- Chimera-users - RBVI Mailing Lists

problem in picking
by Uzma Saqib 27 May '14

27 May '14

Hi , I am not able to pick atoms in Chimera from the graphics window (*picking*). pls help. FYI, snapshot attached. thanks

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script
by Schulz-Gasch, Tanja 22 May '14

22 May '14

Hi there, I hope you could help me with a little script. I am pretty sure, that something must exists already;-) I need to rotate around the y-axis in 2 degree steps for a total of 44 degree and at each step export a high res graphic. Rotation of the camera/view (keeping the look-at point) would be preferable compared to rotation of the object. Anything out there like this??? Thanks for your help, Tanja -- *Dr. Tanja Schulz-Gasch *Head of Communications & Operations, pRED Basel Bldg 69, 308 Grenzacherstrasse 124 4070 Basel Switzerland Mobile: +41 (0) 79 578 4672 Work: +41 (0) 61 688 8309 Email: tanja.schulz-gasch <http://goog_20899098>@roche.com Web: www.roche.com *Confidentiality note: This message is intended only for the use of the named recipient(s) and may contain confidential and/or privileged information. If you are not the intended recipient, please contact the sender and delete this message. Any unauthorized use of the information contained in this message is prohibited.*

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show path in Volume Viewer or Model Panel
by Dieter Blaas 21 May '14

21 May '14

Hi, I am often looking at a number of structures with the same file name but in different directories by using e.g: chimera ./dir*/struct.mrc to look at structures ./dir1/struct.mrc ./dir2/struct.mrc ./dir3/struct.mrc and so on... since all have the same name, it is difficult to identify them in chimera. Is there a way as to let chimera display the path in addition to the file name or any other way of finding out what is what? Thanks, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Custom presets
by Oliver Clarke 20 May '14

20 May '14

Hi all, I posted this last week, but it didn’t appear in the archives, so I guess it didn’t go through - if that is not the case, my apologies for the double post. I notice in the presets menu that there is the option to add custom presets, but I couldn’t find much documentation on this feature. Is it possible to save the current display options as a preset, similar to saving individual preference combinations but as a preset that can be quickly loaded? For example, displaying X-ray maps in a way that looks similar to how they are represented in Coot is a little complicated - I usually turn off “Mesh lighting”, “Cap high values at box faces”, and “Square mesh”, turn off ribbons, display all atoms and set the stick scale to 0.5, change the background to black, and alter the depth cueing - it would be very handy indeed to be able to apply all these settings at once. Also with regards to X-ray maps, I usually normalize (using vop scale #map, factor 1/SD) both the 2fo-fc and fo-fc, and then split the fo-fc into separate +ve and -ve maps, using vop threshold #map minimum 0 and vop threshold #map maximum 0. Would it be possible to assign these steps to macros or commands, and if so how would I go about doing that? Many thanks for your help, Oliver.

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Chimera License
by Chamila Jayasinghe 16 May '14

16 May '14

Hi, I am computer technician from University of Calgary, Department of Biological Sciences. We are hoping to Chimera for one of our Biochemistry tutorials for about 20 students. Is this consider as non-commercial use. Do we need to purchase license for the installation. Many thanks! Chamila Jayasinghe Faculty of Science (IT)

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re Registration
by Anna Lohning 15 May '14

15 May '14

Hi I am using Chimera and tried to register but came up with an error. Are you please able to do so manually? My details are: Dr Anna E. Lohning Asst Professor - Biochemistry Faculty of Health Sciences & Medicine Bond University 4229 QLD Australia alohning(a)Bond.edu.au I intend to use it for Research. Thanks very much. Its a great program. Kind regards Anna Dr Anna Elizabeth Lohning Assistant Professor - Biochemistry Faculty of Health Science & Medicine Bond University ROBINA 4229 (07) 5595 4779 alohning(a)bond.edu.au

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Re: [Chimera-users] Ionisation state of ligand and protein residues processed with chimera
by Elaine Meng 15 May '14

