- Chimera-users - RBVI Mailing Lists

odd chimera benchmark performance
by Dan Lin 13 Aug '15

13 Aug '15

Hello: I was wondering if anyone had any experience tracking down performance problems in chimera. I've noticed that I am getting really sluggish performance when managing a lot of atoms, even when everything is shown as backbone traces only. To take a look at the performance, I ran the benchmark and got the following numbers: Volume benchmark scores surface mesh contour solid recolor 981 1291 280 589 393 Null Wire Stick BStick Ribbon Sphere Ops 6249.5 158.7 1.5 0.9 27.4 0.4 89.3 compared to a benchmark posted on the website of the same graphics card: 2125 2026 302 512 491 213 492 452 3259 169 128 Apparently I'm getting awful benchmarks for most of the molecule benchmarks, while the volume performance is pretty comparable. I re-ran the molecule benchmarks to make sure they were reproducible and got pretty much the same numbers. Would anybody have any suggestions for figuring out what's going on? For reference, I'm running ubuntu 12.04 with up to date nvidia drivers for a GTX 560 Ti. Thanks, Dan

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axis-axis distance definition
by Oliver Clarke 13 Aug '15

13 Aug '15

Quick question - how is the distance between two axes (as reported by Axes/Planes/Centroids) calculated? Is it the minimum distance between two axes (I guess yes, because it does not seem to match the center to center distance)? And does it assume the axes are of infinite length, and calculate the displacement required for them to intersect, or does it measure the minimum distance between the axes with the length and end positions as displayed? Cheers, Oliver.

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place label at arbitrary position in 3D
by Oliver Clarke 13 Aug '15

13 Aug '15

In case it is useful to anyone else - I was trying to figure out a way to place a label at an arbitrary position in 3D, so that I can for example generate a chimera session of a protein with all helices labeled and annotated appropriately. I couldn’t figure out a way to easily do this with the built in tools (rlabel, labelopt etc all seem to require you to set an offset from an atom in the structure), so I made the following alias, which gets around this by placing an invisible marker atom at the center of rotation (which I mostly keep locked to the center of view), and attaching a label to that. Hope it is useful to somebody else too. #Place label here (at center of rotation). #Usage: label_here "label_text" (replace spaces in desired label text with _; they will be replaced by spaces in label) alias ^label_here ~sel; ac mc; color black sel; repr bs sel; vdwdefine 0.01 sel; setattr a label $1 sel; transparency 100,a sel; ~sel Cheers, Oliver.

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curved helices - cylinder representation?
by Oliver Clarke 12 Aug '15

12 Aug '15

Hi all, I’d like to have an extended version of the “Pipes and planks” representation, where helices are represented as cylinders, except as a regular, easily modifiable ribbon representation, and allowing for helix curvature rather than breaking up curved helices. I realize this is not currently implemented and is unlikely to be addressed until Chimera 2.0 due to the many other more important things on the drawing board, so I’m trying to figure out a way to hack something together that will generate acceptable results in the meantime. I figure that one way to do this might be to use a create a pdb file with guide atoms located on the helix axis, which one can approximate by placing a guide atom (P or CA) at the center of mass of a six residue sliding window of C-alpha atoms, and then use these guide atoms to create a thick, smoothed (with B-spline) licorice tube. This works quite well for an individual helix, as you can see in the attached pics, but I am a little at a loss as to how to automate this procedure across all the helices in a structure, or even for a given (selected) helix (and it’s only really the helices I care about - strands are fine as is, but having a curved cylinder representation for helices would be very handy). I guess I can do so using a python script of some sort, but if anyone has any pointers as to how to get started, they would be most appreciated. So I guess I need to loop through all the residues in a selection, calculating the center of mass in a sliding window and placing atoms as appropriate, then write out a pdb file with appropriate atom names. This shouldn’t be too hard, but if anyone can point me towards code that I can adapt for this purpose it would be most helpful. Cheers, Oliver.

