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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

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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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