15 May '14

Dear Tao, Chimera AddH does not have the option to predict protonation state for different pH values, but you can do it using a different tool in Chimera to add hydrogens: menu Tools… Structure Editing… PDB2PQR, or command "pdb2pqr". In the graphical interface opened from the menu, click the triangle next to "Options" to show the options: Use PROPKA to predict protonation states: change to "true" pH value to use with PROPKA: default 7, you can change to the pH you want See documentation for more information: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/pdb2pqr.html> Then Apply or OK will run the calculation using a web service at the NBCR. One thing that might be confusing is that the result is opened as a new model in Chimera (i.e. original could be model 0, results will be model 1 so that there are two copies of the structure open in Chimera). PDB2PQR also assigns charges but the choices are different from Chimera's Add Charge (except for PDB2PQR AMBER and Add Charge AMBER ff99SB, AMBER ff99bsc0 all give the same charges). Depending on which charges you want, you could try running Dock Prep before or after PDB2PQR. If you run Dock Prep after, make sure to do it on the PDB2PQR results (model 1 in my example) and turn off the "add hydrogens" option because you want only the hydrogens from PDB2PQR. There might be errors, however, because PDB2PQR sometimes generates hydrogen names that are not recognized by the Add Charge step of Dock Prep… you may have to re-name some N-terminal -NH3+ hydrogen(s) from H to H1 to get it to run without error. Or, you could do the pKa prediction outside of Chimera using some other program, for example: H++ web server (this also adds the hydrogens) http://biophysics.cs.vt.edu/ PROPKA web server (this just predicts the pKa of each ionizable sidechain, and then you would use this information in combination with your desired pH to add hydrogens with Chimera or some other program): http://propka.ki.ku.dk/ That PROPKA program is the same one that the PDB2PQR server uses. 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 May 14, 2014, at 6:27 PM, 崔涛 <cuitao(a)mail.hzau.edu.cn> wrote: > Dear Elaine > Thanks very much for your quick reply which helped me a lot. > The documentation mentions “AddH aims to generate protonation states reasonable at physiological pH”. Now I have a new question. Is there a way and how to generate protonation states reasonable at other pH (such as 6.0 or 8.0) with chimera? I have found options to specify different tautomers in chimera. However, I didn’t find options for changing pH. > Best regards, > Tao

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Transition from PyMol
by R Michael Sivley 14 May '14

14 May '14

I'm attempting to transition from Chimera to PyMol and I'm struggling to reproduce the results of a visualization script. The script maps numeric values onto certain residues in a protein structure. Those residues are marked by spheres, and those spheres are colored by spectrum according to the residue value. In PyMol I overwrite the atom bfactors, and then display the CA of annotated residues as a sphere, colored by spectrum. The PyMol code (post-bfactor overwrite): cmd.show(selection="name CA and br. b >%f"%min_score-0.0001,representation="spheres") cmd.spectrum("b","blue_red",selection=include,minimum=min_score,maximum=max_score) In Chimera I've generated an attribute file, and used defattr to assign values to residues. I get the spheres by creating spheres centered on the CA atom of the annotated residues: rc("open %(struct_loc)s"%params) rc("defattr %(tempf)s"%params) rc("ribcolor dark grey") # temporary for resi in params['resis']: rc("shape sphere center %s@CA radius 1 color grey"%resi[0]) rc("rangecolor %(anno)s %(minval)s blue %(maxval)s red"%params) At this point, I can color the residues themselves using their attribute values, but I can't color the spheres, because they don't contain the information necessary to color them. I've uploaded the PyMol and Chimera generated images to imgur here: PyMol: http://imgur.com/a/GVfWi#0 Chimera: http://imgur.com/a/GVfWi#1 <http://imgur.com/a/n1PNl#1>Any help in reproducing the PyMol image in Chimera would be much appreciated. I haven't begun working on orientation (PyMol's `orient` equivalent), but any quick tips there would certainly be helpful as well. Thanks! Mike

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search for the conserved domain alignment algorithm
by ce 13 May '14

13 May '14

Hi, Does Chimera constain an algorithm that can generateconserved domain alignment in the exact way as Entrez CDD alignment works ? Yours sincerelly, XY

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x,y coordinates of the Chimera screen
by Jan Kosinski 13 May '14

13 May '14

Hi, When I load a model in Chimera I can move the model on the plane of the screenwith the move command along the x,y axes. Is it possible to get the current range of the coordinates of the x and y axes of the screen, so I could automatically (without setting positions with savepos) move my models to particular points on the screen? For example, move to left upper corner in a movie... Or move the model outside the screen and create nice fly-in effect in movies. Thanks, Jan

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1.9 production release
by Eric Pettersen 13 May '14