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question
by A G Szabo 11 Aug '15

11 Aug '15

Today I was trying to Fetch a series of files from the PDB. Their accession codes are 3J7O, 3J7Q, 3J7R, and 3J7P. These are structures of the ribosome complexed with a trimeric translocon, Sec61. Each time Chimera responded with an error message indicating that there was no such file. The files come from a paper by R M Voorhees, (2014) Cell 157:1632. I went to the PDB website and was able to access each of the files. So they do exist. However, when I tried to visualize them using Protein Workshop the structure that appeared was a mixture of surfaces and ribbon structures. I was not able to do anything with any of the structures using Protein Workshop. I could not delete any of the several components, nor change them to ribbon structures. I have been able to fetch, using Chimera, other PDB files that have the entire ribosome complexed with proteins of interest. I sent a message to PDB relating what I have encountered and am waiting for a response. My question to Chimera is to determine if there is a work around to get at any of these files. Thank you Arthur G. Szabo Professor Emeritus Chemistry Wilfrid Laurier University

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is Chimera able to do spin albeling in silico
by Shu-Hao Liou 10 Aug '15

10 Aug '15

Hi, Thank you for reading this email. I'd like to have a rough protein structure with certain spin label on one of the cysteine. Is chimera be able to provide the reasonable structure for that? Sincerely, Shu-hao Liou UC Davis

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Attribute "distance" generated by shortcut "ac sd" not saved between sessions?
by Oliver Clarke 10 Aug '15

10 Aug '15

Hi all, I use the command “ac sd” to color dotted surfaces such as the attached by pore radius (I generate a molmap surface corresponding to the channel axis and then use "ac sd" to generate an attribute “distance", which in this case corresponds to the pore radius, which I can then use to color the dotted surface pdb using Render by Attribute). The dotted surface is generated using the program HOLE (http://www.smartsci.uk/hole/) along with the attached script to make it readable by chimera. This all works fine, however I have noted that the attribute generated by "ac sd” is not present when I reload the saved session, whereas other attributes (e.g. those created explicitly with defattr) are. I can just regenerate it of course, but it would be convenient if it were saved with the session, as it can take a while (~10 minutes) to calculate for large dotted surfaces. Cheers, Oliver.

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A video of 'view dock'
by Amali Guruge 10 Aug '15

10 Aug '15

Dear All, Can we save the movie play in 'view dock' option? Can anyone help me? Thank you.

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Re: [Chimera-users] PDB: 3NZ4 (Chimera vs Pmol Visualization)
by Elaine Meng 07 Aug '15

07 Aug '15

Hi Kevin, What you are seeing is weird-looking bonds between the ribbon and the residues named MDO. It is an artifact caused by the default smoothing of the ribbon path, the amino acid derivation of MDO, and the default hiding of “backbone” atoms in Chimera when the ribbon is displayed. More on that here, if anybody wants details... <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbo…> As you found, you could just show atoms without ribbons to solve the problem. However, if you really wanted to show ribbons at the same time, here are some choices as to what you could do in Chimera to make it look less deformed: (1) enable display of all atoms of the MDO at the same time as the ribbon, for example with command: ribbackbone .. however, side effects you may not like are that this will also show backbone atoms of the other residues that are displayed, and MDO and these other residues may be obviously detached (as if “floating” away) from the smoothed ribbon. You could try hiding the backbone atoms of the other residues with: ~disp @n,c,o & ~:mdo … or you could go back to the original behavior of disabling simultaneous backbone-atom and ribbon display with: ~ribbackbone (2) use a non-smoothed ribbon path that is forced to go through the CA atoms, for example with command: ribspline cardinal … however, this is still ugly because the ribbon makes a sharp turn near this derived residue, and the methyl group comes off of the ribbon at a strange angle. You can go back to the default ribbon path with: ribspline b Sorry, neither makes a beautiful picture. But I hope this helps to explain what is going on. 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 Pictures before and after using “ribbackbone” command:

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PDB: 3NZ4 (Chimera vs Pmol Visualization)
by Kevin D. Walker 07 Aug '15

07 Aug '15

A specialized prosthesis within the PDB 3NZ4 structure looks proper in Pmol but looks skewed in Chimera (my choice), and I wonder why the prosthesis is rendered as such in Chimera? Kevin ---------------------------------- Kevin D Walker Associate Professor Michigan State University Department of Chemistry and Department of Biochemistry & Molecular Biology 578 S Shaw Lane; Room 208 East Lansing, MI 48824 Phone: 517 355 9715 x 257 Fax: 517 353 1793 websites: 1) http://bmb.natsci.msu.edu/about/directory/faculty/kevin-d-walker/current-re…

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clipping and capping
by George Tzotzos 07 Aug '15

