- Chimera-users - RBVI Mailing Lists

partial failure in addH BUG?
by Francesco Pietra 04 May '11

04 May '11

Hello: i had partial failure in addH to a natural product. H at a quaternary, chiral C was not added in spite of repeated attempts. All Hs were added by my favorite drawer (for organic compounds); however, this changes the coordinates, which is not what I want. I solved the issue by transferring the chimera pdb output to vmd, adding the missing H with Molefacture. On the other hand, Molefacture, if asked to add all Hs, resulted in incorrect stereochemistry at -O-CH3 and some -C-CH3 (inverted umbrella, which could not be reversed). francesco pietra

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building large size polymer
by 윤홍민 02 May '11

02 May '11

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kindly help
by preetam nayak 02 May '11

02 May '11

Respected sir, I am using chimera for the first time.I just want to ask that after successfully removing all clashes/contacts in my pdb file using commandline arguement selectively,I am unable to save this modified pdb file even after trying many a times.Everytime I am saving my pdb file after modifications,the changes are not at all saved and again when I am opening the pdb file ,it is showing the same clashes/contacts.Sir,please help by providing the required steps as to how to save the changes one has made in the pdb file.

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Information request
by Francesco Burresi 30 Apr '11

30 Apr '11

Hi, I've docked a ligand with a receptor and I get a pdb with1 chain (chain A) I'd like to separate recpetor-ligand in two different chians (chain A e chain B). How can I do that in Chimera? regards

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Information request
by elisa carli 28 Apr '11

28 Apr '11

Hi, I'm trying to model a TM protein using a Fugue approach. This method involves to divide a transmembrane protein in fragment (Nter, TM1,LOOP1and so on) Each fragments is predicted separatly. I'd like to assembly and join fragment, superimposing the backbone of a fragment with that of the correspondent segment in the structure of my protein. How can I achieve this goal with Chimera? regards

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Re: [Chimera-users] Chimera: Myosin thick filament movie
by Tom Goddard 28 Apr '11

28 Apr '11

Hi Rogelio, The myosin thick filament movie in the Chimera animation gallery was made in 2006 using a 700 line python program I wrote. Fortunately Chimera animation capabilities are much better now, so I've made a Chimera command script that makes the same movie in Chimera 1.5.2 (Jan 2011), about 150 commands. I've attached the script. It of course requires the myosin data files to work. So I've put the script and data files in myomovie.zip and put a link to that in the animation gallery with the myosin animation (will appear after web site is rebuilt tonight). http://www.cgl.ucsf.edu/chimera/animations/animations.html To create the movie you open the myomovie.py Chimera session then open the myomovie.cmd command script. Rendering this movie takes about 15 minutes (for about 70 seconds of final video, 1760 frames) using the high quality supersample 3 option set in the script. The myosin movie is somewhat complex. There are about a half dozen simpler movie making command scripts with links on the animation gallery page. We don't have a separate movie scripts web page, although that is a nice idea. There is a movie making tutorial on the Chimera tutorials page http://www.cgl.ucsf.edu/chimera/tutorials/tutorials.html and there are details about all the commands in the Chimera User's Guide http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/movies.html Tom > Hi Tom, > > I have been recently looking at the animation gallery of Chimera and I > was wondering if I could get a copy of the script used to make the > Myosin movie, > Do you guys have a repository of scripts used for the displayed movies? > > I am working with a helical map and I would like to try to implement a > similar animation for my maps, > > thanks a lot for your help and consideration > > ROGELIO > > > -- > Rogelio A. Hernandez Lopez > Leschziner Lab > Harvard University > 305.G NWB > 52 Oxford Street, Room 305 > Cambridge, MA 02138 > > http://www.mcb.harvard.edu/Leschziner/

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Information request
by elisa carli 28 Apr '11

28 Apr '11

Hi, I'm working with a pdb file, that have two atoms in an ARG residue , not allowed by Charm H Polar force fields Is it possible to fix the problem with Chimera? Residues: ARG 251 1HH1 ARG 251 2HH2 Regards

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how to write log file in Chimera
by Rogelio A. Hernandez-Lopez 27 Apr '11

27 Apr '11

Hi, Is there any way to create a log file to store all the actions performed by the user during a chimera session, either using the menus or command line? I want to write a script for a movie and it would be very useful to copy and paste commands from such as file thanks, ROGELIO -- Rogelio A. Hernandez Lopez Leschziner Lab Harvard University 305.G NWB 52 Oxford Street, Room 305 Cambridge, MA 02138 rhernand(a)fas.harvard.edu (617)-872-5399 http://www.mcb.harvard.edu/Leschziner/

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trying to add charges
by Irene Newhouse 27 Apr '11

27 Apr '11

I'd like to do a PDB2PQR run of my protein with its 'ligands' - actually substrates & am having problems getting the server to recognize my mol2 file. So I thought I'd use chimera to add charges & write, hopefully, a compatible mol2 file. I'm having problems with that as well. This is a pdb of the ligands:HETATM 8225 MG MG A 291 25.874 25.146 58.617 1.00 0.00 Mg2+ HETATM 8226 C4 FPS A 292 25.754 19.949 62.737 1.00 0.00 C HETATM 8227 C3 FPS A 292 26.088 21.273 63.475 1.00 0.00 C HETATM 8228 C2 FPS A 292 26.021 22.571 63.132 1.00 0.00 C HETATM 8229 C1 FPS A 292 25.656 23.447 61.998 1.00 0.00 C HETATM 8230 S1 FPS A 292 27.204 24.181 62.219 1.00 0.00 S HETATM 8231 P1 FPS A 292 27.928 23.762 60.771 1.00 0.00 P HETATM 8232 O1 FPS A 292 28.873 24.955 60.385 1.00 0.00 O HETATM 8233 P2 FPS A 292 28.554 26.180 59.405 1.00 0.00 P HETATM 8234 O2 FPS A 292 28.206 25.713 57.968 1.00 0.00 O HETATM 8235 O3 FPS A 292 27.331 26.943 59.830 1.00 0.00 O HETATM 8236 O4 FPS A 292 29.622 27.136 59.149 1.00 0.00 O HETATM 8237 O5 FPS A 292 26.862 23.528 59.683 1.00 0.00 O HETATM 8238 O6 FPS A 292 28.976 22.661 61.190 1.00 0.00 O HETATM 8239 C5 FPS A 292 26.754 21.192 64.778 1.00 0.00 C HETATM 8240 C6 FPS A 292 26.118 20.990 66.155 1.00 0.00 C HETATM 8241 C7 FPS A 292 27.084 20.015 66.840 1.00 0.00 C HETATM 8242 C8 FPS A 292 28.144 20.342 67.618 1.00 0.00 C HETATM 8243 C9 FPS A 292 28.586 21.777 67.991 1.00 0.00 C HETATM 8244 C10 FPS A 292 28.618 19.212 68.506 1.00 0.00 C HETATM 8245 C11 FPS A 292 27.622 19.162 69.634 1.00 0.00 C HETATM 8246 C12 FPS A 292 27.899 18.054 70.615 1.00 0.00 C HETATM 8247 C13 FPS A 292 28.127 18.187 71.942 1.00 0.00 C HETATM 8248 C14 FPS A 292 28.131 19.492 72.723 1.00 0.00 C HETATM 8249 C15 FPS A 292 28.358 16.835 72.549 1.00 0.00 C HETATM 8250 H4 FPS A 292 24.677 19.881 62.580 1.00 0.00 H HETATM 8251 H5 FPS A 292 26.263 19.931 61.773 1.00 0.00 H HETATM 8252 H1 FPS A 292 25.472 22.838 61.113 1.00 0.00 H HETATM 8253 H11 FPS A 292 24.694 24.092 62.300 1.00 0.00 H HETATM 8254 H14 FPS A 292 28.310 18.659 67.618 1.00 0.00 H HETATM 8255 H15 FPS A 292 29.626 18.910 68.790 1.00 0.00 H HETATM 8256 H141 FPS A 292 28.344 19.287 73.772 1.00 0.00 H HETATM 8257 H142 FPS A 292 28.897 20.155 72.320 1.00 0.00 H HETATM 8258 H143 FPS A 292 27.155 19.970 72.638 1.00 0.00 H HETATM 8259 H91 FPS A 292 29.470 21.732 68.628 1.00 0.00 H HETATM 8260 H92 FPS A 292 28.821 22.333 67.083 1.00 0.00 H HETATM 8261 H93 FPS A 292 27.779 22.279 68.525 1.00 0.00 H HETATM 8262 H7 FPS A 292 26.852 18.977 66.652 1.00 0.00 H HETATM 8263 H61 FPS A 292 26.054 21.948 66.670 1.00 0.00 H HETATM 8264 H62 FPS A 292 25.117 20.575 66.036 1.00 0.00 H HETATM 8265 H51 FPS A 292 27.451 20.354 64.779 1.00 0.00 H HETATM 8266 H52 FPS A 292 27.298 22.117 64.967 1.00 0.00 H HETATM 8267 H4 FPS A 292 26.087 19.103 63.338 1.00 0.00 H HETATM 8268 H12 FPS A 292 27.905 17.074 70.162 1.00 0.00 H HETATM 8269 H151 FPS A 292 28.547 16.946 73.646 1.00 0.00 H HETATM 8270 H152 FPS A 292 27.455 16.195 72.388 1.00 0.00 H HETATM 8271 H153 FPS A 292 29.246 16.355 72.064 1.00 0.00 H HETATM 8272 H111 FPS A 292 27.646 20.103 70.183 1.00 0.00 H HETATM 8273 H112 FPS A 292 26.622 19.003 69.230 1.00 0.00 H HETATM 8274 H2 FPS A 292 26.305 23.333 63.843 1.00 0.00 H HETATM 8348 O3 IPE A 586 21.257 22.023 59.139 1.00 0.00 O HETATM 8349 C1 IPE A 586 21.725 22.610 60.331 1.00 0.00 C HETATM 8350 C2 IPE A 586 21.891 21.539 61.401 1.00 0.00 C HETATM 8351 C3 IPE A 586 22.135 21.746 62.732 1.00 0.00 C HETATM 8352 C4 IPE A 586 22.476 23.125 63.351 1.00 0.00 C HETATM 8353 C5 IPE A 586 22.090 20.534 63.651 1.00 0.00 C HETATM 8354 P1 IPE A 586 22.541 22.279 58.101 1.00 0.00 P HETATM 8355 O1 IPE A 586 23.289 23.718 58.505 1.00 0.00 O HETATM 8356 O2 IPE A 586 23.635 21.031 58.224 1.00 0.00 O HETATM 8357 O7 IPE A 586 21.980 22.381 56.596 1.00 0.00 O HETATM 8358 P2 IPE A 586 22.517 20.944 55.933 1.00 0.00 P HETATM 8359 O4 IPE A 586 24.120 21.122 55.494 1.00 0.00 O HETATM 8360 O5 IPE A 586 22.398 19.740 57.082 1.00 0.00 O HETATM 8361 O6 IPE A 586 21.597 20.552 54.601 1.00 0.00 O HETATM 8362 H6 IPE A 586 20.970 20.939 61.359 1.00 0.00 H HETATM 8363 H7 IPE A 586 22.711 20.896 61.047 1.00 0.00 H HETATM 8364 H4 IPE A 586 22.660 23.213 64.432 1.00 0.00 H HETATM 8365 H5 IPE A 586 22.534 24.017 62.710 1.00 0.00 H HETATM 8366 H1 IPE A 586 21.090 20.076 63.606 1.00 0.00 H HETATM 8367 H2 IPE A 586 22.843 19.801 63.329 1.00 0.00 H HETATM 8368 H3 IPE A 586 22.303 20.848 64.684 1.00 0.00 H HETATM 8369 H11 IPE A 586 22.687 23.089 60.148 1.00 0.00 H HETATM 8370 H12 IPE A 586 21.008 23.356 60.675 1.00 0.00 H END When I try to add charges, chimera chews on it for a bit, then gives me a message that amber has stopped running, check the log file. When I click on the log file, the only message is that I've had a crash. In the older version of chimera I was running, I also tried this with only the IPE & got the same behavior. Are my compounds just too nonstandard? Thanks! Irene Newhouse

