- Chimera-users - RBVI Mailing Lists

surface ESP in chimera
by sbasu＠ffame.org 30 May '14

30 May '14

Dear Chimera group, Could you please help us resolving the following issues ? 1. Is there a way to load a pre-computed solvent accessible surface (i.e., coordinates of dot surface points stored in a PDB format against source atom types) on top of a protein molecule ? [kindly see the attached example file] 2. Is there a way to print / write the actual dot surface points generated by Chimera into a file (preferably in a PDB format with the source atom records) ? 3. Is there a way to actually compute the electrostatic potentials (ESP) on the solvent accessible surface by chimera using a Delphi interface ? In that case, how can one set the delphi parameters (e.g., partial charges / atomic radii / percentage grid fills / boundary conditions) according to his likings ? 4. We have computed ESP on solvent accessible surface (MS - connolly) using a standalone version of delphi. When we load the phimap.phi onto the chimera-generated surface to obtain the ESP-colored surface map, we find ambiguities between the surface coloring and the actual values of the potentials (almost the entire surface is showing red / white whereas there are obviously positive patches from the actual numbers) ! We suspect that it is due to the inconsistency between two surfaces. Lastly, 5. A trivial question is how to select residue(s) by residue sequence number (e.g., 108 or 108-VAL) from the select drop-down list ? We do not seem to find that option. thanks and regards, Sankar Basu Post Doctoral Fellow Foundation for Applied Molecular Evolution Gainesville, FL 32601

2 2

Saving an EM map to open at a specific Threshold
by Kevin Huynh 30 May '14

30 May '14

Hello, I have finished processing my cryo-EM map and have set the desired volume to threshold=1 with EMAN2; however, I cannot seem to figure out how to save the map in mrc format so that I can open the map at threshold 1. I am wondering if Chimera can save the map in mrc format so that I can open it at threshold 1? If yes, how can this be done? Thanks, Kevin

2 1

merging 2 pdb files
by Adrian Javaherian 30 May '14

30 May '14

Hi, My name is Adrian. I am a graduate student at Bar Ilan University in Israel. I have 2 pdb files, each containing rRNA sequences and I would like to combine the 2 to make 1 pdb file displaying all of the rRNA subunits. I download the Chimera program. Is it possible to do this on your program and if so, can you please tell me how? Thank you so much, Adrian

2 1

Electron density maps
by lecan 30 May '14

30 May '14

Hello Chimera's users, I would like to know if there are a way to see density maps from .mtz files with chimera. I have tried opening a .mtz file after opening a .pdb file, but I got the next error message after choose CCP4 density map in the Type Selection window: Error reading file abc.mtz format ccp4 File size 631624 too small for grid size (1297373728,929300992,1145110528) and 64 bytes of symmetry operators Does anyone could telling me if what I'm trying to do is possible and what is the way to do it? Thank you for your help, Luis L.

3 2

part-time job for Chimera professionals
by Andrew Voronkov 30 May '14

30 May '14

Dear Chimera users, if anyone may be interested in part-time job and additional income through Chimera usage, please let me know. I am looking for someone, who can regularly make nice-looking Chimera pictures. It can be 2-3 hours per week for example. Best regards, Andrew

1 0

Save to a file
by sette＠uniroma2.it 29 May '14

29 May '14

Dear all, I created a simple text file with a list of distances to be measured How to save in a file the measured distances? The saveFile options does not seems to be the solution. I use 1.7 version of Chimera on Windows 7. Thanks, Marco ---------------------------------------------------------------- Invito da parte dell'Ateneo: Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del tuo aiuto. Dona il 5 x mille all'Universita' di Roma Tor Vergata codice fiscale: 80213750583 http://5x1000.uniroma2.it

2 5

merging 2 pdb files
by Adrian Javaherian 28 May '14

28 May '14

Hi, My name is Adrian. I am a graduate student at Bar Ilan University in Israel. I have 2 pdb files, each containing rRNA sequences and I would like to combine the 2 to make 1 pdb file displaying all of the rRNA subunits. I download the Chimera program. Is it possible to do this on your program and if so, can you please tell me how? Thank you so much, Adrian

3 3

mmCIF support
by Greg Couch 28 May '14

28 May '14

Hello, I'm working on improving Chimera's mmCIF support. So if anyone has a mmCIF file that is not from the PDB and that they are willing to share, please send it to me. Many thanks, Greg

2 1

domain colouring
by ce 28 May '14

28 May '14

Hi, Could You send me instruction about domain colouring (the quickest way if possible) ? Cheers, J.

2 5

After fitting a PDB into a cryo-EM density, is it possible to color the PDB atoms by the local EM density in the cryo-EM map?
by Lai, Jonathan 27 May '14

27 May '14

Dear Chimera-users, I have several cryo-EM maps of an assembly process and a PDB of the final product; what I want to do is to have a visual depiction of how the local EM density around structural elements in the final product changes over time. After fitting the PDB into the cryo-EM density, I am wondering if it is possible to color the PDB atoms by a reference EM density at each point. For example, I want to color every residue that intersects isosurface == 0 blue, every residue that intersects isosurface == 1 red, and have a continuous color scheme for all intermediate values from (0 to 1). I already have fitted the PDBs into the cryo-EM maps. Is there any easy way to do this? Cheers, Jonathan Lai University of Illinois at Urbana-Champaign

3 2

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

2 1

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.*

3 5

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 ------------------------------------------------------------------------

2 1

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.

3 17

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)

2 1

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

2 1

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

1 0

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

2 3

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

2 3

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

2 4

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

1 0

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

3 4

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

3 2

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

3 2

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

2 3