- Chimera-users - RBVI Mailing Lists

IMOD model reader question
by William Jeffrey Triffo 12 Aug '08

12 Aug '08

I have an IMOD model (just a bunch of contours, representing filaments) that I tried to load into Chimera, but it threw some errors. This was odd, because it was a model I had augmented (added more contours) from a previous model that did load correctly (and I re-verified after the load error). is it helpful to forward the model file in question? best, -Jeff

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MatchMaker and Find Clash in nogui mode
by Ryan 11 Aug '08

11 Aug '08

Hi. I read in the archive (2004) that someone was looking to use MatchMaker in the nogui mode / command line, but that was not a possibility at the time. I am wondering if this ability has ever been implemented, and if so, how does one go about scripting this. Additionally, i would like to use the 'Find Clashes/Contacts' function in nogui mode. Is this possible? Thanks a lot, ryan

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protonating the protein
by Elaine Meng 11 Aug '08

11 Aug '08

Hi Francesco, > However, if you are using charges assigned in Chimera for something > (Dock Prep with AddH, Add Charge, and write Mol2 for input to DOCK > scoring grid calculations, for example), you would need to add the > protons in Chimera before assigning charges. This could be done by > selecting the carboxylate oxygens you want to get protonated (no more > than one per carboxylate group, of course) and changing their atom > types with the command: > setattr a idatmType O3 sel > prior to running AddH and Add Charge (alone or as steps in Dock > Prep). It is not necessary to rename the residues. Add Charge will > then recognize the neutral forms of ASP and GLU and use the > corresponding partial charges. I just tested this in the Chimera > production release, 1.2540 (July 9). The above is definitely true, you do not need to rename the residues in Chimera, but further tests reveal to get the correct charge distribution on the protonated carboxylic acid, the atom names also need to match the AMBER lib files: the protonated oxygen should be named OE2 (if glutamic acid) or OD2 (if aspartic acid) and the "free" oxygen should be named OE1/OD1. This will already be true sometimes, but not always. If you need to switch the atom names around before adding charges, it can be done by text-editing the PDB file or with commands. For example, you could change the name of an atom by selecting it and then using a command like: setattr a name OE2 sel After assigning charges, you can see the values as labels, for example: labelopt info charge la :6.a Again all this was tested in the production release 1.2540. Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Volume planes tool
by Elaine Meng 08 Aug '08

08 Aug '08

Hi Jeff, Here is another idea, still not exactly what you were asking for, but perhaps worth a look. You can use the Per-Model Clipping tool (under Tools... Depiction) to show a thin slab of the data, and you can interactively rotate and translate the slab any way you want relative to the data with the mouse. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/per-model/ per-model.html Just choose which model to clip, enable clipping, turn on slab mode and adjust clipping with mouse. You may also want to adjust the contour level in Volume Viewer. I tried it on emd_1274.map in the production release (1.2540). You can use it on solid, surface, or mesh volume displays. Below I attach an image of a slab surface display together with an unclipped solid display (a second copy of the same data). There is also a command to control per-model clipping in a script, mclip. It lets you specify location/orientation in the data coordinate system or the viewing coordinate system. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mclip.html Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Chimera: doubt on axes measurement
by Giovanni Cardone 07 Aug '08

07 Aug '08

Hi everybody, I have a doubt about my proper using the tool Axes for measuring angle between helices. After aligning two model and generating the axes corresponding to the helices of interest, I select them in the 'Structure Measurements' dialog windows. As you can see from a snapshot, they look properly selected. They are almost overlapping, but in the Reply Log I get the following info: col_best_001.pdb helix 10/col_best_005.pdb helix 2 crossing angle: 36.9 degrees, distance: 15.3 angstroms Beside the value of the angle seeming to me too high, shouldn't the distance between the helices be within few angs (at least according to how I interpret the documentation)? Probably I am missing something. Thanks in advance, Giovanni Cardone

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Protonating the protein
by Francesco Pietra 07 Aug '08