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3D labels
by matheus froeyen 26 Apr '11

26 Apr '11

Dear all, I try to change the size of the 3D labels in my structure via the preferences/background menu but there is no effect! Strange but changing the font type & bold, italic etc works. I tried a previous version of chimera and there I have the same problem. The font is always small (about 12?) The 2D labels I can change font size without problem. But I know it has worked before. I have no idea what is going on. I work on A Macintosh G5 with Leopard. Thanks for any suggestions mathy

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labels
by Jean-Paul Armache 26 Apr '11

26 Apr '11

hello, i was wondering, whether there is a way to make the 2d labels appear slowly, stepwise (meaning, through some rounds of opacity to the normal text) ? best regards, jean-paul

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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 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

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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 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.

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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

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

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

3 2

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

2 2

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

2 1

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

3 6

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. ****************************************************

2 1

Controling the configuration of chiral atoms.
by vincent zoete 07 Apr '11

07 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.

2 2

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

2 1

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

2 1

salt bridges
by Simon Sham 07 Apr '11

07 Apr '11

Hi, I have tried to find out salt bridges with chimera. According to the archive: "findhbond selRestrict both saveFile ~/mydir/myfile" 1. I could not find "selRestrict" under "FindHbond". I am using the latest version of CHimera. Thanks for your help in advance. Best, Simon Sham

4 6

Scrollbar in Structure/sequence associations
by Lucio Ricardo Montero Valenzuela 06 Apr '11

06 Apr '11

Hello. I want to suggest that a vertical scrollbar be added to the Structure/sequence associations dialog box, because whenever there are more than ~17 models, the last ones are not reachable. Lucio

2 1

Suggestion
by Davis, Derick C. (MU-Student) 04 Apr '11

04 Apr '11

Hello, I was wondering if the developers have considered creating an application of Chimera for the iPhone or iPad? If not, they should :) Thank you, Derick Davis

2 1

Map's Box size
by יוכבד 04 Apr '11

04 Apr '11

Hi Can I please get your help with map resizing. I have a map with a box size 250,269,108. To run a map fitting script I need the map to have a cubic size. Using the volume viewer- Region min max step x - I was able to play with the box size the problem is I can't get the entire map into a cubic box (Z axis is to small). Is there a way to enlarge the box on the Z axis? Thank you Yocheved

3 2

Thermal ellipsoids are not updated when playing multi-frame PDB trajectory
by Lukasz Walewski 01 Apr '11

01 Apr '11

Hi, I am looking at the trajectory with thermal anisotropy factors that change from frame to frame, i.e. I have a multi-frame PDB file that contains ATOM and ANISOU records. The components of the anisotropy tensors change during the simulation (the data I am analyzing has a redefined meaning). I am able to properly read and play the trajectory. Ellipsoid representation of the thermal U factors works excellent for a single frame. However it seems that the ellipsoids are not updated when I play the trajectory, i.e. the atoms move as expected but the ellipsoids retain both their positions and shape from the first frame. Is there any way around ? In any case I find Chimera wonderful software that I came upon only recently. Thanks guys for developing it! With best regards, Lukasz

2 2

Script for getting the map values of fitted residues.
by Robert Ford 29 Mar '11

29 Mar '11

I was wondering if there was a script available that would get the map density values of amino aid residues in a model fitted to an EM or X-ray density map and then write the data to a text file? Essentially what I need is something that does something like this (but not laboriously by hand) e.g. in command line mode select #1:1.B then I use Tools>Volume Data>Fit in Map and click 'Update' to get the average map density value for the atoms in amino acid residue number 1 in chain B of model 1. Many thanks for your help Bob Ford, Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, 131 Princess St., The University of Manchester Manchester M1 7DN, UK. Tel: +44(0)161 2004187 Fax: +44 (0)161 3068918 bob.ford(a)manchester.ac.uk www.ls.manchester.ac.uk

2 1

Ask a question
by ding kevin 29 Mar '11

29 Mar '11

Hi, I am a freshman to use Chimera. When I run "add charge" of ligand by the tutorial, and the error below appears. I would like to know the reasons and how could I solve this problem. Thank you very much! Charge model: AMBER ff99SB Assigning partial charges to residue ARA (net charge +0) with am1-bcc method Running ANTECHAMBER command: D:/drivers/Chimera 1.5.3rc/bin/amber11/bin\antechamber -ek qm_theory='AM1', grms_tol=0.02, tight_p_conv=0, scfconv=1.d-10, -i c:\users\dingzh~1\appdata\local\temp\tmpkghulj\ante.in.mol2 -fi mol2 -o c:\users\dingzh~1\appdata\local\temp\tmpkghulj\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 (ARA) cygwin warning: (ARA) MS-DOS style path detected: c:\users\dingzh~1\appdata\local\temp\tmpkghulj\ante.in.mol2 (ARA) Preferred POSIX equivalent is: /cygdrive/c/users/dingzh~1/appdata/local/temp/tmpkghulj/ante.in.mol2 (ARA) CYGWIN environment variable option "nodosfilewarning" turns off this warning. (ARA) Consult the user's guide for more details about POSIX paths: (ARA) http://cygwin.com/cygwin-ug-net/using.html#using-pathnames (ARA) /usr/bin/antechamber.exe: error while loading shared libraries: ?: cannot open shared object file: No such file or directory (ARA) Error: cannot run ""D:/drivers/Chimera 1.5.3rc/bin/amber11/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in judgebondtype() of antechamber.c properly, exit (ARA) Running: "D:/drivers/Chimera 1.5.3rc/bin/amber11/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac Failure running ANTECHAMBER for residue ARA Check reply log for details -- Zhaoyang Ding East China University of science and technology Shanghai China

2 1

recovering saved pseudobonds; or convert pseudo to bond?
by Kelly Dryden 28 Mar '11

28 Mar '11

Hi, I have a series of saved selections that contain a combination of bonds and pseudobonds, but when I save the session and return to it, only the bonds are recalled. All my attempts to convert the pseudobonds to "real" bonds have failed. This is from a manually created cage model, without real atoms. Is there anyway to either make all the connections into bonds, or to save the pseudobonds in the "named selections"? Thanks, Kelly

3 4

Re: [Chimera-users] [chimera-dev] Energy Minimisation Citation
by Nancy 28 Mar '11