07 Aug '15

I’m a real novice in this kind of operation so I shall try in some detail what I’m trying to achieve. I’m dealing with a long serendipitous ligand that spans through a homodimer (2erb) (see screenshot1). I would like to generate something like the B-factor colouring feature (http://www.cgl.ucsf.edu/chimera/features.html <http://www.cgl.ucsf.edu/chimera/features.html>). I’ve opened the Depiction tool and tried surface clipping and capping to no avail. Reading the manual, I figured out that first I have to generate a volume and then use the sop clip command. If this is the routine, I’m seeking advice on how to generate the volume data and then pass it to the sop clip command. As always grateful for your kind help Regards George

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Changing license agreement email
by Flaherty, Daniel P 07 Aug '15

07 Aug '15

Hello, I am using the academic license agreement for Chimera from my previous position at the University of Kansas. However, I have now moved to Purdue and am starting my own laboratory. I would like to utilize Chimera in my lab. I sent an email earlier regarding generating spheres when preparing a protein for docking from my Purdue email and it told me I was not a registered user. I subsequently re-sent the email from my KU email since that is what I was licensed under. Long story short. How to I switch the license agreement to recognize my Purdue email as the registered user? Do I need to un-install Chimera and go through the steps to accept the academic licensing again using my new Purdue email account? Sorry for the confusing email. Thanks! Dan Daniel P. Flaherty, Ph.D. Assistant Professor Department of Medicinal Chemistry and Molecular Pharmacology Purdue University dflaher(a)purdue.edu Office - (765) 494-4761 [cid:8F36A2D2-6664-4FA0-B72D-D785C950B081]

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Placing markers in specific points of an EM map using command line
by Ana Lucia Alvarez Cabrera 07 Aug '15

07 Aug '15

Dear colleagues, I would like to know how can I place markers in specific points within an EM map, using commands (and not the Volume Tracer option in the graphic interface). I am doing a movie and I need to place markers in different regions of a map. By placing the markers first manually with the mouse (using the Volume Tracer option in the graphic interface) into the map and saving the respective marker set I can know the specific coordinates for each marker by reading the output marker file "suffix.cmm" (for example: <marker id="1" x="22.28" y="24.608" z="17.976" r="1" g="0.49804" b="0" radius="2"/> ), but I still don't know how to use this information when writing the command for placing the marker in that position. Thanks in advance, Ana-Lucia

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Re: [Chimera-users] Help Generating Spheres
by Repic Matej 07 Aug '15

07 Aug '15

Dear Daniel, The error you are getting only says that the sphgen program is not in your $PATH and therefore the shell cannot find the executable to run. Make sure you have installed DOCK6, which is not bundled with Chimera. You need to apply for the DOCK6 license (free for academia) and the "sphgen" program will be bundled with it. Apply here: http://dock.compbio.ucsf.edu/Online_Licensing/dock_license_application.html After you have made sure DOCK6 is properly installed by following the instructions below, you can follow all the tutorials available online. http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Installation Best, Matej ------------------------------------------------------ Dr. Matej Repic Ecole Polytechnique Fédérale de Lausanne Laboratory of Computational Chemistry and Biochemistry SB - ISIC – LCBC BCH 4108 CH - 1015 Lausanne ------------------------------------------------------ From: <chimera-users-bounces(a)cgl.ucsf.edu<mailto:chimera-users-bounces@cgl.ucsf.edu>> on behalf of "Flaherty, Daniel P" <dflaher(a)purdue.edu<mailto:dflaher@purdue.edu>> Date: Friday, August 7, 2015 at 04:38 To: "chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>" <chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: [Chimera-users] Help Generating Spheres Hello, I’m teaching myself to perform molecular modeling and docking using your tutorials. I am trying to prepare a protein for a vHTS and I have run into a snag during the sphere generation tutorial (http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_…) In the section where it says,"To generate the spheres, simply use the command "sphgen" in the same folder that contains the INSPH and the rec.ms files. The output will be two files: rec.sph<http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/rec.sph>, which contains the spheres in clusters, and OUTSPH<http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/OUTSPH>, which contains general information about the calculation.” I am getting an error that says Unrecognized command: “sphgen”. I downloaded the INSPH text file but I have no idea what to do with it. I don’t know what “folder” the tutorial refers to when it says,”use the command ‘sphgen’ in the same folder that contains the INSPH and rec.ms files." Any help would be greatly appreciated! Thanks, Dan

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Help Generating Spheres
by Flaherty, Daniel P 06 Aug '15

