- Chimera-users - RBVI Mailing Lists

PDB file format for movie
by Mingfeng Yang 05 Feb '07

05 Feb '07

Dear Chimera users and developers, I'd like to use chimera to view the motions of a protein. If all the snapshots are to be saved in a single PDB file, what's the correct format for them? I tried the following, but chimera complained that a single structure is included only. Thanks, Mingfeng ------------------ MODEL 1 ATOM 1 N ALA 1 -4.564 -7.956 -6.531 1.00 0.00 N ATOM 2 CA ALA 1 -5.237 -8.746 -5.532 1.00 0.00 C ATOM 3 C ALA 1 -4.360 -9.172 -4.378 1.00 0.00 C ... ATOM 81 HN ALA 10 0.195 11.398 3.736 1.00 0.00 H END MODEL 2 ATOM 1 N ALA 1 -5.031 -8.234 -5.174 1.00 0.00 N .... END

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Re: [Chimera-users] question about mac laptops / workstations and chimera stability
by Thomas Goddard 05 Feb '07

05 Feb '07

Hi Jeff, I have not seen any graphics driver bug reports with the MacBook Pro with X1600 graphics. I just ordered this machine to replace my four year old Dell with Quadro 4 graphics -- I am confident it will work well using volume data in Chimera. Here is our graphics driver bug page of problems observed with Chimera http://www.cgl.ucsf.edu/chimera/graphicsbugs.html It only has about 1/3 of the driver bugs and I will be adding more from our Chimera bug tracking system when I have time. Tom

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volume path tracer / render surface with marker set
by Jeff 02 Feb '07

02 Feb '07

hello, is there a way to render a surface of arbitrary thickness using a marker set? as in, fit some sort of spline to a marker set, with the constraint being that the algorithm assumes they all lie on the same surface? this would be useful for modeling membranes, perhaps it is already implemented and I am not seeing it in the dialogs. thanks, -J

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Copying volume settings to a second data set
by Thomas Goddard 02 Feb '07

02 Feb '07

Hi Jeff, There is no capability to copy settings (thresholds, colors, brightness, display style, rendering options) that are specific to each volume data set to another data set. That would be useful and I'll add it to the feature request list. Here are some hacks to achieve this. I don't think they are worth the trouble to use but you can decide. If you save a Chimera session with a volume having settings you want to reuse you can edit the session file changing the line: 'path': 'F:\\cygwin\\home\\Tom\\work\\volume\\emd\\emd_1282.map', to 'path': 'F:\\cygwin\\home\\Tom\\work\\volume\\emd\\XXX.map', Then when you reopen that session Chimera will say it cannot find the map file and ask you to select a new map file with a file open dialog. You can choose some other map. The settings from the original map will then be applied to this newly opened map. Another hack is to use the Volume Series tool available on the experimental features web page: http://www.cgl.ucsf.edu/chimera/experimental/experimental.html You can open your maps that you want to use the same settings for as a "volume series". That tool copies settings when you use it to flip between volume in a series. It can even adjust thresholds so they have the same rank position on the histogram (e.g. greater than 94% of voxel values). Tom Jeff wrote: > thanks Tom, > > is there a way to save the thresholds (and color settings) in the > volume viewer, so that when I close a map and reopen a > similar/filtered one, I don't have to re-do all the settings > (brightness and transparency too, for instance) > > i realize the histrogram changes for each map, but even if it saved > how many control points (and their colors) were there, that would > work. is there a 'save volume viewer state' button? I could not find one. > > -Jeff >

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Question on how to represent only chain A of Chimera
by nsomboon＠berkeley.edu 02 Feb '07

02 Feb '07

Hi, I need help. I received the modeling structures of my query (black) and the best representative 1qopB (magenta) through MODWEB, and used Chimera to visualize them (please see attached file). However, the magenta structure also contains 1qopA, in which I only want the 1qopB and don't want the 1qopA. I read through tutorials but cannot find a way to get rid of the chain A of the 1qop. Hence, could you please direct me of how to cut out chain A of 1qop in this attached file? Thank you very much. Sincerely yours, Nara

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Saving modified PDB files
by Bernard Heymann 02 Feb '07

