- Chimera-users - RBVI Mailing Lists

how to make simmetric dimer
by Francesco Biagi 26 Apr '11

26 Apr '11

Hello everyone. I have a question about Chimera: I want to put two monomers (of a dimer) in simmetry. I tried to do this with mouse, with poor results.I would like to know if there is a method or a script that can help me. Thanks to all.Francesco

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PDB reference frame
by Roberto Kopke Salinas 25 Apr '11

25 Apr '11

Dear All, Is there a way to draw and visualize the three axes of the PDB reference frame in Chimera? Thank you for your help, Roberto

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Re: [Chimera-users] Changing charge of protein
by Elaine Meng 22 Apr '11

22 Apr '11

Dear Monisha, If you get a Chimera daily build (version 1.6, whereas you probably have 1.5), there will be AddH options for all those residue types I mentioned. The options in AddH are for the side chains. The N-terminus of the backbone will already get a +1 charge, and the C-terminus -1. If the backbone N is not the N-terminus, it is in an amide group and will not be formally charged. However... There is a limit as to what total charge is reasonable for a given protein sequence. If you just arbitrarily increase positive charges everywhere to try to reach some value (why??), it will become less representative of reality. Another approach you might consider if you are trying to make your "system" more neutral is to add counterions (see Tools... Structure Editing... Add Ions). 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 22, 2011, at 11:47 AM, Monisha Hajra wrote: > Dear Elaine, > > Thank you for your reply. > > However I find in AddH option, its only Histidine specific, what should I do if I want to alter specific protonation state of Lys, Arg. > > Also, read from the link that you had send is that > "lysine positive or neutral > • charges for the neutral LYN residue are assigned if the atom named NZ has atom type N3 and thus two attached hydrogens rather than three" > Is that mean that I can't create +2 charge for Lys, by adding another H to N (which is attached to alpha C)? > > I tried even by command line " addh #0: 34@N", its showing error, though chain #0: 34@N is showing the N atom. > > Kindly provide some solution. Right now charge of my protein is -22, I have to bring it up to +10. Really appreciate on general comment of yours on how do do that? > > Regards > Monisha > > On Fri, Apr 22, 2011 at 9:38 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Dear Monisha, > The charge of the protein is the sum of the charges of its residues, but charges are not saved in PDB format. > > Maybe you mean you want to control the protonation state and thus the formal charges of certain residues (for example, specifying which histidines should be positive and which should be neutral)? That can be done when you are adding hydrogens. In the AddH tool (under Tools... Structure Editing) there is "Protonation states for" setting for controlling protonation states of histidine, glutamic acid, aspartic acid, lysine, and cysteine residues. You would have to decide yourself which residues should be in which states. You could indicate that by editing the input PDB file to contain special residue names, or just choose "specified individually" for it to go through and ask you about each one. Details: > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addh/addh.html> > > Then, you could save the PDB file including the hydrogens using "File... Save PDB" in the Chimera menu. > > Charges are a somewhat separate matter, and are not saved in PDB files. There would not be any charge assignments until after you used Add Charge (under Tools... Structure Editing). Then, you could see the atom and residue charges in histograms in Render by Attribute, or save them to a file using that tool. If you really meant you wanted to assign specific charges to specific atoms yourself, you could do that with Define Attribute or the command setattr. You can label atoms with their charges as described here > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharg…> > but we don't have that for whole residues. > > 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 22, 2011, at 5:20 AM, Monisha Hajra wrote: > > > Dear User, > > Is there any way to increase or decrease total charge of the protein in Chimera? Can I see the residue wise (not atom wise) charge and modify, and should be able to save the modified protein in pdb. Trying to look to add charge / "render by attribute" section, but didn't get much help. > > Any help will really be appreciated. > > Regards > > Monisha > >

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Why sym # group h did't work
by Fang, Shunming (NIH/NIDDK) [C] 22 Apr '11

22 Apr '11

Hello, There, I tried several time to use the commend sym #1(or 2,3..), group h, 11.75, 101.32 to my em map, it always show errors saying unknown keyword 11.75, 101.32? Please help me, Thanks Shunming

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Changing charge of protein
by Monisha Hajra 22 Apr '11

22 Apr '11

Dear User, Is there any way to increase or decrease total charge of the protein in Chimera? Can I see the residue wise (not atom wise) charge and modify, and should be able to save the modified protein in pdb. Trying to look to add charge / "render by attribute" section, but didn't get much help. Any help will really be appreciated. Regards Monisha

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Command line
by Ryan Doherty 21 Apr '11

21 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

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help with command line selections
by Corey Fugate 21 Apr '11

21 Apr '11

I'm having a hard time figuring out how to select secondary structural elements from the command line. Can someone help me with this? Corey

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Command line
by Ryan Doherty 21 Apr '11

21 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

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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

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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

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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.

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measure volume for protein subsections
by Anke Mulder 20 Apr '11

20 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.

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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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Controling the configuration of chiral atoms.
by vincent zoete 08 Apr '11

08 Apr '11

Dear Chimera team, We are very satisfied daily users of Chimera for drug design and protein engineering applications in our lab. Congratulations for your great work! I would like to come back on the point raised by Dr. Charbel MAROUN recently. Having the possibility to change the configuration of whatever chiral atom would be very useful for drug design applications. It's true that we can do it using other software like Pymol or HyperChem, to cite just two of them arbitrarily. But it would be much more convenient to rapidly and graphically do it in Chimera, without the need to switch to another program for that particular and single action. We are often working with D-amino acids and chiral small molecules. We apreciate a lot the "Build Structure" module to construct or modifiy such compounds, and allowing more control on the chiral center configuration would be very useful. Do you think you could consider adding such chirality inversion command in the future? Sincerely, Vincent Zoete, Molecular Modeling group - SIB www.click2drug.org =========================================================== Hello, Sorry, Chimera does not do that. I am pretty sure that SYBYL and probably some other programs will do it, but you may want to ask on a more general list such as CCL.net for a more certain and detailed answer about other programs. Best, 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 Jan 28, 2011, at 6:15 AM, R. Charbel Maroun wrote: > Hi everybody, > Is there an easy and quick way to invert the chirality of an atom, say a Ca ? > Greetings, > ----------------------------------------- > R. Charbel MAROUN, Ph.D., H.D.R.

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Hydrogen bond cut off
by Simon Sham 07 Apr '11

07 Apr '11

Hi, First, I don't have access to the reference by JE Mills in Journal of Comp. Aided Design 1996. Secondly, can someone please tell me that in chimera is the cut off distance between the donor and acceptor atoms 3.5 angstroms and cut off angle 35 degrees? Thanks for your help in advance. Simon

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Problem for selecting the Recepter and ligand
by Bishwajit Das 07 Apr '11

07 Apr '11

Hi I am using chimera,i am a new user of this and i open a docking model in .pdb format. Now my question is how i seen that model which is recepter and which is ligand.How i differentiate with recepter and ligand with two another colour. Please help me with step by step Thank you -- * BISHWAJIT DAS*** KOLKATA

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