06 Aug '15

Hello, I’m teaching myself to perform molecular modeling and docking using your tutorials. I am trying to prepare a protein for a vHTS and I have run into a snag during the sphere generation tutorial (http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_…) In the section where it says,"To generate the spheres, simply use the command "sphgen" in the same folder that contains the INSPH and the rec.ms files. The output will be two files: rec.sph<http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/rec.sph>, which contains the spheres in clusters, and OUTSPH<http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/OUTSPH>, which contains general information about the calculation.” I am getting an error that says Unrecognized command: “sphgen”. I downloaded the INSPH text file but I have no idea what to do with it. I don’t know what “folder” the tutorial refers to when it says,”use the command ‘sphgen’ in the same folder that contains the INSPH and rec.ms files." Any help would be greatly appreciated! Thanks, Dan

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Morphing with pipes and planks
by Tom Goddard 06 Aug '15

06 Aug '15

Hi Corey, Pipes and planks depictions don’t update when the molecule changes shape. It is also slow to compute so it wouldn’t work interactively. But if you want to make a movie it can be done with some trickery. The tricky part is that there is no command to make the pipes and planks depiction. But a few lines of Python (file updatepp.py attached) can update the pipes and planks. So after creating the morph and the initial pipes and planks I can record a movie with the following command sequence: movie record super 3 ; coordset #2 0,100 ; perframe "open /Users/goddard/ucsf/chimera/libs/PipesAndPlanks/updatepp.py" frames 100 ; wait 100 ; movie encode ~/Desktop/planks.mp4 Tom > On Aug 6, 2015, at 2:35 PM, Corey Dambacher wrote: > > Hi Tom, > > Gabe lander suggested I email you regarding morph maps between two models: > > Is there a way to do a morph using pipes and planks? I have a couple of models I would like to morph, and this works very well when in ribbon, but it doesn't seem to work when I have the pipes and planks depiction... > > Thanks for your time and consideration, > > Corey

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vop cover for maps from EDS server?
by Oliver Clarke 05 Aug '15

05 Aug '15

Hi all, I would like to use the command ‘vop cover’ (https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover) with option fbox so that I can easily extend 2fo-fc maps downloaded from the EDS using ‘Fetch by ID’ to cover multiple unit cells. At the moment, this command does not seem to respect the lattice symmetry of the input map (see attached) - is there any way to make it do so? I have tried explicitly specifying the option ‘useSymmetry true’, but it shows the same behaviour. The example PDB ID I used for the attached screenshot was 3CH3. Cheers, Oliver.

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How to find a specific motif from a protein structure?
by Jing Tang 05 Aug '15

05 Aug '15

Hi, I would like to know how to identify a given motif such as DFG in a protein kinase structure. I have thought to use "select: asp,phe,gly" but it found all the residues rather than the motif. A related question would be then how to identify the activation loop or other more specific domains such as p-loop p+1 loop etc. from a structure. Thanks, Jing

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How to record the movie in the main window as well as in the sideview window?
by zhongjun hu 05 Aug '15

05 Aug '15

Hello, Everyone: I want to record the movie of main window as well as the side view window. Until now, I haven't find any simple way. Are there any suggestions or ideas? Thank you so much! Best, Zhongjun Hu 08/05

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opening *cif format
by Dmitry 05 Aug '15

05 Aug '15

Dear Colleagues, I'm trying to open 4fe1-sf.cif file with chimera 1.10.2. But nothing is happening. Although the program saying : "Done opening ....." Could you please explain how to open *cif files ? Sincerely, Dmitry

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FoxS in Chimera for SAXS curve fitting
by Eugene Valkov 05 Aug '15

05 Aug '15

I was wondering what version of FoxS the current release of Chimera employs for goodness-of-fit calculations to small-angle X-ray scattering curves using crystal structure models? Also, if any specific parameters are used other than what is default? I obtain quite different values using standalone FoxS binary or using the online server versus what is output by Chimera. Thanks, Eugene

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multiple (redundant) distances in command line >file.txt
by Olexandr Dybkov 04 Aug '15