28 Mar '11

Thank you very much for your explanations, I greatly appreciate it. Nancy On Mon, Mar 28, 2011 at 1:47 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Konrad, > Thanks for the MMTK citation link. The force field information is in the > Chimera minimization man page, for example: > > < > http://www.cgl.ucsf.edu/chimera/1.5.3/docs/ContributedSoftware/minimize/min… > > > > To summarize, Amber ff99 is used for standard residues and monatomic ions, > Antechamber/GAFF for nonstandard residues. Of course, the page above also > mentions MMTK and links to its documentation. 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 Mar 28, 2011, at 10:24 AM, Konrad Hinsen wrote: > > > On 28 Mar, 2011, at 5:26 , Nancy wrote: > > > >> I used the "Minimize Structure" feature of Chimera to minimize several > ligand molecules in preparation for docking (with the "Gasteiger" charges > option). I need to cite this in an article that I am to submit for > publication, and I need a bibliography of the software, including a > description of the minimisation algorithm, force field, etc... Please let > me know how I should go about this? > > > > The minimization code used by Chimera comes from MMTK, whose reference is > this paper: > > > > > http://dirac.cnrs-orleans.fr/plone/publications/all-publications/H_2000_2 > > > > The force field is some dialect of Amber, though I don't know which one > exactly is used by Chimera. I hope someone else can provide that > information. > > > > Konrad. > >

1 0

(no subject)
by Hernán Costa 28 Mar '11

28 Mar '11

Hi I need to obtain mutation on differents sites on a protein but i can´t. How can I create a mutual mutation an know if the rotamer selected is Ok? Thanks Hernán Costa

2 3

Energy Minimisation Citation
by Nancy 28 Mar '11

28 Mar '11

Dear All, I used the "Minimize Structure" feature of Chimera to minimize several ligand molecules in preparation for docking (with the "Gasteiger" charges option). I need to cite this in an article that I am to submit for publication, and I need a bibliography of the software, including a description of the minimisation algorithm, force field, etc... Please let me know how I should go about this? Thank you very much, Nancy

2 1

RMSD Calculation
by Nancy 26 Mar '11

26 Mar '11

Hi All, I need to determine the RMSD of a small molecule cocrystallized ligand, against a large number of predicted docked conformations. Please let me know what is the best method for doing this. Thank you very much, Nancy

1 0

displaying DelPhi results
by Knut Langsetmo 25 Mar '11

25 Mar '11

Hi, I have done a DelPhi calculation on my protein, and when I try to display it, I get the error: "File cam.phi, format delphi Record size 1852798752 > file size 26826676" Any suggestions would be greatly appreciated. Thanks, --Knut

2 1

Automated RMSD Calculations
by Nancy 25 Mar '11

25 Mar '11

Hi All, I would like to calculate RMSDs of a large number of small molecule conformations against a reference conformation, is there a simple software program or method that can be used to perform such calculations? Thanks in advance, Nancy

2 1

Chimera production release candidate (1.5.3)
by Elaine Meng 25 Mar '11

25 Mar '11

A Chimera production release candidate (version 1.5.3) is now available: <http://www.cgl.ucsf.edu/chimera/download.html> Please try it and report any problems. The 1.5 series includes 64-bit versions and will be the last for X11 on Mac (not to worry, the native Mac versions will still be supported). See the release notes for changes relative to previous versions of Chimera: <http://www.cgl.ucsf.edu/chimera/1.5.3/docs/relnotes/1.5.html> Relative to 1.5.2, version 1.5.3: - corrects line width in saved images (affects mesh, silhouette edges, and other lines such as H-bonds) - fixes error on Windows associated with non-Unicode usernames - turns multisampling off by default on Macs (it was associated with bad behaviors on some Mac systems) Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

installation problem
by estrella＠cartuja.csic.es 23 Mar '11

23 Mar '11

Hi, I´ve tried hardly to intall the last Chimera version for Windows (chimera 1.5.3rc), but at the phyton execution time, I have this message: "Unable to execute file: C\Archivos de programa\Chimera 1.5.3rc\phyton.exe Create process failed; code 14001" Ifound this error and it possible solution in internet, without any success. Could you help me? Thanks so much Estrella

2 1

Re: [Chimera-users] chimera help...please...
by Eric Pettersen 23 Mar '11

23 Mar '11

On Mar 23, 2011, at 2:32 AM, Amit Kumar wrote: > > Dear Pettersen, > first of all I like to thanks you as i am getting always nice > graphics from chimera software and hope you still involve in > improving it to compete all over good structure visualizers.... > I am a frequent user of this visualizer and already cited in all my > papers internationally published. I am struggling in getting ... I'm happy you've gotten good results with Chimera, and thanks for the citations -- they help us get our funding renewed! > 1) user guide of UCSF Chimera in pdf version as whole If you go to the Chimera home page and click on the "Documentation" link, there will be a list of links to various documentation. One of those links will be for a PDF of the 1.5 version of the User's Guide. It's about 12.5 MB (828 pages). The Chimera documentation was always designed to be hyperlinked web pages, so the PDF version is not as well organized or concise as it would be if the documentation was PDF-based. I hope you know that the HTML User Guide is bundled with each Chimera download and therefore all the Help buttons in dialogs, the "help" command, and the various functions in the Help menu just access your local copy and don't go over the web. > 2) if i build structure - add atom in structure ----whether we can > plced the atom at my desired place or coordination...if yes > how...and whether i can dragg that atom specifically to some unique > place....how? The atom gets placed in the center of the view, so if you can get the center of the view to be your desired location then you're set. Otherwise, you can use the "Movement Mouse Mode" tool (in the Movement tools category) to move the atom wherever you want it positioned. > 3)whether we can allign the specific atom/residue and accordingly > whole molecule....how? Although i use match maker that allign whole > molecules but my specific residue miss out Use the "match" command to match specific atoms/residues. Open the command line (Favorites->Command Line) and type "help match" for details. As an example if you wanted to match residue 14 in model 0 with residue 20 in model 1 (and they were the same residue type with the same atom names) then "match #0:14 #1:20" will move model 0 so that its residue 14 will be superimposed on model 1's residue 20. > 4)how i can allign heteroatom like in my case i am trying to allign > heme from different hemoglobin molecule with maximum efficiency...as > heme are chemically same for both molecule it should allign > perfectly and accordingly their globin (apoprotein) part... Similarly, if the hemes have the same number of atoms and the same atom names then something like "match #0:HEM #1:HEM" would work (also assuming only one heme per model). If the hemes have differing numbers of atoms or different atom names then you would have to use a more detailed match command where you actually specify the atom names so Chimera knows which atoms to pair up in the match. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

DNA atomic structure fitting with an envelope
by Damien Larivière 22 Mar '11

22 Mar '11

Dear all, James Stroud or Thomas Bishop webservices among others enable to create a portion of DNA in the PDB format. Is it possible in Chimera to import a mesh envelop (see image), the PDB structure of the DNA portion and to force the DNA to fit with the envelope (which has the length and the diameter of the DNA portion)? Many thanks for your help Damien ps: As far I understand, the MDFF tool by Klaus Schulten allows to conform a PDB structure to a mesh (interesting for cryoEM). I have not tested it yet.

2 1

Offsetting residue numbering
by Sumitro Harjanto 22 Mar '11

22 Mar '11

Hi Elaine, Is there a way to introduce a systematic offset to the residue numbering in a model? The numbering in my model is different from the convention. Eg. the methionine that's supposedly in position 5 is labeled as MET 4, alanine in position 6 as ALA 5, and so on. I can't do it manually cos there are many residues. Is there an easy way to resolve this other than using a script to automatically assign the labels? It'll be good if i can resolve this from the root , such that my atom specification is also consistent with the naming convention I use. :) Cheers, Sumitro Institute for Infocomm Research disclaimer: "This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you."

3 3

matchmaker output
by Tiziano Tuccinardi 18 Mar '11

18 Mar '11

Dear all, I am using MatchMaker for aligning about 100 structures, and it works very well!! Is it possible to automatically save the pairwise alignment without opening the MultAlignViewer? Due to the large number of structures, I cannot use the Match-Align tool but it would be enough to save the pairwise alignments Thanks in advance Tiziano -- +++++++++++++++++++++++++++++++++++++ Tiziano Tuccinardi, PhD Dip. Scienze Farmaceutiche Via Bonanno 6, 56126 PISA Tel ++39 050 2219595 Fax ++39 050 2219605 E-mail tuccinardi(a)farm.unipi.it <mailto:tuccinardi@farm.unipi.it> http://www.mmvsl.farm.unipi.it/staff/tiziano-tuccinardi/ Adjunct Assistant Professor SbarroInstitute for Cancer Research and Molecular Medicine Centerfor Biotechnology TempleUniversity PhiladelphiaPA 19122 (USA) +++++++++++++++++++++++++++++++++++++

2 3

Movie frames are blank
by Gökhan Tolun 17 Mar '11

17 Mar '11

Dear all, I am trying to create a very simple movie, but my movies turn out blank. I am using the Spin Movie example script on http://www.cgl.ucsf.edu/chimera/tutorials/movies08/moviemaking.html My movie seems to render, and the movie file is created, but when I open the file and play it, its just a blank (all black) video. When I examined the captured frames, theyre also all blank black frames. If I choose Save image, it saves it just fine, so I guess the image capturing algorithm for movies is different the one for saving the images. This is on Windows 7 64-bit, Chimera 1.5.2, Intel Mobile 965 express Chipset GPU (its a TabletPC, hence the GPU). Any suggestions to fix this would be appreciated. Thank you. _______________________________________ Gökhan Tolun, M.S., PhD. Post-doctoral Research Associate Lineberger Comprehensive Cancer Center University of North Carolina 450 West Dr., CB#7295, Room 11-119 Chapel Hill, NC, USA 27599