02 Feb '07

I have a problem saving PDB files relative to density maps in recent versions of Chimera. When I load a PDB file and move it relative to a density map, and then try to save it relative to the density map, it does not apply the transformation to the PDB coordinates. This used to work in older versions. My workaround is to have another molecule open and save the transformed one relative to that. However, I would prefer to be able to save a transformed molecule relative to a density map. Can this be fixed? Bernard Heymann, Research Fellow Rm 1515, 50 South Dr., MSC 8025, NIAMS, NIH Bethesda MD 20892-8025 Tel. 301-451-8241, Fax. 301-480-7629

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Chimera to visualize MOLDEN-generated VRML2.0 files
by Kalju Kahn 01 Feb '07

01 Feb '07

Dear Chimera users, I am looking for advice on how to make chimera work with VRML 2.0 files generated by MOLDEN. MOLDEN seems to generate valid VRML files (octagaplayer reads these in all right) but chimera crashes with Segmentation fault (core dumped) This happens both on 32-bit Suse 9 system and 64-bit recent Ubuntu system. Any ideas are appreciated! Kalju ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry University of California, Santa Barbara

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anyone using chimera on a an IBM T43p
by Jeff 01 Feb '07

01 Feb '07

hello, I have an IBM T43p (June '05 or so release) which has an ATI FireGL v3200 (Mobility). In XP, it isn't possible to try out drivers from the vendor, I am limited to drivers from IBM. In Linux, I have been able to install proprietary drivers from ATI, but there is no selection for the 'Mobility' version of the v3200 on ATI's website; the install has not complained though, and basic stuff appears to be fine (GUI is ok, glxgears, etc). In both XP and Linux, chimera will crash when attempting to use volume maps. It appears fine with pdb files, although I typically work with volume data so haven't rigorously tested that. I have been assuming that the FireGL v3200 (Mobility) is the same logic as the v3200, at least documentation I have been able to find seems to imply that. Does anyone know (or suggest) a chimera-stable driver version from ATI that I might test? I might at least be able to get it to work in Linux, as the driver suite downloaded from ATI appears to cover most late-generation cards. thanks for any suggestions, -Jeff

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Re: [Chimera-users] access to pdb parser
by Jean Didier Pie Marechal 01 Feb '07