04 Aug '15

Dear UCSF Chimera team, I am trying to measure and draw multiple distances by pasting into the command line respective commands. As outcome I would like to have: 1. the dashed lines between each pair of atoms that I am checking 2. the distances shown above/on the lines 3. a log or a file with all the distances checked (one line per each distance command I executed) For example, dist :540@ca/pdbSegment=A :573@ca/pdbSegment=A dist :453@ca/pdbSegment=B :479@ca/pdbSegment=B dist :695@ca/pdbSegment=B :395@ca/pdbSegment=A dist :2059@ca/pdbSegment=B :1421@ca/pdbSegment=B dist :426@ca/pdbSegment=B :944@ca/pdbSegment=B dist :2059@ca/pdbSegment=B :1514@ca/pdbSegment=D dist :2059@ca/pdbSegment=B :1417@ca/pdbSegment=B dist :1421@ca/pdbSegment=B :2059@ca/pdbSegment=B dist :421@ca/pdbSegment=C :439@ca/pdbSegment=C dist :453@ca/pdbSegment=B :487@ca/pdbSegment=B and so on Resulting in Distance between #50 LYS 540 CA and #50 LYS 573 CA: 13.0 Distance between #35 LYS 453.B CA and #35 LYS 479.B CA: 22.7 Distance between #35 LYS 695.B CA and #50 LYS 395 CA: 8.8 Distance between #35 LYS 2059.B CA and #35 LYS 1421.B CA: 20.5 Distance between #35 LYS 426.B CA and #35 LYS 944.B CA: 25.7 Distance between #35 LYS 2059.B CA and #53 LYS 1514.T CA: 115.7 Distance between #35 LYS 2059.B CA and #35 LYS 1417.B CA: 15.2 Distance monitor already exists That is, 8 out of 10 distances were checked. Since the 8th line was a swap of atom1 and atom2 of 4th, the Chimera Error window popped up and execution of further commands was stopped Similarly, the execution is interrupted if: - one or both atoms are missing - one or both atoms are present in multiple copies - if such distance was checked already Is there a way to ignore/skip this kind of check points and just report such cases in the log? I used to do this in pymol and the python script reported all distances (even redundant) and errors (atom 1 or/and atom 2 are missing) without stopping. At the end I had a txt file with exactly one line for each command. It would be nice to have the same functionality in UCSF Chimera as well. Thank you very much for your help! Kind regards, Olexandr -- ----------------------------------------------------------------- Dr. Olexandr Dybkov Max-Planck-Institute for Biophysical Chemistry Department of Cellular Biochemistry Am Fassberg 11 37077 Göttingen Germany Tel. ++49-551-201 1979 Fax ++49-551-201 1197 email: odybkov(a)gwdg.de ----------------------------------------------------------------

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Coloring an specific area along a morphing serie among several maps
by Ana Lucia Alvarez Cabrera 04 Aug '15

04 Aug '15

Dear Srs, I made a chimera movie where six different conformations of the same complex are morphed in a sequence, changing on to the next one (the aim is showing a conformational change occurring in a number of steps, in this case the six electron microscopy maps). My complex has an specially flexible domain and I need to highlight this area along the morphing sequence of the six maps. I suppose that this can be done using the markers and color zone options, but I don't know how to implement this orders in the .cmd script of my movie. Thanks in advance for your help. Sincerely, Ana-Lucia ________________________________ Ana Lucia Alvarez Cabrera Unidad de Bioinformática. Lab. B-13 Dept. Estructura de Macromoléculas Centro Nacional de Biotecnología (CSIC) C/ Darwin 3, Campus de Cantoblanco 28049, Madrid, España Tel: (34) 915854510

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Re: [Chimera-users] Mirror image proteins
by Elaine Meng 04 Aug '15