2 1

Average Backbone B-factor
by Simon Sham 17 Mar '11

17 Mar '11

Hi, I need to read a pdb file and calculate the average backbone (CA, C, & N) B-factor for each residue and compare it with the result some MD. Is there anyway I can do it in Chimera? Thanks, Simon

2 1

Re: [Chimera-users] error: from DockPrep import prep
by wascm 16 Mar '11

16 Mar '11

Dear sir: Thanks for the detailed reply! When the following code was added to the start of sciprt: import chimeraInit chimeraInit.init(nogui=True, silent=True) The interpreter print the following confused error: --------------------------------------------- Traceback (most recent call last): File "./xx.py", line 5, in <module> chimeraInit.init(nogui=True, silent=True) TypeError: init() takes at least 1 argument (2 given) ----------------------------------------------- it's really easy and convenient to running python script with chimera. The reason for i want to run python script independently is that i want add some custom command option. However, if i run python script with chimera, it's hard for me to add some custom command option and handle it in the script though getopt module. For example, when i run some command like this: chimera –nogui test.py -t test test.py ################### #!/usr/bin/python t=None try: opts, args = getopt.getopt(sys.argv[1:], "t:") except getopt.GetoptError, err: pass finally: for arg_k, arg_v in opts: if (arg_k =="-t"): t=arg_v #################################### This will raise running exception! is there a way for me to add the coustom option to python script and run the script with chimera? the exception message as follow: ------------------------------------------------- Executing test.py... Traceback (most recent call last): File "/home/wascm/chimera/share/chimeraInit.py", line 588, in init chimera.openModels.open(a, prefixableType=1) File "/home/wascm/chimera/share/chimera/__init__.py", line 1537, in open models = func(filename, *args, **kw) File "/home/wascm/chimera/share/chimera/__init__.py", line 972, in _openPython loadFunc(sandboxName, fileName, f) File "test.py", line 10, in <module> for arg_k, arg_v in opts: NameError: name 'opts' is not defined Error while processing test.py: NameError: name 'opts' is not defined File "test.py", line 10, in <module> for arg_k, arg_v in opts: See reply log for Python traceback. Traceback (most recent call last): File "/home/wascm/chimera/share/chimeraInit.py", line 588, in init chimera.openModels.open(a, prefixableType=1) File "/home/wascm/chimera/share/chimera/__init__.py", line 1503, in open raise ValueError, "Unknown model type" ValueError: Unknown model type Error while processing -t: ValueError: Unknown model type File "/home/wascm/chimera/share/chimera/__init__.py", line 1503, in open raise ValueError, "Unknown model type" See reply log for Python traceback. Traceback (most recent call last): File "/home/wascm/chimera/share/chimeraInit.py", line 588, in init chimera.openModels.open(a, prefixableType=1) File "/home/wascm/chimera/share/chimera/__init__.py", line 1503, in open raise ValueError, "Unknown model type" ValueError: Unknown model type Error while processing test: ValueError: Unknown model type File "/home/wascm/chimera/share/chimera/__init__.py", line 1503, in open raise ValueError, "Unknown model type" See reply log for Python traceback. ---------------------------------------------------------- At 2011-03-15 09:02:09，"Greg Couch" <gregc(a)cgl.ucsf.edu> wrote: (This is really achimera-dev(a)cgl.ucsf.edu mailing list question.) My guess is that your problem is that chimeraInit.init() was never called, so the chimera internals were never set up. So in the beginning of your Python script, add: import chimeraInit chimeraInit.init(nogui=True, silent=True) before using chimera's modules. But, in general, you would be better off running those python scripts with chimera. For example: % chimera --nogui --silent script.py That would set up the the appropriate environment for chimera, execute the python script, and exit. And you would be protected against any future changes in how chimera is initialized. If you want to use other Python modules with chimera, set your CHIMERAPATH environment variable with a list of directories that hold the Python modules (same syntax as PYTHONPATH, but just for chimera). If you want to install other Python packages into chimera's Python that have a setup.py file, use: % chimera --nogui --silent setup.py install It is also possible to make easy_install work with chimera by temporarily putting chimera's bin directory on your path and running the appropriate egg (seehttp://pypi.python.org/pypi/setuptools for details). Right now, chimera is using Python 2.7. HTH, Greg

3 2

radial clipping
by Kelly Dryden 16 Mar '11

16 Mar '11

Hi, I would like to radially clip a density map. There are nice ways to do radial coloring, but I haven't found anything that allows a similar cropping (preferably with capping). Is there an easy way to do this? I do not want to erase the density, but rather be able to see the surface at varying radii, just as you can do with planes. (At the moment, I can only run v1.4). Thank you, Kelly

3 5

Re: [Chimera-users] [chimera-dev] error: from DockPrep import prep
by wascm 15 Mar '11

15 Mar '11

Dear sir: Your suggestions do work well! The problems have been resolved well by your help. Thank you very much! Best Wishes Tao Cui From:Eric Pettersen Date:2011-03-16 05:12 Subject:Re: [chimera-dev] [Chimera-users] error: from DockPrep import prep To:wascm Cc:Greg Couch,chimera-dev BB,UCSF Chimera Mailing List On Mar 15, 2011, at 5:37 AM, wascm wrote: Dear sir: Thanks for the detailed reply! When the following code was added to the start of sciprt: import chimeraInit chimeraInit.init(nogui=True, silent=True) The interpreter print the following confused error: --------------------------------------------- Traceback (most recent call last): File "./xx.py", line 5, in <module> chimeraInit.init(nogui=True, silent=True) TypeError: init() takes at least 1 argument (2 given) There was an oversight in the code Greg provided: chimeraInit.init takes a mandatory "argv" argument, which is exactly like sys.argv. ----------------------------------------------- it's really easy and convenient to running python script with chimera. The reason for i want to run python script independently is that i want add some custom command option. However, if i run python script with chimera, it's hard for me to add some custom command option and handle it in the script though getopt module. For example, when i run some command like this: chimera –nogui test.py -t test test.py ################### #!/usr/bin/python t=None try: opts, args = getopt.getopt(sys.argv[1:], "t:") except getopt.GetoptError, err: pass finally: for arg_k, arg_v in opts: if (arg_k =="-t"): t=arg_v #################################### This will raise running exception! is there a way for me to add the coustom option to python script and run the script with chimera? Yes. Use a --script argument, like this: chimera --nogui --script "test.py -t test" --Eric

1 0

I am having a problem
by Burt Goldberg 15 Mar '11

15 Mar '11

Dear, Chimera, as I opened the program it prompted me to re-register. I tried 3 time but got a Error message PKCS7. HELP!!!! Burt -- Burt Goldberg, PhD Professor of Chemistry & Biochemistry Chemistry Department Affiliated Research Professor Medical Parasitology New York University School of Medicine New York University

2 1

Re: [Chimera-users] Selection through bond and fragment naming
by Jean Didier Pie Marechal 14 Mar '11

14 Mar '11

Dear all, thanks a lot for your answers. I seem to have a problem though. When running the script, one way or another I always ends up with something like: a.residue.removeAtom(a) AttributeError: 'NoneType' object has no attribute 'removeAtom' AttributeError: 'NoneType' object has no attribute 'removeAtom' File "M:\REUNIONS\dibuixos\Manipulate_structure\newres.py", line 20, in <module> a.residue.removeAtom(a) See reply log for Python traceback. I think I got the origin of the problem but can't figure out how to solve it. What I observed is that, before running the script if I do the following after selecting my atoms: >>> for a in at: print a.residue I have the following list printed UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 but doing the same AFTER having run the script gives : None UNK 1 UNK 1 UNK 1 UNK 1 UNK 1 ... It seems like the residue type of the first atom disappeared. Any clue? all the best, JD Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://asklipio.qf.uab.es ----- Missatge original ----- De: Eric Pettersen <pett(a)cgl.ucsf.edu> Data: Divendres, Març 11, 2011 8:29 pm Assumpte: Re: [Chimera-users] Selection through bond and fragment naming > On Mar 11, 2011, at 7:42 AM, Jean Didier Pie Marechal wrote: > > > Hi, > > > > I have a system from which I only have xyz coordinates. What I > would > > like to do is to define myself residue attribute on different > > fragments of the molecules. Could you tell me how (or if there is > a > > way to ): > > > > 1. expand a selection to bonding atoms (i.e. I click on one atom > and > > expand selection through one bond after each actions) This would > be > > of the easiest way for me to select the fragments I want to. > > Hi JD, > My only idea as to how to do this is with a short Python script: > > from chimera.selection import currentAtoms, addCurrent > addAtoms = set() > for a in currentAtoms(): > addAtoms.update(a.neighbors) > addCurrent(addAtoms) > > You could then use the open command to run it: > > open <script folder location (e.g. ~marechal/scripts)>/expand.py > > which you could short to "xp" with the alias command: > > alias ^xp open blah-blah/expand.py > > > > > 2. set a residue attribute to the given selected fragment. I > think I > > remember how to do so in scripting, but what is the command line > to > > do so? > > So, do you really want to set a residue-level attribute, or do you > want to organize the selected atoms into a residue? Setting a > residue- > level attribute for the atoms is easy: > > setattr r myAttrName my-attr-val sel > > Organizing the atoms into a residue again requires Python, and not > as > simple a script as for your first question, e.g.: > > # script designed to run under "runscript" command, therefore has > an > "arguments" variable available... > try: > rname, rnum = arguments > except ValueError: > raise chimera.UserError("must supply residue name and number > arguments") > > try: > rnum = int(rnum) > except ValueError: > raise chimera.UserError("residue number (second arg) must be an > integer") > > atoms = chimera.selection.currentAtoms() > if not atoms: > raise chimera.UserError("No atoms selected") > > # make a new residue > newRes = atoms[0].molecule.newResidue(rname, "A", rnum, ' ') > > # withdraw atoms from their current residues > for a in atoms: > a.residue.removeAtom(a) > if len(a.residue.atoms) == 0: > a.molecule.deleteResidue(a.residue) > > # add atoms to new residue > for a in atoms: > newRes.addAtom(a) > > So you would run this script with the command "runscript blah- > blah/ > newres.py TYR 1", which could again be shorted using aliasing: > > alias ^nr runscript blah-blah/newres.py $1 $2 > > --Eric > > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > >

2 1

registration and user group
by SteffenVfx 14 Mar '11

14 Mar '11

Hi there. I've been trying to register with you all for some time, but it always comes back with a registration error. I'd like to enroll in your mailing list and user group forum. can you pass along my information? thanks casey *Steffen VFX ~the science of storytelling~* *| Casey Steffen M.S. | President/Chief Creative Officer | 211 6th Ave. #2a | Brooklyn, NY 11215 | **Web:**www.steffenvfx.com | **Twitter:**SteffenVfx<http://twitter.com/steffenvfx> | **Blog:**http://blog.steffenvfx.com | **Phone:347-875-0423 |*

2 1

bond selection
by Elisabeth Ortega 11 Mar '11

11 Mar '11

Dear Chimera Dev. Team, I have a little question for you. How can I select a bond using the Command Line (or the IDLE)? Thanks in advance. Elisabeth Ortega-Carrasco Universitat Autònoma de Barcelona

3 2

Selection through bond and fragment naming
by Jean Didier Pie Marechal 11 Mar '11

11 Mar '11

Hi, I have a system from which I only have xyz coordinates. What I would like to do is to define myself residue attribute on different fragments of the molecules. Could you tell me how (or if there is a way to ): 1. expand a selection to bonding atoms (i.e. I click on one atom and expand selection through one bond after each actions) This would be of the easiest way for me to select the fragments I want to. 2. set a residue attribute to the given selected fragment. I think I remember how to do so in scripting, but what is the command line to do so? Kind regards, JD Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://asklipio.qf.uab.es

4 3

error: from DockPrep import prep
by wascm 10 Mar '11

10 Mar '11

Dir sir I try to write a indenpendent python script and run it from command line some global variables was first set: export LD_LIBRARY_PATH=/home/wascm/chimera/lib:$LD_LIBRARY_PATH export PYTHONPATH=/home/wascm/chimera/share:/home/wascm/chimera/lib:$PYTHONPATH export CHIMERA=/home/wascm/chimera the script work well when import following module import chimera from chimera import runCommand, openModels, MSMSModel from WriteMol2 import writeMol2 from WriteDMS import writeDMS however, when add the code: from DockPrep import prep the error information as follows: ####################################### Traceback (most recent call last): File "./xx.py", line 12, in <module> from DockPrep import prep File "/home/wascm/chimera/share/DockPrep/__init__.py", line 15, in <module> from prefs import prefs, defaults, INCOMPLETE_SC, MEMORIZED_SETTINGS File "/home/wascm/chimera/share/DockPrep/prefs.py", line 13, in <module> from Rotamers.prefs import defaults as rotamerDefaults File "/home/wascm/chimera/share/Rotamers/__init__.py", line 574, in <module> from prefs import defaults, CLASH_METHOD, CLASH_THRESHOLD, HBOND_ALLOWANCE File "/home/wascm/chimera/share/Rotamers/prefs.py", line 13, in <module> from DetectClash.prefs import CLASH_THRESHOLD, HBOND_ALLOWANCE, PB_COLOR, \ File "/home/wascm/chimera/share/DetectClash/__init__.py", line 157, in <module> val = getColorByName(val) File "/home/wascm/chimera/share/chimera/colorTable.py", line 87, in getColorByName color = chimera.MaterialColor(r/255.0, g/255.0, b/255.0) ValueError: missing default material ################################################# how can i solve this problem? best wishes Tao Cui

1 0

error: from DockPrep import prep
by wascm 10 Mar '11

10 Mar '11

Dir sir I try to write a indenpendent python script and run it from command line some global variables was first set: export LD_LIBRARY_PATH=/home/wascm/chimera/lib:$LD_LIBRARY_PATH export PYTHONPATH=/home/wascm/chimera/share:/home/wascm/chimera/lib:$PYTHONPATH export CHIMERA=/home/wascm/chimera the script work well when import following module import chimera from chimera import runCommand, openModels, MSMSModel from WriteMol2 import writeMol2 from WriteDMS import writeDMS however, when add the code: from DockPrep import prep the error information as follows: ----------------------------------- Traceback (most recent call last): File "./xx.py", line 12, in <module> from DockPrep import prep File "/home/wascm/chimera/share/DockPrep/__init__.py", line 15, in <module> from prefs import prefs, defaults, INCOMPLETE_SC, MEMORIZED_SETTINGS File "/home/wascm/chimera/share/DockPrep/prefs.py", line 13, in <module> from Rotamers.prefs import defaults as rotamerDefaults File "/home/wascm/chimera/share/Rotamers/__init__.py", line 574, in <module> from prefs import defaults, CLASH_METHOD, CLASH_THRESHOLD, HBOND_ALLOWANCE File "/home/wascm/chimera/share/Rotamers/prefs.py", line 13, in <module> from DetectClash.prefs import CLASH_THRESHOLD, HBOND_ALLOWANCE, PB_COLOR, \ File "/home/wascm/chimera/share/DetectClash/__init__.py", line 157, in <module> val = getColorByName(val) File "/home/wascm/chimera/share/chimera/colorTable.py", line 87, in getColorByName color = chimera.MaterialColor(r/255.0, g/255.0, b/255.0) ValueError: missing default material ---------------------- how can i solve this problem? best wishes Tao Cui

1 0

Re: [Chimera-users] using chimera command in batch mode
by cuitao＠webmail.hzau.edu.cn 10 Mar '11

10 Mar '11

Dear sir I am so grateful to you for your detailed answer. Thanks a million. best wishes Tao Cui ------------------ 原始邮件 ------------------ >From: Eric Pettersen <pett(a)cgl.ucsf.edu> >Reply-To: UCSF Chimera Mailing List <chimera-users(a)cgl.ucsf.edu> >To: "cuitao(a)webmail.hzau.edu.cn" <cuitao(a)webmail.hzau.edu.cn> >Cc: UCSF Chimera Mailing List <chimera-users(a)cgl.ucsf.edu> >Subject: Re: using chimera command in batch mode >Date: Wed, 9 Mar 2011 13:11:31 -0800 > On Mar 8, 2011, at 5:30 PM, Tao Cui wrote: Dear sir: I have seen one message you posted in dock-fans mail list. http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html The batch mode solution you privided is really helpful to me. I wnat to know if I can complete similar batch mode works for other applation? for example, delete all H atoms, save molecule to pdb format and writedms. Thank you very much! Hi Tao, You can use the same approach outlined in the dock-fans post to write scripts for other purposes. The script in that post uses Python since that is the only way to call DockPrep from a script, but if the things you want to do are available as Chimera commands you can just write a Chimera command script and use it the same way (the script would need to end in .com or .cmd instead of .py though). So deleting all H atoms would just be the command "del H". You would save a file in PDB format with the "write" command (type "help write" in Chimera to see what arguments you would want). Writing a DMS file isn't available as a command, so you would need to use Python scripting for that, along the lines of: from chimera import runCommand, openModels, MSMSModel # generate surface using 'surf' command runCommand("surf") # get the surf object surf = openModels.list(modelTypes=[MSMSModel])[0] # write DMS from WriteDMS import writeDMS writeDMS(surf, "output.dms") You would need to keep in mind that Chimera's surface generation will fail for some structures, more so on Windows than other platforms, so you might want to check that the output file actually has some surface points in it. Alternately, in Chimera, the surface attribute "calculationFailed" will tell you if the surface calculation succeeded or not, so you could do something other than try to write the DMS file if that attribute is False. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

2 1

Re: [Chimera-users] Internal water molecules
by Tom Goddard 10 Mar '11

10 Mar '11

Hi John, Here's an idea about how to define internal water molecules and identify them in Chimera. Make a density map of the molecule at some resolution, say 5 Angstroms, using the Chimera "molmap" command, then define internal waters to be the ones that are located at a point above a certain density threshold. You can use the Chimera "Values at Atom Positions" dialog (menu Tools / Volume Data) to get the interpolated density map value at each atom position. It assigns the density value to each atom. Then you can use the Render by Attribute dialog (menu Tools / Structure Analysis) to select just those atoms with values above the threshold density. Then you can intersect that list of atoms with waters since it will also include protein atoms. All this is easy to do but since you want to do it for many frames of a molecular dynamics simulation you need a script that can be run for each MD frame. Unfortunately the values at atom positions and the render by attribute selection capability don't have Chimera command equivalents. But those capabilities (like all Chimera capabilities) can be used with a Python script. I could provide you a script if this sounds useful. Also I'll add to our feature request list the need for Chimera commands that would allow you to do it without resorting to Python. Tom > Hello, > > Is it possible, in Chimera, to select only the internal water > molecules of a protein structure? I need to find out how many water > molecules enter the protein structure from the outside during a > molecular dynamics simulation. > > Thanks! > > John