13 May '14

Hello everybody, A new production release of UCSF Chimera (version 1.9) is available: http://www.rbvi.ucsf.edu/chimera/download.html Download is free for noncommercial use. Platforms: Windows, Mac, Linux, including 64-bit versions (recommended for working with large datasets on machines with at least 4GB memory). New features include multiple sequence alignment using Clustal Omega or MUSCLE web services, building double-helical nucleic acids, "colorkey" command, "struts" command to reinforce structures for 3D printing, "vseries" volume series playback and processing options, more efficient save/restore of coordinates in sessions, Dynameomics amino acid rotamer library, WMV2 movie output, COLLADA export. More details are given below; see release notes for the full list: http://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.9.html Display, Interface: * icon for menu selection mode: Append, Intersect, Replace, Subtract * distance monitor line style and color can be saved as preferences * silhouette outlines can be controlled per-model * Axes/Planes/Centroids objects can be recolored with Actions menu * "colorkey" command implementation of Color Key tool Structure Analysis and Modeling: * new Align Chain Sequences tool for multiple sequence alignment of structure chains using a Clustal Omega or MUSCLE web service (these can also be called to realign the sequences in an existing Multalign Viewer window) * "mda" command to Blast-search and retrieve structures similar to a query sequence, lay them out left->right by N->C along the query * APBS interface omits explicit solvent by default * "coulombic" command allows specifying atoms/charges to use for ESP calculation independent of the surface to color * Build Structure tool allows generating nucleic acid double helices, specifying phi angle when joining peptides * "adjust" command to change bond angle or length * MD Movie session support for partly loaded trajectories * Morph Conformations pairs chains by ID if the sets of IDs are same * "ramachandran" command can assign probabilities as attributes * Rotamers/swapaa include Dynameomics rotamer library (Daggett group) Volume Data (density maps, ESP maps): * "vop" volume operations to take pointwise maximum or multiply maps * "vseries" command options to open and close volume time series, jump playback to a specific frame, perform various processing such as alignment, normalization, cropping, compressing, save to file * new volume input format VTK structured points (ASCII) General, I/O: * some Preferences reorganization, new categories: Labels, Selection * more efficient save/restore of coordinates in sessions * new output movie format WMV2 * new export formats COLLADA, VTK * "struts" command to add strengthening bonds for 3D printing * "leap" command for using Chimera with a Leap Motion Controller Enjoy! On behalf of the Chimera team, --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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how to get translation and rotation vectors for move and turn commands
by Jan Kosinski 13 May '14

13 May '14

Hi, I have the same model loaded in Chimera twice. One model has been moved to a different position and rotated manually using mouse. How can I get x,y,z coordinates for the centers of the to models to calculate x,y,z axis definition compatible with the move command? And how to get rotation information for turn command? I tried with cofr command but it seems to give coordinates in different reference frame. I would like to avoid using savepos/reset/fly commands in this case. Python solution would be fine. Thanks in advance for your help, Jan

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EM density map rescaling issue???
by Christian Geiss 13 May '14

13 May '14

Dear Chimera User list, I have a fundamental problem when loading pdb structures and EM density maps as *.em. The scale doesn't fit at all, with other words my pdb structure is tremendously bigger than the EM structure. One work-around is to resample the EM structure from current 64 px boxsize with 8.6 A pixelsize to 1 A pixelsize, giving ~ a 500 pixel volume, but then the volume gets quite big und my chimera gets really slow in handling those structures (pdb and big EM map at once)...is there any other way to solve this issue like scaling the EM structure on the fly in not such a memory consuming way...I also wonder if there is any information about the pixelsize in the EM header, because then the scaling should be done usually automatically??? Thanks in advance, Chris P.S. I couldn't find anything related to this in the chimera archive... -- *Christian Geiss, M.sc.* Universitaet Frankfurt BMLS Frangakis Group Max-von-Laue-Strasse 15 D - 60438 Frankfurt am Main Phone: +49-(0)69-79842597 Fax: +49-(0)69-79846467 geiss(a)biophysik.org

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threshold level problem
by 李智海 13 May '14

13 May '14

Hello, I am a freshman for Chimera, sorry for a possibly stupid question but i seem to be confused by the difference between threshold level in volume view and the sigma value that is used to contour the density map in some articles. please help me out! Thank you very much! Zhihai Li

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help with surface coloring
by Benda, Christian 09 May '14

09 May '14

Hello, sorry for a possibly stupid question but I seem to have a problem getting a molecular surface colored the same way as the atoms or ribbons of the underlying structure. Here’s what I did: - selected two domains of a larger protein separately (sequence viewer) and colored each domain differently (say green and blue, ribbons and atoms are in the respective color) - then selected the molecule in the model panel and clicked surface main - I get a surface, but it is either transparent grey or a solid color (pink) of the color well displayed in the model panel (not the domain colors I selected). - when opening the attributes of the surface, I can toggle between color source “atoms" or “model" but that only toggles between transparent gray and pink. I tried all kinds of combinations and clicks but I don’t manage to get the surface colored in the colors of the two domains. Any hint? It would be highly appreciated! Many thanks! Christian

