April 2011 - Chimera-users - RBVI Mailing Lists

Command line
by Ryan Doherty 20 Apr '11

20 Apr '11

I searched the online documents and was unable to find out how to perform certain actions via the command line. Can you let me know how to perform the following commands via the command line: Color secondary structure (and set color for Helix, Strand & Coil) Create a text file with a summary of attributes (ie. # of ions, # of ligands, # of chains, areaSAS for each selected residue) Color surface based on hydrophobicity Thanks! Ryan

1 0

dock prep error in chimera
by Daron Standley 20 Apr '11

20 Apr '11

Hi- I just submitted the following bug report to chimera. Sorry if this is a redundant report, but I thought perhaps an experienced chimera user could identify my problem, since I am new to using this tool. I am trying to prepare a ligand for docking. I want to prepare the 4 ribonucleotide monophosphates AMP, GMP, UMP, and CMP. First, I tried extracting these from the Zinc database, but I kept getting related but not quite correct molecules. So, I then tried preparing the molecules in Chimera. My procedure was: 1. Chop up an RNA molecule from the PDB (e.g., 2xnz.pdb) into 'residues' (that is, a single ribonucleotide monophosphate) using a simple perl script. 2. Optional step 2 (I tried both with and without this step): add an oxygen fromt the previous residue to the phosphate and name it ' OP3'. 3. Save each molecule as an individual pdb file (e.g., 2xnz-G-1.pdb for the first GMP) 4. Read one of the newly created pdb files into chimera 5. run Tools->Structure Editing-> AddH In either case (with or without step 2) I get the error below. I have attached both pdb files (bug.zip) for reference. ####################### Error Log ####################### Error in ':ALA': underlying C++ Selectable object is missing Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 346, in command getattr(s, buttonFuncName(txt))() File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 564, in OK self.Apply() File "/Applications/Chimera.app/Contents/Resources/share/AddH/gui.py", line 265, in Apply hisScheme=hisScheme, okCB=self.cb) File "/Applications/Chimera.app/Contents/Resources/share/AddH/unknownsGUI.py", line 272, in initiateAddHyd okCB() File "/Applications/Chimera.app/Contents/Resources/share/DockPrep/__init__.py", line 194, in <lambda> cb=lambda pap=_postAddPrep, mols=mols, kw=kw: pap(mols, **kw)) File "/Applications/Chimera.app/Contents/Resources/share/DockPrep/__init__.py", line 259, in _postAddPrep method=method, cb=lambda ur, uc, m=mols, kw=kw: File "/Applications/Chimera.app/Contents/Resources/share/AddCharge/__init__.py", line 117, in initiateAddCharges chargeModel=chargeModel, nogui=nogui, showCharges=labelStandard) File "/Applications/Chimera.app/Contents/Resources/share/AddCharge/__init__.py", line 199, in addStandardCharges for r in m.residues: ValueError: underlying C++ Molecule object is missing ValueError: underlying C++ Molecule object is missing File "/Applications/Chimera.app/Contents/Resources/share/AddCharge/__init__.py", line 199, in addStandardCharges for r in m.residues: See reply log for Python traceback. ####################### End Error Log ####################### Best regards, Daron

2 2

animation
by Jean-Paul Armache 20 Apr '11

20 Apr '11

hello, i would like to ask a question about animation. i would like to achieve the following: 1. i have 3 different volumes, so when i put them next to each other, i would like to have each of them to rotate around it's own axis. an additional feature would be to start the rotation of each of the volume at a different point of time. 2. i would like to make certain parts of pdb appear slowly, either through change of colors from transparency or nucleotide/aminoacid at a time. 3. i would like the colors of a specific volume/pdb to "pulsate", meaning to start up with color nr 1, through 2 or 3 different colors to color nr 2. at the present moment i don't really know how to do those, would you have any hints ? thank you best regards, JP Armache

3 2

trajectories for movie making
by Justin Pahara 20 Apr '11

20 Apr '11

Hello All, I am interested in learning how to write and implement code that defines a pathway through a molecular model in chimera (I want to make movies this way rather than moving and rendering frame by frame through the scene. I'm far more biochemist than computer scientist, so I'm hoping to find material that will allow me to learn from the basics. Q's that I have: 1)how do I define a trajectory start point and end point in the chimeraff 3D viewing space 2)how do I define movement and/or velocity through the 3D space (how do I find define particular reference points in 3D space using chimera) 3)how do I define the incremental steps in in the trajectory (so I can achieve high frame rate or low frame rate videos) 4)can I use the utility function to make a movie/export pov files of the pathway? I greatly appreciate all suggestions! thanks, Justin.

2 1

measure volume for protein subsections
by Anke Mulder 19 Apr '11

19 Apr '11

Hi, I have used segger to divide my reconstruction into protein monomers, and I know how to measure the volume and other attributes of the protein monomer, however, I would like to be able to measure subsections of the monomer so that I can have an idea of what the volume of protein is that, for example, is buried in the lipid bilayer, etc. I thought that I could use clipping planes to do this, but from what I can tell the volume measurement still takes into account the volume of the entire protein. Thanks so much. Anke M.

3 4

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

3 2

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

2 2

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

3 4

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

2 1

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

2 1

Chimera-users April 2011