04 Aug '15

Dear Dikran, You would need to open the structure before running the script, otherwise the script has nothing to work on. Elaine > On Aug 4, 2015, at 12:22 PM, Sarko, Dikran <dikran.sarko(a)yahoo.com> wrote: > > Dear Elaine, > > Thank you very much for your reply. > I am not familiar with programing, however, I did exactly as described in the page you had refered to. > > import chimera > m = chimera.openModels.list()[0] > for a in m.atoms: > crd = a.coord() > crd.x = 0 - crd.x > a.setCoord(crd) > > then I opened the 4LLZ pdb file as a test, however when I saved the structure and tried to combare it with the original one. Chimera opened only one structure (not tow as I expected). > > Is there anything wrong, ore any additional advice. > > PS: I suggest to incorporate an additional function in the next release of Cheimera that consider the generation of mirror image protein of pdb file as a function within the tools, or other appropriate function. Such function will attract a lot of attention, and Cheimera will be (to my knowledge), the 1st modeling program that offer such a function. > > Thank you very much > Dikran > > Von: Elaine Meng <meng(a)cgl.ucsf.edu> > An: "Sarko, Dikran" <dikran.sarko(a)yahoo.com> > CC: Mailing List <chimera-users(a)cgl.ucsf.edu> > Gesendet: 19:54 Montag, 3.August 2015 > Betreff: Re: [Chimera-users] Mirror image proteins > > Hello Dikran, > Only with a little scripting, but somebody asked the same thing a few years ago and a simple python script was posted to the list. Please see: > > <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-January/005882.html> > <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-January/005883.html> > > Remember that in python the indentation is important. > 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 Aug 2, 2015, at 1:11 PM, Sarko, Dikran <dikran.sarko(a)yahoo.com> wrote: > > > > Hello, > > is there any way to generate mirror image proteins (All AA in D-form) from an already exsist pdb file. > > Thank you in advance > > Dikran > >

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segment map & mesh view
by Dmitry 04 Aug '15

04 Aug '15

Dear Colleagues, Does anybody know how to: 1. Delete selected segment from segment map and save the result. 2. Change the mesh view properties - because for the volume the mesh size is different then for the segment map. Sincerely, Dmitry

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Feature suggestion - turn about pre-defined axis.
by Oliver Clarke 03 Aug '15

03 Aug '15

Hi all, Just have a minor feature suggestion that I think would make the command “turn” more useful in certain circumstances. Currently, one can use “turn” to rotate about the x,y or z axes; an arbitrary vector; or about a bond or pair of selected atoms (http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/turn.html) Would it be possible for chimera to treat a predefined axis (e.g a helix axis, or the symmetry axis of an ion channel) as an atom-spec for the purposes of turn? As an example, “turn a1 45” would rotate 45 degrees about axis a1, with the default center of rotation corresponding to the midpoint of the axis. This would be very helpful for adjusting the relative orientations of symmetric oligomers, amongst other use cases. Cheers, Oliver.

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Mirror image proteins
by Sarko, Dikran 03 Aug '15

03 Aug '15

Hello, is there any way to generate mirror image proteins (All AA in D-form) from an already exsist pdb file. Thank you in advanceDikran

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Average structure
by George Tzotzos 03 Aug '15

03 Aug '15

Hi everybody, I’m analysing the Principal Components of an Amber trajectory. I have generated a number of representative pdb files which are concatenated for each PC. Question: Is there a way to generate an average structure in Chimera from the concatenated PDB files? I know this can be done using MD movie but this solution requires that I generate a new topology file for my complex (the original topology file contains ligands and water molecules). Thank you in advance for any suggestions Regards George

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Re: [Chimera-users] Chimera-users Digest, Vol 148, Issue 6
by feisun＠ibp.ac.cn 03 Aug '15

03 Aug '15

From: feisun(a)ibp.ac.cn Subject: I am in a vacation. I am now taking a vacation from Aug. 1st to Aug. 9th. I will reply to you after Aug. 10th. Sorry for the delay. Fei

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Re: [Chimera-users] Chimera-users Digest, Vol 148, Issue 5
by feisun＠ibp.ac.cn 03 Aug '15

03 Aug '15

From: feisun(a)ibp.ac.cn Subject: I am in a vacation. I am now taking a vacation from Aug. 1st to Aug. 9th. I will reply to you after Aug. 10th. Sorry for the delay. Fei

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Morphing a residue through MD trajectories
by George Tzotzos 02 Aug '15

02 Aug '15

Hi, I have an MD trajectory which I can load successfully on Chimera. My objective is to monitor changes in conformations of one particular residue in the receptor (:123) throughout the trajectory and generate a movie. If I could do this in tandem with a bound ligand so much the better. I’ve tried to follow the instructions but obviously, I get it wrong. I opened the Morph Conformations tool, I selected the trajectory and clicked on Add. This generated a 2nd MD Movie panel of just one frame. Any help would be most welcome Regards George

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Re: [Chimera-users] Chimera-users Digest, Vol 148, Issue 4
by feisun＠ibp.ac.cn 02 Aug '15

02 Aug '15

From: feisun(a)ibp.ac.cn Subject: I am in a vacation. I am now taking a vacation from Aug. 1st to Aug. 9th. I will reply to you after Aug. 10th. Sorry for the delay. Fei