3 5

Re: [Chimera-users] castp visualization
by Elaine Meng 09 Mar '11

09 Mar '11

On Mar 9, 2011, at 9:06 AM, Irene Newhouse wrote: > Remember a few days ago, I sent you an image from a Chimera castp visualization & it looked really weird, with strips connecting two apparently disconnected regions? Well, I put up PyMol & its castp viewer & it manages to plot the surface understandably - blackish represents the 'outside' of the cavity... I think my protein is nonetheless somewhat pathological, because if I try to render the same surface in mesh, it swells to occupy nearly the whole molecule, which is not right - mesh & solid should enclose the same volume. However, the solid rendering does reproduce where the substrate goes, and how on earth it gets in there is now my problem:-) > > I just tried something else -- I have the new Chimera on my linux station, & that's where I was seeing the odd renderings. On my PC, I have the previous version of Chimera & it shows the same surfaces as PyMol! The image chasurfs.png shows the odd effects [from the current release on my linux station], for only one of the dimer units [I thought maybe the dimer was the issue. No.] Possibly the surface rendering of cavities in the current release of Chimera is correct most of the time, but it looks as if it's not for a protein as odd as this one. For debugging purposes, the PDB is 1X09 [I used Chimera to generate the other dimer unit]. > Hi Irene, Given your observations, it may be a graphics driver problem on your linux machine. I.e. the salient difference may be the platform, not the Chimera version. However, wasn't what you sent before from Surfnet, not CASTp? In any case, my understanding is that the same Chimera code is used on the different platforms, and I don't think these tools have been changed for months. I just tried "open castp:1x09" in the 1.5 release and a recent daily build (v1.6 Feb 24) and looked at a few pockets, and the surfaces seemed fine. Since I deal with the user interface and not programming or hardware issues, I included the list in case others have suggestions or comments. Best, Elaine

3 2

Re: [Chimera-users] using chimera command in batch mode
by Eric Pettersen 09 Mar '11

09 Mar '11

On Mar 8, 2011, at 5:30 PM, Tao Cui wrote: > Dear sir: > > I have seen one message you posted in dock-fans mail list. > > http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html > > The batch mode solution you privided is really helpful to me. I > wnat to know if I can complete similar batch mode works for other > applation? for example, delete all H atoms, save molecule to pdb > format and writedms. > > Thank you very much! Hi Tao, You can use the same approach outlined in the dock-fans post to write scripts for other purposes. The script in that post uses Python since that is the only way to call DockPrep from a script, but if the things you want to do are available as Chimera commands you can just write a Chimera command script and use it the same way (the script would need to end in .com or .cmd instead of .py though). So deleting all H atoms would just be the command "del H". You would save a file in PDB format with the "write" command (type "help write" in Chimera to see what arguments you would want). Writing a DMS file isn't available as a command, so you would need to use Python scripting for that, along the lines of: from chimera import runCommand, openModels, MSMSModel # generate surface using 'surf' command runCommand("surf") # get the surf object surf = openModels.list(modelTypes=[MSMSModel])[0] # write DMS from WriteDMS import writeDMS writeDMS(surf, "output.dms") You would need to keep in mind that Chimera's surface generation will fail for some structures, more so on Windows than other platforms, so you might want to check that the output file actually has some surface points in it. Alternately, in Chimera, the surface attribute "calculationFailed" will tell you if the surface calculation succeeded or not, so you could do something other than try to write the DMS file if that attribute is False. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

select by atom number
by Francesco Pietra 09 Mar '11

09 Mar '11

Hello: Is any trick to select by atom number? Having NAMD files with CHARMM FF, i.e., SEGID and no chain ID, I find now difficult to use CHIMERA the way I used it. Thanks francesco pietra

3 2

color bond distance, angle and so on
by Jean-Didier Maréchal 08 Mar '11

08 Mar '11

Hi guys, How can I change the color of the labels associated to distance between atoms, angles etc (both the for the text and the dashes). Thanks a lot JD **************************** Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://asklipio.qf.uab.es

5 8

Re: [Chimera-users] How to model a 4Fe4S cluster on conserved Cys residues
by Elaine Meng 08 Mar '11

08 Mar '11

On Mar 8, 2011, at 1:03 PM, Ingmar Buerstel wrote: > Dear Elaine, > thanx a lot for your quick answer. In fact I have already a modelled structure (made with swiss model) of the protein. > I was looking for a possiblitiy to fit a 4Fe4S-cluster in the position of the original cluster. The cysteines are conserved, thus, I just need to copy/paste the 4Fe4S-cluster into my structure. I would be glad, if you could help me concerning this problem. Dear Ingmar, You could superimpose your model and the related structure that does contain this cluster (residue SF4) and then merge the SF4 residue into your model. However, the result may be rough, depending on how well the structures match in 3D. It might be better to start over and use Modeller as described in my previous message, because it can make a model that already includes the cluster. However, if you want to try the superimposing approach, here are more details. (a) In Chimera, open your model and then open the known related structure that contains the cluster. (b) Superimpose the two structures, for example with the Matchmaker tool. Here is some discussion of different ways to superimpose structures in Chimera. You will want to make sure that the structures match well at the four cysteines. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html> (c) Delete everything in the known structure except for the part you want to paste into your homology model, and then combine the two models into one. For example, if your model is open as #0 in Chimera and the known structure is open as #1, you could use commands delete #1 & ~:sf4 combine #0,1 The delete command gets rid of all atoms in #1 except the SF4 residue. The combine command creates a new model, #2, by merging the SF4 residue in #1 with the homology model in #0. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> You can save the new model #2 to a file (for example, with File... Save PDB). However, you would hope that the cysteine sidechains in your model are pointing in the correct orientations to bind the cluster. If not, you might have to paste in those residues from the known structure too, and delete them from your homology model, before merging. Then you might have to manually text-edit the PDB to add bonds between the merged cysteines and the rest of the homology model. Again, it might be better just to start over and use a modelling method that can include the cluster in the first place. 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 > > > > Subject: Re: [Chimera-users] How to model a 4Fe4S cluster on conserved Cys residues > > From: meng(a)cgl.ucsf.edu > > Date: Mon, 7 Mar 2011 09:38:45 -0800 > > CC: chimera-users(a)cgl.ucsf.edu > > To: ingmar_b(a)hotmail.com > > > > Dear Ingmar, > > It sounds like you want to model your whole protein including the 4Fe4S cluster, am I right? Or is there a structure of your protein but that does not include the cluster? > > > > I would not recommend modeling this "from scratch" (building one atom by one atom) in Chimera but instead, homology-modeling your protein and cluster from the structure of a related protein that contains the cluster. Of course, this all depends on the existence of a known structure for a related protein. > > > > Chimera includes an interface to the Modeller program for homology-modeling. To use it, you would have to first go to the Modeller website > > <http://www.salilab.org/modeller/registration.html> > > and register to get a license key (free for academic use). In Chimera, you could choose "Tools... Sequence... Blast Protein," paste in the sequence of your protein, and then blast it against the PDB to see if there are any structures related to your protein. If there is a hit that seems good enough to you, you could use the Blast results dialog to open the structure and also the alignment of the two sequences. > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/blast.html> > > Then, in the sequence alignment window, choose "Structure... Modeller Tools" to show the interface to Modeller. Use "Advanced Option" to "Include non-water HETATM residues from template" so that the FeS cluster will be included in the model. > > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mo…> > > > > Or, you could simply see if there is already a model of your protein available in ModBase by using "File... Fetch by ID" in the Chimera menu. However, those models probably wouldn't contain the FeS cluster. > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/fetch.html> > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modbase.html> > > > > Some related references I just saw but didn't read in detail: > > > > Fee, J. A.; Castagnetto, J.M.; Case, David A.; Noodleman, L.; Stout, C.D.; Torres, R.A.; "The circumsphere as a tool to assess distortion in [4Fe-4S] atom clusters". J. Biol. Inorg. Chem. 2003, 8: 519-526. > > <http://dx.doi.org/10.1007/s00775-003-0445-8> > > > > Atomic resolution structures of oxidized [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus in two crystal forms: systematic distortion of [4Fe-4S] cluster in the protein. > > (2002) J.Mol.Biol. 315: 1155-1166 > > <http://dx.doi.org/10.1006/jmbi.2001.5292> > > (goes with PDB entries 1iqz, 1ir0 ... I see that the residue name of the cluster is SF4, so you could also use the searching tools at the PDB website to find structures that have this cluster) > > > > I hope this helps, > > Elaine > > > On Mar 6, 2011, at 6:44 AM, Ingmar Buerstel wrote: > > > Dear users, > > > i hope anybody out there can help me. I would like to model a 4Fe4S cluster in between a set of four highly conserved Cys residues. From compoarative analysis with crystal strucutre I know there belongs a 4Fe4S but for my respective protein no such crystal exists, so I would like to model my 4Fe4S cluster by my self. I am not very familiar with Chimera, yet, but the "Build structure" function did not work quite well for me. > > > > > > So would kindly ask those who have experince with this kind of models to give me some hinds to model such a FeS-cluster > > > Thanx in advance, > > > Ingmar > >

