writing a script for which I need the number of clashes for a given selection for continuing. My first thought was to simply run in my script: runCommand("findclash selection ignoreIntraRes false") after having selected the region I was interested in. However, I realize that I come to the recurrent problem: having the information I am interested in printed in the reply log. I don't know how to have the info passed into an array or any kind of variable in the python environment. Could you tell me how to do so please? On the other side, I would be pleased if you could tell me what is the correct arguments I have to pass and syntax I have to use for the functions detectClash and/or cmdDetectClash (which I guess is the basis of the same findclash). All the best, JD Dr. Jean-Didier Maréchal Lecturer Computational Bioorganic and Bioionorganic Chemistry @ Transmet 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

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python for finding clashes
by Jean Didier Pie Marechal 28 Oct '08

28 Oct '08

Hi everyone, I am writing a script for which I need the number of clashes for a given selection for continuing. My first thought was to simply run in my script: runCommand("findclash selection ignoreIntraRes false") after having selected the region I was interested in. However, I realize that I come to the recurrent problem: having the information I am interested in printed in the reply log. I don't know how to have the info passed into an array or any kind of variable in the python environment. Could you tell me how to do so please? On the other side, I would be pleased if you could tell me what is the correct arguments I have to pass and syntax I have to use for the functions detectClash and/or cmdDetectClash (which I guess is the basis of the same findclash). All the best, JD Dr. Jean-Didier Maréchal Lecturer Computational Bioorganic and Bioionorganic Chemistry @ Transmet 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

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Re: [chimera-dev] Chimera-dev Digest, Vol 57, Issue 5
by Patrick Ladam 23 Oct '08

23 Oct '08

>The reason your code did not work is that "ribbonData" is recomputed >whenever the molecule representation is changed (thereby wiping out >your changes). The attribute that actually controls the atoms being >used for ribbon representation is in "ribbonResidueClass" (the name >made sense when I wrote the code :-). Attached is a script that >changes the guide atom for all residues to "C". Please let me know if >you have any questions or suggestions. > >Conrad Hello Conrad, Thank you for your answer and the script, I'll try that right away. Thanks again Patrick

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Changing guide atom - repost
by Patrick Ladam 21 Oct '08

21 Oct '08

Hello list, I received an answer concerning this topic but via the chimera menus which I tested in the first place and works fine. Actually I want to do this from the python shell, so here is my repost: ----------------------------------------------------------------------- I'd like to change the guide atom in res.ribbonData to use C instead of CA as an example. Here is what I did: for r in mol.residues: for a in r.atoms: if a.name == 'C': r.ribbonData.guide = a # Set C as guide Atom if r.isHelix: # Update the display r.ribbonDisplay = True r.ribbonDrawMode = chimera.Residue.Ribbon_Round This does not seem to redisplay/recompute the helix through C Atoms, the helix still goes through CA but not C atoms. I am not confident with the way I altered the guide Atom or maybe is it another problem like updating the ribbon or so... If someone can help... Thanks to all PL

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Bild in python without open/write/close/makecommand ?
by Patrick Ladam 20 Oct '08

20 Oct '08

Hello to all, I have a serie of vectors to draw and update repeatidly. Is it possible to avoid the file open/write/close and makeCommand( 'open myfile.bild' ) process and rather do it in memory within python. In other words, is there a way to interpret bild commands directly in the chimera python module ? Thanks to all Patrick Ladam

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Changing guide atom
by Patrick Ladam 17 Oct '08

17 Oct '08

Hello list, I'd like to change the guide atom in res.ribbonData to use O instead of CA as an example. Here is what I did: for r in mol.residues: for a in r.atoms: if a.name == 'O': r.ribbonData.guide = a # Set O as guide Atom if r.isHelix: # Update the display r.ribbonDisplay = True r.ribbonDrawMode = chimera.Residue.Ribbon_Round This does not seem to redisplay/recompute the helix through O Atoms. I am not confident with the way I altered the guide Atom or is it another problem like updating the ribbon or so... If someone can help... Thanks to all PL

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Problem with sleap II
by Dr. Jean-Didier Maréchal 17 Oct '08

17 Oct '08

Hi guys, I could test again the solvation script. As you said, the problem with the cygwin library is completely solved. I am now running with the following problem: Running sleap command: C:\Archivos de programa\Chimera\bin\amber10\exe\sleap -f d:\docume~1\jean\config~1\temp\tmpfqkue6\solvate.cmd (solvate) [gtkleap]$ source leaprc.ff03 (solvate) Error: can not find file leaprc.ff03 in all the search path. Failure running sleap Check reply log for details Thanks for any help, JD *************************************************** Dr. Jean-Didier Maréchal Lecturer Computational Bioorganic and Bioionorganic Chemistry @ Transmet 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

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mixing names
by Patrick Ladam 14 Oct '08

14 Oct '08

Hello to the list, I start trying to write my first py code in chimera (not that easy without too much doc strings) and have a first question to submit. Here is what I am doing in IDLE: >>> import chimera >>> opened = chimera.openModels.open('1zik.pdb') >>> mol = opened[0] >>> for i in mol.atoms: print i.name N CA CB CG CD .../... # Now I want to instanciate an atom and set its name attribute: >>> at1=chimera.Atom >>> at1.name="BC1" >>> print at1.name BC1 >>> # Now I redo the previous loop: >>> for i in mol.atoms: print i.name BC1 BC1 BC1 BC1 BC1 BC1 BC1 BC1 BC1 BC1 BC1 BC1 .../... They're all BC1!!! How come ? My created atom 'at1' and my 'mol' are supposed to be completely seperated objects no? Can someone help, I am afraid I missed something really basic here... Bye to all

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Chimera-dev October 2008