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Re: [Chimera-users] Chimera-users Digest, Vol 148, Issue 3
by feisun＠ibp.ac.cn 01 Aug '15

01 Aug '15

From: feisun(a)ibp.ac.cn Subject: I am in a vacation. I am now taking a vacation from Aug. 1st to Aug. 9th. I will reply to you after Aug. 10th. Sorry for the delay. Fei

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Re: [Chimera-users] Chimera-users Digest, Vol 148, Issue 2
by feisun＠ibp.ac.cn 01 Aug '15

01 Aug '15

From: feisun(a)ibp.ac.cn Subject: I am in a vacation. I am now taking a vacation from Aug. 1st to Aug. 9th. I will reply to you after Aug. 10th. Sorry for the delay. Fei

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Re: [Chimera-users] Chimera-users Digest, Vol 148, Issue 1
by feisun＠ibp.ac.cn 01 Aug '15

01 Aug '15

From: feisun(a)ibp.ac.cn Subject: I am in a vacation. I am now taking a vacation from Aug. 1st to Aug. 9th. I will reply to you after Aug. 10th. Sorry for the delay. Fei

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Open model from pdb with designated model id?
by Oliver Clarke 31 Jul '15

31 Jul '15

Hi all, I would like to write an alias to load a pdb and the associated 2fo-fc and fo-fc maps with a single command (and adjust the contours and appearance of the maps and model). To do this, I need to be able to open the models with specific output ids, so I can issue commands to alter their appearance later in the alias. Looking at the documentation (http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/open.html <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/open.html>), it seems like this should be possible, but when I give an output model id it seems that chimera is ignoring it and still choosing the lowest available id. I have tried the following commands, “open 1bl8 100”, “open 1bl8 #100”, “open 1bl8 model-id:100” but they all either fail or load 1bl8 with model id 1. Am I missing something about the syntax here? Or is there another flag for the output model id? Cheers, Oliver.

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Option to not record duplicates in the command history?
by Oliver Clarke 31 Jul '15

31 Jul '15

Hi all, I like the command history in chimera a lot - it makes it very quick to repeat previous commands. One minor alteration that might make it a little bit better would be to have an option (maybe in the Command Line section of the preferences?) to not record sequential duplicate commands in the history (like the “ignoredups” option for the bash history). I will often repeat the same command a bunch of times (for example “turn x 5” or one of the various aliases I use for navigation and recentering), and so not having all these duplicates recorded in the history would make it a lot faster to find recently used commands. Cheers, Oliver.

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Addh function and fake N, C-terminii
by gaelle garet 31 Jul '15

31 Jul '15

Hi, I want to use Addh function to add hydrogens and protonate N, C-terminii but I don't understand very well how you detect if a terminus is fake or not. For example, for the structure 3L4F, I obtain the following log : Chain-initial residues that are actual N terminii: MET 586.A, MET 586.B, MET 586.C Chain-initial residues that are not actual N terminii: GLY 652.D Chain-final residues that are actual C terminii: LEU 646.A, LEU 646.B Chain-final residues that are not actual C terminii: ASP 638.C, ARG 758.D I don't understand why GLY 652.D, ASP638.C and ARG 758.D are not terminii, can you explain me why and how the algorithm detect that ? Thank you in advance for your answer. -- Gaëlle

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How to explore two protein structures on the same screen?
by Jing Tang 31 Jul '15

31 Jul '15

Hi, I opened two protein structures, say 2JIT and 4WA9 and they were partially overlapped on the screen. How to move one protein so that they can be separated more? I can only move the two proteins as a whole but not individually. Further, I would like to highlight one residue for a particular protein and I could not find a way to first select a protein and then a residue. Thanks, Jing

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Recent problems with linux x64 version
by Peter L. 30 Jul '15

30 Jul '15

Hello, Recently I used Chimera for a internship/volunteer work with my older brother, and it did not start up due to some seemingly graphics drivers problems. I'm running Ubuntu 15.04 on a AMD radion 5450M on this machine and NVidea gtx 760 on another. Both would not start up due to having libGL error: unable to load driver: nouveau_dri.so etc etc, as so documented here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015February/010734.html (Error from the NvIdia machine) and would not load r600. However both had the same fix, that seemigly works by removing the file /Chimera64-1.10.2/lib/libstdc++.so.6, I renamed it to libstdc++.so.6.bak in case I might need it, but it works on both machines now. It seems as some older libs are colliding with mesa drivers, and casung them to break, and removing this fixes the problem. Its been documented before with other programs here, where the fix is simular. http://askubuntu.com/questions/614422/problem-with-installing-steam-on-ubun… I also found that in the chimera mail I found, it was recommend to update some drivers, or Nvidia drivers, however, nvidia drivers for linux tend to break the system a lot or cause other problems. Hope this helps!, Peter