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Re: [Chimera-users] Display a spider volume data in a specific orientation
by Elaine Meng 08 May '14

08 May '14

Hi Zongli, This is not my area of expertise (our expert is currently out of town) -- at first I thought you could use "Transform Molecule Coordinates" (under Tools... Movement), but now I see that it works only on atomic structures rather than maps: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transfor… > It only works on molecular structures because it actually changes the atomic coordinates, without changing the model transformation. I've figured out one workaround, but it is both crazy and slightly tedious: (1) open your map (say as model 0). (2) open any atomic-resolution structure, it doesn't matter what, and open it twice -- now you have three models. Don't move them separately from the map (yet). Let's say the atomic structures are models 1 and 2. (3) use "Transform Molecule Coordinates" with desired Euler angles and shift on one copy of the atomic structure (say model 1). (4) use the match command to superimpose the other copy of the atomic structure on the one that was transformed: match #2 #1 (the command can use the whole models since they should have exactly the same atoms) (5) use the matrixcopy command to apply the transformation matrix of the second copy of the atomic structure to the map: matrixcopy 2 0 You might think "why do I need two copies of the atomic structure? can't I just transform one copy and then use matrixcopy?" ... in fact that's what I tried first, but after it didn't work, I realized it was because the Transform tool works by changing the coordinate values and not the stored matrix of the model. It is necessary to match the second copy to generate a corresponding matrix, and then matrixcopy can be used. I'm CC-ing the chimera-users(a)cgl.ucsf.edu list in case other Chimera users have suggestions. Our expert Tom G should be back next week and he might also have ideas. In general, it's better to send Chimera questions to that mailing list instead of just me, because I could be away from work or (like now) lacking a good answer! 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 7, 2010, at 11:51 AM, Li, Zongli wrote: > Hi Elaine, > I have a spider volume data (or mrc density map) from which I got a > serious 2D projections. I have the Euler angles for each projection. > Is there a way in Chimera that I can use those Euler angles to > display the 3D spider volume data (or mrc density map) in a specific > orientation that corresponding to that 2D projection? > Thank you very much in advance. > Best, > Zongli > > **************************************** > Zongli Li, Ph.D. > > Howard Hughes Medical Institute > Department of Cell Biology > Harvard Medical School > C Building, Room 420B > 240 Longwood Avenue > Boston, MA 02115 > > Tel: 617-432-4095 (Office) > 617-432-4708 (EM Suite) > 617-432-4091 (Computer room) > Fax: 617-432-1144 > Email: zongli_li(a)hms.harvard.edu > *************************************** >

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Enquiry: Match Maker
by Anna Hernandez 06 May '14

06 May '14

Hi, I have a question regarding structural alignments with Match Maker. I would like to know if there is any way to obtain a list of all possible alignment solutions (or a subset) tested by Match Maker, instead of only the "best" one, so that I can further assess the different options manually. Specifically I am trying to find an homologous substructure/motif from my template structure within a query structure. The pattern to be searched is rather small as compared to the whole protein and it can be aligned in multiple positions. I would like to assess each of the possibilities more carefully based on the biological knowledge of the protein. Thank you in advance. Best wishes, Anna Hernandez

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Re: [Chimera-users] how to save distance to a file
by Eric Pettersen 05 May '14

05 May '14

On May 5, 2014, at 4:07 PM, chang YG <changyg2008(a)gmail.com> wrote: > Hi Eric, > > Thank you very much for the quick response. I can't wait to try the script you provided. > > For the RMSD, I have two conformers for the same sequence. If I encounter any problem, I will give it my best shot before posting questions. In that case it should be easy: from chimera import openModels, Molecule m1, m2 = openModels.list(modelTypes=[Molecule]) import Midas rmsd = Midas.rmsd(m1.atoms, m2.atoms) etc. --Eric > > Yonggang > > > On Mon, May 5, 2014 at 3:59 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > On May 5, 2014, at 3:57 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > >> print>>f, a1, a2, diet > > Stupid auto-correct spelling. "diet" should be "dist". > > --Eric > >

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how to save distance to a file
by chang YG 05 May '14

05 May '14

Hi, Thanks for taking time to answer the questions. Could you advise me of how to save distances using a python script. Here is what I have: from chimera import runCommand as rc rc("open 1t4y") rc("distance :33@H :34@H") #how to save distance. Another related question: how to save "rmsd" of two structures using a python script? Thanks, Yonggang

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patching ACE NME
by Francesco Pietra 05 May '14