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Searching chimera-users archive
by Tom Goddard 08 Mar '11

08 Mar '11

Hi Conrad, Searching the Chimera mail archives from the Chimera documentation web page does not work at all well. http://www.cgl.ucsf.edu/chimera/docindex.html I tried searching for "Beale" and it produced no results. > Your search - *Beale site:www.cgl.ucsf.edu/pipermail/chimera-users > -filetype:gz* - did not match any documents. > > Suggestions: > > * Make sure all words are spelled correctly. > * Try different keywords. > * Try more general keywords. > * Try fewer keywords. > There is a message in August 2010 from John Beale. If I search for that message using www.google.com (chimera "startup options" John Beale) I do get the message. So it has been indexed. Some other revealing problems. Searching the Chimera archives from the documentation page for "chimera" produces only 20 hits, all but 5 are attachments. Likewise a search for "windows" produces just 4 hits (one from 2005, one 2006, one 2007, one 2010). Obviously this isn't working. Maybe we should remove the search field from the documentation until we have time to fix it because users (even ones who should know better like me) sometimes believe the search results that there are no archived messages on the topic. Tom > On Mar 8, 2011, at 10:58 AM, Tom Goddard wrote: > >> Hi Eric, >> >> How do I reply to an old chimera-users message and keep my reply in >> the same mailing list thread? I guess there is some mail header line >> that allows the mailing list to recognize which messages belong to >> the same thread. But I don't have the old chimera-users email I want >> to reply to. The web interface to the archive doesn't appear to >> provide a way to reply. > > Well, I don't know for sure, but I assume it is threaded based on the > In-Reply-To header and/or the References header. Now, the archive > doesn't show you either of those so I assume they're buried in some > internal location, so you're stuck. Besides, threading is broken > across month boundaries anyway, so isn't the point moot really? > > --Eric >

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saving charmm layout
by Francesco Pietra 07 Mar '11

07 Mar '11

Hello: Is it possible to save pdb conserving as much as possible charmm layout (in particular the segments (P1, P2, etc)? I find speedy to edit graphically with Chimera but, afterward, much time is required to restore charmm layout. thanks francesco pietra

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How to model a 4Fe4S cluster on conserved Cys residues
by Ingmar Buerstel 07 Mar '11

07 Mar '11

Dear users, i hope anybody out there can help me. I would like to model a 4Fe4S cluster in between a set of four highly conserved Cys residues. From compoarative analysis with crystal strucutre I know there belongs a 4Fe4S but for my respective protein no such crystal exists, so I would like to model my 4Fe4S cluster by my self. I am not very familiar with Chimera, yet, but the "Build structure" function did not work quite well for me. So would kindly ask those who have experince with this kind of models to give me some hinds to model such a FeS-cluster Thanx in advance, Ingmar

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question on volume viewer usage
by Bala subramanian 04 Mar '11

04 Mar '11

Friends, I am using chimera version 1.5 (build 31401 downloaded on 2010-09-16). I have three pdb files (of same protein) and for each pdb file, i have an electro static potential file (.dx file). I opened the three pdb files and then the .dx potential files successively through volume viewer. Each time i open the .dx file, the isosurfaces are mapped on to the first pdb file. Why is it so ?. 1) Precisely 1.dx should be mapped on 1.pdb, 2.dx on 2.pdb...etc. How can i do this ? 2) Is there any way to have a universal setting of volume display options. Like in isosurface threhold (+2 and -2 in my case), color for +ve and -ve surface, transparency etc. Because presently i am doing these settings individually for each .dx file. Thanks, Bala

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1 out of many helices shown as pipe
by odonnell＠chem.fsu.edu 03 Mar '11

03 Mar '11

Hi all, I have a pdb with many alpha helices but I only want one or two to stand out as a pipe. I tried highlighting that particular sequence(s) and going to Depiction => pipesAndPlanks but it will change all of them. Many thanks for a push in the right direction. -Jason ------------------------------------------------------------------------- Sent via webmail for Chemistry & Biochemistry @ Florida State University https://webmail.chem.fsu.edu -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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ambient lighting mode for simple drawing style missing
by Benda, Christian 03 Mar '11

03 Mar '11

Hi possibly a simple question but it has kept me buffled for two weeks now, so I decided to ask: how can I set lighting mode to ambient? I am trying to create images using a simple drawing style like exemplified in http://www.cgl.ucsf.edu/chimera/ImageGallery/ p53 simple drawing or Clathrin but I don't find ambient lighting mode in the viewing tools - lighting menu. The only options given are lights (head light, 1, 2) or quality (normal, glossy). I am using Chimera 1.5 build 30417 fir darwin 64bit, aqua on a MacBook Pro with Mac OS X 10.6.6. Many thanks in advance Christian ________________________________ Dr. Christian Benda Max Planck Institute of Biochemistry Structural Cell Biology Am Klopferspitz 18 D-82152 Martinsried Germany Phone: +49 (0)89 85 78 23 37 Fax: +49 (0)89 85 78 22 19 Email: benda(a)biochem.mpg.de

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Re: [Chimera-users] Problem with Nvidia Quadro FX 880M and Stereocopic view
by Veli-Pekka Kestilä 02 Mar '11

02 Mar '11

Thank you, I had missed the settings on that other place. Now it works quite well. (barring some issues with external monitor) I also noticed that overlay setting in same menu should be on or whole desktop would get blurry (with or without stereo glasses on). -vpk On 3/1/11 10:36 PM, Greg Couch wrote: > If both Chimera and PyMol are complaining, then you've haven't > configured OpenGL stereo correctly. The NVidia Quadro driver > configuration has two places to setup stereo. There are the > "Stereoscopic 3D" settings that are not helpful for chimera (except for > making NVIDIA's stereo image viewer work). So in addition to that, you > want to setup stereo in the "3D Settings / Manage 3D Settings" dialog. > In there, turn on "Stereo - Enable" and select the appropriate kind of > stereo in "Stereo - Display mode". > > Good luck, > > Greg > > On 02/28/2011 09:11 PM, Veli-Pekka Kestilä wrote: >> >> I have done all of these and as I said in my original e-mail I got the >> full screen tests nvidia provides working. Problem is that when I try to >> start Chimera or PyMol it fails complaining that 3d vision mode isn't >> available. So question still basically is if it's possible to get it >> working with Quadro 880M >> >> On 2/23/11 4:40 PM, Sabuj Pattanayek wrote: >>> also see : >>> http://www.pymolwiki.org/index.php/Stereo_3D_Display_Options#NVidia_NVision… >>> >>> . It has some instructions on how to setup 3d vision on windows. >>> >>> On Wed, Feb 23, 2011 at 8:36 AM, Sabuj Pattanayek<sabujp(a)gmail.com> >>> wrote: >>>> IIRC there's an option in the windows nvidia configuration utility >>>> that enables and disables nvidia 3d vision. I assume that's the setup >>>> you're trying to use, so check that to see if it's enabled or >>>> disabled. >>>> >>>> 2011/2/23 Veli-Pekka Kestilä<veli-pekka.kestila(a)helsinki.fi>: >>>>> Hi Tom, >>>>> >>>>> On 2/22/11 8:12 PM, Tom Goddard wrote: >>>>>> Hi Veli-Pekka, >>>>>> >>>>>> This is either a driver configuration problem or driver limitation or >>>>>> driver bug. Your driver is from Oct 2010 and there are newer ones. >>>>>> The >>>>>> following 266.58 driver was released Jan 18, 2011 and the notes >>>>>> say it >>>>>> adds support for various "3d vision notebooks". Maybe the new >>>>>> driver is >>>>>> needed. >>>>>> >>>>>> http://www.nvidia.com/object/notebook-win7-winvista-64bit-266.58-whql-drive… >>>>>> >>>>> I installed back the newest driver and problem still persist. So it's >>>>> problem either with driver or the card. >>>>> 880M isn't very high end on the Quadro Cards. >>>>> >>>>>> If it is a driver configuration problem, I don't know about that. Our >>>>>> expert on stereo and Windows is on vacation this week but can >>>>>> advise you >>>>>> next week. >>>>> Seems that I will be waiting for that. Thank you for your reply. And >>>>> hope to hear from you next week. >>>>> >>>>> -vpk >>>>> >>>>>> Tom >>>>>> >>>>>>> Hello, >>>>>>> >>>>>>> I have problem with Nvidia Quadro FX 880M and Stereoscopic view. >>>>>>> When I >>>>>>> switch the stereoscopic view on in Chimera it gives me following >>>>>>> error: >>>>>>> >>>>>>> stereo viewing (Unable to find hardware stereo support >>>>>>> (couldn't choose pixel format >>>>>>> Couldn't configure togl widget)). >>>>>>> >>>>>>> I have installed the Quadro drivers version 259.57 in Windows 7 >>>>>>> 64bit. >>>>>>> And separate 3D driver for Quadro. >>>>>>> >>>>>>> Greetings, >>>>>>> Veli-Pekka Kestilä >>>>>>> >>>>>> >>>>>> >>>>> >>>>> -- >>>>> University of Helsinki / Institute of Biotechnology / >>>>> veli-pekka.kestila(a)helsinki.fi / +358 9 191 58921 / Room 4316, >>>>> Biocenter 3 >>>>> _______________________________________________ >>>>> Chimera-users mailing list >>>>> Chimera-users(a)cgl.ucsf.edu >>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> > > -- University of Helsinki / Institute of Biotechnology / veli-pekka.kestila(a)helsinki.fi / +358 9 191 58921 / Room 4316, Biocenter 3

