- Chimera-users - RBVI Mailing Lists

Adjust angle
by Thomas Mitterfellner 19 Apr '11

19 Apr '11

Hello! My question is: it possible not just to measure but to change the angle between three atoms (e.g. A1 and A2 fixed, A3 rotated in the plane spanned by A1-A2-A3 with radius A2-A3)? What I really like in Chimera (and miss in other molecular modelling software) is the possibility to move/rotate only the atoms selected, which is great e.g. for pre-aligning two molecular fragments when modelling transition states. I know chimera is actually rather intended to be used for large molecules but it could be a great tool for modifying/building structures if only it was easier to modify structural parameters like bond lengths, angles and torsions (which I saw is possible). Kind regards, Thomas Mitterfellner

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Re: [Chimera-users] Alteration of C-terminal AA-sequence within an X-ray model data set with Chimera
by Elaine Meng 14 Apr '11

14 Apr '11

Dear Heinrich, I can think of a couple possibilities. First you would open the structure and the density map. Opening the density map will automatically start Volume Viewer, in which you can adjust the display type (surface, mesh, etc.) and contour level by moving the slider on the histogram. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/frame…> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum…> Then... (A) you could select those 30 residues, then use "Movement Mouse Mode" (under Tools... Movement) "move selection" option to manually reposition them. However, that would not automatically fit the residues to density, it would just let you rotate and translate them as a rigid body yourself with the mouse, which can be difficult if you are trying to dock into density. The selecting could be done in several ways, such as by command (e.g. "select #0:356-end.a" to select model 0 chain A residues 356 to the end) or interactively in the Sequence tool (under Favorites in the menu). After the movement you could save the modified structure with "File... Save PDB" in the Chimera menu or the "write" command, and you would probably want to save "relative to" the map model. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movemode/movemode.…> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb> (B) you could make those 30 residues a separate model and then automatically fit them as a rigid whole into the density using "Fit in Map" (under Tools... Volume Data). You would delete the rest of the structure, for example with command "delete ~#0:356-end.a" to delete all atoms EXCEPT model 0 residues 356-end in chain A. Next, using the mouse, manually move it to an approximate position relative to the map. You can freeze the map and move only the structure by un-checking the "Active" box for the map model below the Command Line or in the Model Panel (both tools are under Favorites in the menu). Then use Fit in Map, which will perform a local optimization. You may want to run it a few times to see if the result improves. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.ht…> Saving a whole model is less convenient than in (A). You would need to open another copy of the structure, delete the opposite part (e.g. command "delete #0:356-end.a") and probably also fit that one into the density. You could either save both as PDB relative to the map model and then manually combine them into one PDB file, or in Chimera merge the models (see command "combine" or the "copy/combine" function in the Model Panel), possibly add the bond if you need it (see command "bond" or the Build Structure tool) and then save the PDB of the combined model relative to the map model. Even if method (B) is not too long for you, I can think of two problems: (1) It is not flexible fitting. Each part is treated as a rigid body, and you have to decide yourself how to split a structure into parts. (2) The parts do not "see" each other, there is nothing to stop them from bumping into each other or even going to the same place in the density map. In the Chimera daily builds, we have recently added a tool that addresses this problem: MultiFit (under Tools... Volume Data) will perform simultaneous fitting of multiple rigid structures. However, it currently assumes overall Cn (cyclic) symmetry, so it cannot be applied to your problem. We hope to have it working for structures without cyclic symmetry soon, but that is not yet available. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multifit/multifit.…> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 14, 2011, at 2:01 AM, Heinrich Lünsdorf wrote: > Dear Elaine, > here I'm again to ask for your constructive help on another item. My question: Is it possible with Chimera functions and commands to pick up and activate an AA-sequence, i.e. the last 30 C-terminal AAs, and to 'move' or 'bend' them in parts or as a whole but without changing or moving the rest of the X-ray model to get the C-terminal AA-tail fit along with an overlaid EM-density model?? Can such alterations be stored for the original X-ray model? > Thank you cordially for your help in advance. > Sincerely yours, > Heinrich

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rebuild DNA
by Damien Larivière 14 Apr '11

14 Apr '11

Dear all, Here is a PDB file of a DNA portion. It contains only the atoms of the backbone chain trace. Is there a way to rebuild the remaining parts (sugar,...)? Many thanks for your help Damien

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Problem for docking result analysis
by Bishwajit Das 12 Apr '11

12 Apr '11

Hi, I load a docking results in .pdb format,now how can i view inter-molecular bonding information with chimera. please help me. -- * BISHWAJIT DAS*** KOLKATA

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Merging of two pdb files
by Monisha Hajra 11 Apr '11

11 Apr '11

Hi, I have modeled one protein. I have pdb file of the protein. I want to merge the protein with one co-factor (I have the pdb file for the same). Can I merge them in one file using Chimera? If not, then any other tool can you suggest? Regards Monisha

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NMR average structure
by Lucio Ferella 11 Apr '11

11 Apr '11

Hi all, I need to calculate an average structure (or select the most representative member of), from an NMR emsemble structures in Chimera. Is it possible? Thanks for any helps. Lucio

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recording path through centroid
by Francesco Pietra 11 Apr '11

11 Apr '11

Hello: Is it anything new about recording path by the way of the centroid? I did not use it since September 2000. It worked nicely, though -being at illustrations for a candidate publication - my question is whether it has been improved further. thanks francesco pietra

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Hydrophoic and Hydrophilic solvent accessible surface area
by Monisha Hajra 09 Apr '11

09 Apr '11

Hi Team, Can I calculate Hydrophoic and Hydrophilic solvent accessible surface area in Chimera? If so, let me know how? Really appreciate help. Regards Monisha

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Labeling 3D structures in Chimera (and saving them as such)
by Bilal Asif 08 Apr '11

08 Apr '11

Hello, I am a senior undergraduate student at Stony Brook University, part of a team currently attempting to design an introductory biology lab for biology undergraduates. We are attempting to use Chimera as a way to introduce students to structural biology and research. However, we have run into a problem, one which we hope you can help us solve. We have discovered that if one attaches a label to a molecule in Chimera, one cannot save it as a .pdb, and open it again with the same labels attached. Is there a way to preserve labels attached to 3D structures, perhaps by saving it in a different file format? Thank you for your time and consideration. Any insight would be greatly appreciated. Bilal Asif Stony Brook University

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problems in chimera display
by manidip_rs＠iicb.res.in 08 Apr '11

08 Apr '11

  I have downloaded and installed chimera-1.5.3-linux_x86_64.bin, release date April 05,2011.  But after opening a volume data the volume is appearing as random slices.  I have checked all the other necessary requirements. I am using RHEL 5.4 and NVIDIA graphics.  Please suggest.                                                                                                                                                                                                      Thanks,                                                                                                                                                               Manidip Shasmal, Research Fellow,                                                                                                                                                               Indian Institute of Chemical Biology, kolkata -700032 Do not Remove: [HID]20110408124249826[-HID] **************************************************** VirusFree, Spamfree, power packed email service. ****************************************************

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