05 May '14

Hello; In parameterizing a new metal cluster, I would like to patch the various amino acids (which stand isolated from one another) with what are called by AMBER ACE and NME. I would like to do that within the whole block, not for each amino acid isolated from the block. Also, I would like to avoid tleap, which gets into troubles here. I could do that by modifying structure, but a problem arises of residue names, i.e, the original residue takes the name ACE or NME, or viceversa the capping groups take the name of the amino acid being capped. Is there a specific tool with chimera? thanks francesco pietra

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A question on tunnelling chimera through ssh between a linux server and OSX client
by Miguel Ortiz Lombardía 30 Apr '14

30 Apr '14

Hi all, I understand that this is not a typical use of chimera, so I don't expect much support, but I would appreciate if someone can give me a clue to solve the issue... We have a GNU/Linux server (Debian wheezy) with some EM software installed on it. One of these programs calls at some point chimera to show something on which the user has to act upon (or just check, not sure, I'm not the user as you've guessed) This machine is accessed from client OSX machines via ssh. All permissions are set so X11 is seamlessly tunnelled between them (checked with many graphical programs) Now, for a OSX client running on 10.6.8 (snow leopard) and using Apple's X11 the whole process works without problems. But for a OSX on 10.7.5 (lion) with a parallel installation of Apple's X11 and Xquartz 2.7.5 the first small window opens and then the chimera process hangs (it can be killed via Ctrl-C, which returns the control to the program that launched chimera and things can proceed, though without the information provided by chimera) If I connect to the Linux server from the lion machine and directly execute chimera I make a different observation: the first small window opens but then chimera crashes leaving this error in the terminal: Error of failed request: GLXBadCurrentWindow Major opcode of failed request: 149 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1360 Current serial number in output stream: 1360 Now, I would appreciate any clues on the meaning and possible solution of this error or at least any directions on how to properly remove both Apple's X11 and Xquartz (they are supposed to be able to work side-by-side but I presume that a possible source of problems could arise from some conflict between them) AND re-install them to test them in a fresh install. Downgrading the lion machine to snow leopard does not seem to be an option... Thank you! Cheers, -- Miguel Ortiz Lombardía Architecture et Fonction des Macromolécules Biologiques (UMR7257) CNRS, Aix-Marseille Université Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 86 44 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombardia@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

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Preparation of the protein-ligand system for the amber simulation
by James Starlight 30 Apr '14

30 Apr '14

Dear Chimera Users, I wounder to know if it's possible to use combination of the amber ff with the cgenff for the both parametrization of the small ligands in complex with the proteins using amber tools built in Chimera's? Does it possible to use some scripts instead of GUI for such tasks ? I'll be thankfull for some tutorial or example Thanks for help, James

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multi-channel solid rendering
by Nick Walter 29 Apr '14

29 Apr '14

Hello, I've been attempting to create a movie in Chimera using multiple data files in solid style volume rendering, and I have been running into an issue where Chimera consistently shows the last channel to be loaded on top, regardless of the spacial position of the data with respect to the other solid channels. I found this message ( http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-May/006329.html) which explains that multi-channel solid rendering was removed in 2008. I was wondering, if there are any plans to reinstate this feature, or if you were aware of any work-arounds that would work well for creating movies. Thank you for your time, Nick Walter

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related with Fit in map option
by SRDA.DRAKULIC.599589 29 Apr '14

29 Apr '14

Hi, I have a question related to Fit in Map option and how to evaluate subsequently given results. I have a EM map at 19 ang. resolution of protein at yet non-characterised activity state, and there are two atomic structures of homologue of that protein, at clenched and open, active state. I would like to relate that state to one of the atomic structures, thus, both of them were fitted in my EM map and for the clenched state I got following values: cross correlation: 0.8447; average map value 9.526; and number of atoms outside the contour: 1709/7621 (or 22.42%) For the open state: cross correlation: 0.8385; average map value 9.085; and number of atoms outside the contour: 2064/8124 (or 25.42%) Are those differences big enough to say with certainty that my protein is at conformation similar to the clenched one or due to the EM map resolution this can not be said. Sincerely, Srdja Drakulic

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Saving ribbons as PDBs?
by Maja Divjak 29 Apr '14

29 Apr '14

Hello Chimera Gurus, Is there a way to save ribbon structures as PDBs for import into Maya? I've found only the surface structures are saved in the PDB, even though I am working with the ribbon structure in chimera initially. If there is a way to do this, I would be mightily pleased! I used to export chimera domains as vrml files and then convert them to maya files and both the ribbon and surface structures would be included. You can reply to my work email at divjak.m(a)wehi.edu.au if you prefer. Thank you so much and best wishes, Maja Divjak, PhD Biomedical Animator Walter and Eliza Hall Institute of Medical Research

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