01 Feb '07

Hi Eric, Well, the truth is that these are two good news. Most likely I didn't explain myself correctly. In reality, for practical reasons, I'd like to use only chimera for the teaching. So, I am planning to only use its internal python shell for python applications. Therefore the tips you gave me are perfect. Thanks a lot for the help! Cheers JD Dr. Jean-Didier Maréchal Professor Lector Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdonyola (Barcelona) Tel: +34.935814988 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: Eric Pettersen <pett(a)cgl.ucsf.edu> Data: Dimecres, Gener 31, 2007 10:31 pm Assumpte: Re: [Chimera-users] access to pdb parser > Hi JD, > I have good news and I have bad news. The good news it that using > > PDBio to do what you want is pretty easy. The bad news is that you > > can't use it in a generic Python shell, only in Chimera's own > Python > shell. This is because we use a modified version of Python so that > > the types we define in the C++ layer (Molecule, etc.) can have > attributes added to them in the Python layer -- otherwise they > would > behave like the built-in Python types (dict, list. etc.) that can't > > have arbitrary attributes added to them. We intend to improve our > own code to make modifying Python unnecessary, but haven't gotten > to > it so far. > Nonetheless, you can basically use Chimera in place of a Python > interpreter. "chimera --nogui script.py" will execute the Python > script named script.py without bringing up the Chimera interface. > Also, you can start Chimera normally and bring up the graphical > interface to its interactive Python shell, IDLE (under Tools- > >General > Controls) and type Python commands to that. > Here's a session of me using PDBio in IDLE. I've added some > comments. > >>> from chimera import PDBio # import PDBio > >>> pdbio = PDBio() # create a PDBio instance > >>> mols = pdbio.readPDBfile("/mol/pdb/gc/pdb1gcn.ent") # read a > PDB file given its file name > >>> m = mols[0] # readPDBfile() returned a list of models (NMR > can > have many) so get the model itself > >>> m.pdbHeaders["HEADER"] # each model will have a pdbHeaders > dictionary, keyed by the record type, the values will be a list of > strings -- the PDB records > ['HEADER HORMONE 17-OCT-77 > 1GCN 1GCN 3'] > >>> > > --Eric > > On Jan 31, 2007, at 12:42 PM, Jean Didier Pie Marechal wrote: > > > Hi Eric, > > > > Yes, that would be better to explain more what I'd like to do. > > > > I am planning to give a practical on computational (bio)chemistry > > > in my department next year. I'd stongly like to have the students > > > using chimera and python as their main tools (though both are > tools > > I am in process of learning :-)). > > > > One of the "simple things" I have in mind, is to obtain pdb infos > > > directly from the shell e.g list the SEQRES entry or access to > the > > resolution (REMARK 2), the crystallization conditions etc. The > > students will be chemists and I think that from a didactic point > of > > view, obtaining infos from the python shell would be better that > > reading the pdb files, especially if we want to compare different > > > structures e.g. Writing a comand that gives you ALL the > resolutions > > of the 10 structures you loaded would be interesting. I looked at > > > the PDBio, but I can see how to catch REMARKS infos. > > > > I'd really like to have this work going on, but as you can see, I > > > am a bit lost in where to begin. > > > > Any help to tell me where to start would be fantastic! > > > > Cheers > > > > JD > > > > > > > > > > Dr. Jean-Didier Maréchal > > Professor Lector > > Unitat de Química Física > > Departament de Química > > Universitat Autònoma de Barcelona > > Edifici C.n. > > 08193 Cerdonyola (Barcelona) > > Tel: +34.935814988 > > e-mail: JeanDidier.Marechal(a)uab.es > > > > ----- Missatge original ----- > > De: Eric Pettersen <pett(a)cgl.ucsf.edu> > > Data: Dimarts, Gener 30, 2007 1:25 am > > Assumpte: Re: [Chimera-users] access to pdb parser > > > >> Hi JD, > >> Chimera does its PDB parsing in the C++ layer (the PDBio class in > >> > >> the Python layer). There is a file named PDB.py in the mmCIF- > >> parsing > >> module, but it's not for parsing PDB files. Perhaps if you > >> described > >> why you need Python PDB parsing I could suggest options -- using > >> PDBio possibly being one of them. > >> > >> --Eric > >> > >> Eric Pettersen > >> UCSF Computer Graphics Lab > >> pett(a)cgl.ucsf.edu > >> http://www.cgl.ucsf.edu > >> > >> On Jan 29, 2007, at 1:49 PM, Jean Didier Pie Marechal wrote: > >> > >>> Hello everyone, > >>> > >>> a short question. What is the right call for importing the > >>> pdbparser module in the chimera python shell? I found the PDB.py > >> > >>> module in the site-package mmlib, but I don't know how to import > >> it...> > >>> Thanks a lot, > >>> > >>> JD > >>> > >>> > >>> Dr. Jean-Didier Maréchal > >>> Professor Lector > >>> Unitat de Química Física > >>> Departament de Química > >>> Universitat Autònoma de Barcelona > >>> Edifici C.n. > >>> 08193 Cerdonyola (Barcelona) > >>> Tel: +34.935814988 > >>> e-mail: JeanDidier.Marechal(a)uab.es > >>> > >>> > >>> _______________________________________________ > >>> Chimera-users mailing list > >>> Chimera-users(a)cgl.ucsf.edu > >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > >> > >> > > > > > >

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TER Cards and Rainbow Colors
by Albion Baucom 31 Jan '07

31 Jan '07

Is there any way to introduce TER records between breaks in a chain, and still have N->C coloring continuous through a single chain? I have for instance a structure with missing loops that were not observed in density. Therefore there are breaks in the main chain. This is a very common occurrence. To prevent spuriously long bonds I have introduced TER records between the breaks. Then when I apply rainbow coloring from N->C terminus I get the spectral coloring between TER records rather than from the beginning of the chain to the end. I tried the card BREAK, but evidently that is not interpreted by Chimera. Coloring by chain, or by model in the Rainbow panel does not produce the desired effect. Thanks Albion

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