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odd output from surfnet
by Irene Newhouse 02 Mar '11

02 Mar '11

I'm trying to get an image of channels in the attached protein. It's actually a dimer, & the surfaces looked bizarre for the dimer, so I thought maybe surfnet was choking on the repeated residue numbers when you use chain ID, so I clipped it down to the monomer. That' still odd. I've attached a png of the result, using the defaults, & the pdb file of the monomer. What am I doing wrong? Is there a way to get the n largest channels, instead of all of them? Thanks! Irene Newhouse

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morph problem
by Andres Palencia 02 Mar '11

02 Mar '11

Dear Chimera Users, I am trying to morph the complex1 and complex2 from the same system (protein-RNA) to make a video monitoring the conformational changes. As complex 1 is missing one domain and a helix (not visible in the crystal structure), I need to remove these parts in complex 2 to have an equal number of atoms in both complex and could morph it. The resulting video is not so nice because shows the gaps corresponding to the missing part. So, to avoid that, I have modelled the missing part in the complex 1 to have the same atoms, and afer morph it again to make the video, but this is not working. In the transition between complex 1 and complex 2, the RNA encounter one helix on the way that needs to move out to let the RNA to get the position observed in complex 2. If I take out this helix, the video can perfectly be done, but still is not perfect because show gaps. Anybody could give an idea in how to solve the problem? We need the video to include in a publication,. Thanks in advance, Andrés Palencia -- Andres Palencia, PhD Protein RNA Group EMBL Grenoble Outstation 6 rue Jules Horowitz BP181, 38042 Grenoble Cedex 9, France email: palencia(a)embl.fr phone: + 33 (0)476 20 7860(office)/ + 33 (0)476 20 7014(lab) fax: + 33 (0)476 20 7199 http://www.embl-grenoble.fr/

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3-D
by Jason Bouvier 02 Mar '11

02 Mar '11

Hi, how do I view proteins in 3-D in Chimera? And would I use standard 3-D glasses or are special ones required? I viewing in stereo with some old 3-D glasses that I had around but to no avail. Thank you. Cordially, Jason Bouvier Jason Bouvier | Graduate Student, <http://mcb.illinois.edu/departments/biochemistry/> Biochemistry | <http://www.life.illinois.edu/gerltlab/research.html> Gerlt Lab | <http://www.igb.illinois.edu/> Institute for Genomic Biology | Rm 3200 | <http://illinois.edu/> University of Illinois at Urbana-Champaign | 1206 W. Gregory Dr. | MC-195 | Urbana, IL 61801 | office 217.333.2673 | lab 217.333.2699 | <mailto:jbouvier@illinois.edu> jbouvier(a)illinois.edu

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Problem with Nvidia Quadro FX 880M and Stereocopic view
by Veli-Pekka Kestilä 01 Mar '11

01 Mar '11

Hello, I have problem with Nvidia Quadro FX 880M and Stereoscopic view. When I switch the stereoscopic view on in Chimera it gives me following error: stereo viewing (Unable to find hardware stereo support (couldn't choose pixel format Couldn't configure togl widget)). I have installed the Quadro drivers version 259.57 in Windows 7 64bit. And separate 3D driver for Quadro. Greetings, Veli-Pekka Kestilä -- University of Helsinki / Institute of Biotechnology / veli-pekka.kestila(a)helsinki.fi / +358 9 191 58921 / Room 4316, Biocenter 3

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chimera ?
by Alexander Spyros Maris 01 Mar '11

01 Mar '11

Hi, I was attempting to start part of the tutorial by fetching "1d86" from the PDB on my windows PC when I got the error message "No connection because the target refused." Do you know how I can fix this? Thanks! -- Alex Maris

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Internal water molecules
by Beale, John 28 Feb '11

28 Feb '11

Hello, Is it possible, in Chimera, to select only the internal water molecules of a protein structure? I need to find out how many water molecules enter the protein structure from the outside during a molecular dynamics simulation. Thanks! John John M. Beale, Jr., Ph.D. Professor of Medicinal Chemistry and Pharmacognosy Saint Louis College of Pharmacy 4588 Parkview Place Saint Louis, Missouri 63110 314-446-8461 Cell: 314-315-0409 FAX: 314-446-8460 jbeale(a)stlcop.edu<mailto:jbeale@stlcop.edu>

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hem group
by "dr. R�szer Tam�s" 28 Feb '11

28 Feb '11

Hello, I would like to add HAEM group to a protein reconstructed from pdb data. I am working on Windows platform. Could you please help me how can I do that? many thanks Tamas

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How to
by M. Amin Arnaout 28 Feb '11

28 Feb '11

I am running Cimera 1.5.2 on Mac. I am now unable to show a cabonyl O, N or CA of a residue while ribbon is also displayed. Could do that in the earlier version. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Re: [Chimera-users] [chimera-dev] clashes and contacts with hidden models
by Elaine Meng 28 Feb '11

28 Feb '11

On Feb 28, 2011, at 5:28 AM, Elisabeth Ortega wrote: > > I have a question related to the calculation of the clashes between two (or more) models. What I have to do to count only the clashes of the Active or Displayed models? I mean, if I have 3 models in the model panel and I only want to calculate the clashes between the models 1 and 2 without close the model 3, what I have to do? > Hi Elisabeth, With either the graphical interface of Find Clashes/Contacts or the command findclash, you can specify which two groups of atoms to examine for clashes. The remaining atoms will be ignored. I believe it doesn't matter whether the atoms are displayed or active. With the command, it would be something like findclash #1 test #2 [other options] Another example: findclash ligand overlap -0.4 hb 0 test aromatic Use command "help findclash" to see the manual page, or view it here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> With the GUI, the procedure is slightly different: you would select one group (say #1), click Designate, choose option "second set of designated atoms", select the second group (say #2), click "Designate selection as second set", Apply. Click the Help button to see the manual page, or view it here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclas…> This is more of a chimera-users(a)cgl.ucsf.edu question (how to use Chimera) than chimera-dev (programming related to Chimera), so I'm also CC-ing the former list. 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

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suggestion: sym option
by Dougherty, Matthew T 25 Feb '11

25 Feb '11

add an SYM command option to specify the model number of the resulting model Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

2 1

morph shape/bild objects
by Do-Nyun Kim 25 Feb '11

25 Feb '11

Hello, I'm using shapes in bild format to make spheres and cylinders in Chimera. Is there a way of morphing these shapes, spheres in one conformation to spheres in another conformation? Thanks you. Best regards, Do-Nyun Kim.

2 1

Chain/Structure ID as label
by Berhane Temelso 25 Feb '11

25 Feb '11

Hi, I often read in 1-30 hydrogen-bonded molecular clusters from XYZ files and tile them for analysis. It would be great to label each cluster/model with its chain ID or file name. Labeling them using the 2Dlabel command is inconvenient especially when I have a large number of models. Is there an easy way of doing this? Thanks in advance. Berhane

2 2

Inter-helical angle?
by Brian Cannon 24 Feb '11

24 Feb '11

I need to calculate the angle between two helices in a protein. Do you have any instruction about how I could go about doing this? Any help would be greatly appreciated. Thanks! Brian

2 4

color key creation
by Bala subramanian 23 Feb '11

23 Feb '11

Friends, I am using chimera version 1.5 (build 31401 downloaded on 2010-09-16). I have opened two pdb files A and B. I also opened two attribute files corresponding to A and B and colored the ribbon based on the attribute. I want something like the following A B Colorkey 1 Colorkey2 My problem is creating the individual Colorkey. I chose model A (in the Depiction-> render by attribute -> create color key ) and created Colorkey1. When i did the same for model B and use my mouse for colorkey2 creation. Colorkey1 is deleted and Colorkey2 is created below the model B. Is it a bug. Precisely, if i hve to create two Colorkeys corresponding to two different models, how can i do that ? Thanks, Bala

2 1

X,Y,Z coordinates in GUI
by Sujata Sovani 23 Feb '11

23 Feb '11

Wondering if it is possible to see the X,Y,Z coordinates of a particular atom in the GUI using a command? Thanks, Sujata

2 1

need coordinates from volume data
by Terry Lang 23 Feb '11

23 Feb '11

Hey Everyone, I'm am trying to do some unorthodox analysis of volume data using a script. As part of the analysis, I need to access the x,y,z coordinates of each of the points of a ccp4 map. How would I go about that in Chimera scripting once the data is read in? Thanks, Terry -- Paula Therese Lang Postdoctoral Scholar Alber Lab UC Berkeley/QB3

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Displaying double-bonds of small molecules
by Rocco Varela 23 Feb '11

23 Feb '11

How do I display double-bonds of small molecules in Chimera?

2 1

Ray Tracing Transparent Surfaces
by Damian Ekiert 22 Feb '11

22 Feb '11

Hello, Is it possible to raytrace a transparent surface in Chimera? I tried raytracing the frames of a movie where I fade in a surface, but the surface just appears abruptly, solid and black, then fades to the desired colors as the transparency approaches zero. Do I need to fiddle with the POVray settings or what? Any suggestions/work-arounds would be appreciated! Thanks, Damian Ekiert

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