07 Aug '08

Hi: I am not saying anything new. I have a (for me) difficult problem of protonating a protein homology model (built with Modeller) where there are several halogen ion ligands. Actually I succeeded in getting a workable model. Chimera loads it and add hydrogens. I could even prepare the model for DOCK6, generating spheres. Now, however (and also because, before docking small ligands with DOCK6, I want to dock polypeptides, probably with DOT2) I would like to assign specific protonation states to certain carboxylic acids. That is, I want to create an overall model where certain facing carboxylic acids actually face as "carboxylate-carboxylic acid" or as "carboxylic acid-carboxylic acid", or, finally, as "carboxylate-carboxylate", the latter also with metal ligand in between or not. Question: to which extent can Chimera aid the task? And which other package (pdb2qr, H++, ...) may aid Chimera? Or no other package, but simply renaming the said residues in the pdb file and let Amber 10 (which is the package I'll use for MD, with ff99B ff for the protein) do the job of eliminating clashes? All that shows that I have no experience in selective protonation, and the halide ions (in the above said work, I have them simply under "ATOM" under the specific chain of the amino acid residues, not "HETATM", as the latter caused a lot or problems) create difficulty to protonating packages. Thanks for giving me a general guideline along with best moving. francesco pietra

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Chimera 1.2540 installer options and unattended installation
by Frank Thommen 07 Aug '08

07 Aug '08

Hi chimera-users, the Chimera installer seems to know some options and modifiers, but I could not find out what they mean: # ./chimera-1.2540-linux.exe -help UnZipSFX 5.41 of 16 April 2000, by Info-ZIP (Zip-Bugs(a)lists.wku.edu) Valid options are -tfupcz and -d <exdir>; modifiers are -abjnoqCLMVX. # Does anybody know what these options and modifiers do or where I can read about them? My motivation is, that I'd like to install Chimera in a non-interactive way (batchscript) in a non-standard location. Is there a way to achieve that? Thanks in advance frank -- Frank Thommen - Structures IT Management and Support - EMBL Heidelberg structures-support(a)embl-heidelberg.de - +49 6221 387 8353

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ConSurf display in Chimera
by Elaine Meng 06 Aug '08

06 Aug '08

Hello everybody, The ConSurf Server <http://consurf.tau.ac.il/> now provides results as Chimera Web data: a single click displays the color-coded query structure and multiple sequence alignment in your locally installed copy of Chimera. For a screenshot and example Web data file, see: http://www.cgl.ucsf.edu/chimera/consurf/consurf.html More about Chimera Web data: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/webdata/webdata.ht… Special thanks to Elana Erez and the Ben-Tal and Pupko groups at Tel Aviv University, and to Fabian Glaser. Enjoy! Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Re: [Chimera-users] mouse selection problem
by Eric Pettersen 06 Aug '08

06 Aug '08

Meikel Diepholz wrote: > Hi, > just a small problem I hope. > When I am selecting residues with ctrl +left mouse > button, chimera is always replacing the earlier selection, > independent on the selection mode I chose (append, subtract). > > Is it possible to change this? Hi Meikel, This behavior isn't a bug per se, but rather a deliberate design decision. We decided to not have the mouse selection honor the selection mode since it is possible to emulate all the selection modes directly with the mouse (except for intersect). If you hold down the Shift key as you are making a mouse selection then everything chosen with the mouse will have it's selection state toggled (selected items become unselected and vice versa), and other items will not have their selection state changed. So you can "subtract" by shift-control clicking/dragging on selected items, and you can "append" by shift- control clicking/dragging on unselected items. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Text statistics from Matchmaker
by nettles 04 Aug '08

04 Aug '08

I have found MatchMaker in Chimera an incredibly useful alignment tool. Thank you to the UCSF team! Now, I want to do do a mutliple alignment of many structures (~100) off a single reference structure, and output a text record of the residue pairings involved in the individual alignments along with their RMSD. In this particular case, I'll be looking at only small sequence variations of the same protein (with different drugs and cofactors). Accordingly, I would also like to output the RMSD of residue pairs beyond the alignment cut for relatively easy identification of regions having maximal variations. Advise is appreciated, With regard, Jim ________________________________________________________ James Nettles, Ph. D. Assistant Professor Department of Pediatrics, Emory University School of Medicine ________________________________________________________

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