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Volume level rms option
by Oliver Clarke 30 Jul '15

30 Jul '15

Hi all, Just a minor usability suggestion - I was wondering if it would be possible to add a flag to the ‘volume level’ command that allows the user to directly set the map threshold to x*RMS or x*SD? E.g. volume level rms 5 to set to 5xRMS of the map, using the values reported by measure mapstats? At present it is possible to normalize the map to rms, which is very handy, but it would be also convenient (for the purposes of reporting absolute threshold levels in figure legends etc) to be able to set the level as 5*rms but still check the absolute e-/Å^3 contour that this corresponds to. Also on a completely different matter, is there any way to access the “Zone” feature of Volume viewer from the command line? I would like to write an alias that places a dummy atom at the CoFR and displays a spherical zone of the selected map (without generating a new map using vop zone), but I can’t find the corresponding command line function. Cheers, Oliver.

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Useful aliases
by Oliver Clarke 30 Jul '15

30 Jul '15

Attached are a bunch of aliases that I find very useful in Chimera. Usage and intended purpose of the alias is described in the #comments immediately preceding the alias. Some of these will only work in the latest nightly build because they take advantage of command options that were only added recently. Hopefully someone else finds these useful too! If any other chimera users have aliases or shortcuts they find particularly handy maybe we could exchange ideas/code snippets in this thread? Oliver.

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Center of rotation cross-hair
by Tom Goddard 28 Jul '15

28 Jul '15

Hi Oliver, I added display of a cross hair (plus sign) at the center of rotation in the graphics window. You turn it on with command set showCofR and turn it off with ~set showCofR The crosshair is white on black (and dark) backgrounds and black on white (or light) backgrounds. This will be in tonight’s daily build. Tom

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"newmap" command? (Or other way to resample on arbitrary grid?)
by Oliver Clarke 28 Jul '15

28 Jul '15

Hi all, Is there any way to use vop to resample on an arbitrary grid, that is, not the grid of an existing map? This would be useful, for example, when one wants to interpolate to finer grid spacing than is present in the input map (but otherwise keeping the original dimensions and origin). I note in the old chimera documentation that there used to be a command called “newmap” (http://www.cgl.ucsf.edu/chimera/experimental/resample_map/resamplemap.html) which allowed for the generation of an arbitrary map which one could use for exactly this purpose, but this command does not seem to be recognized by modern Chimera builds. Does this command still exist somewhere under a different name? Or is there another way to accomplish this? Cheers, Oliver.

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Hydrogen Bond Criteria
by jjeon＠caltech.edu 28 Jul '15

28 Jul '15

Hello, I would like to learn more about the distance/angle settings that Chimera uses for hydrogen bonds. I have read that the criteria are outlined in the paper Three-dimensional hydrogen-bond geometry and probability information from a crystal survey. I have been waiting to be granted access to the full version since I can only seem to find the abstract on other sites. Is there a website that offers access to the full paper for free? Thank you, Janice

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hbonds
by leila karami 27 Jul '15

27 Jul '15

Dear chimera users I have 2 models in my system (#0 for protein and #1 for ligand). I want to use hbonds command for showing the hydrogen bonds between #0 and #1 models? (I know how to do this using FindHBond, but I want to know related command). What is the best options for hbonds command to get above state? Best, Leila

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DNA ladder different color than backbone
by Belle Lin 25 Jul '15

25 Jul '15

Dear Chimera users/developers, Is there a way to make the DNA ladders a different color than the backbone? I am able to do so when the side (sugar/base) is shown in the "tube/slab" mode, but when I change it to the "ladder" mode I am unable to change the color of the rungs. I have included photos below which hopefully make my question more clear. Thank you in advance for your help!! Thanks, Belle Lin _____________________________________________________________ Able to create: [image: Inline image 3] [image: Inline image 2] Trying to create: [image: Inline image 1]

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Announcing the 2015 EMDataBank Map Challenge
by Cathy Lawson 23 Jul '15

23 Jul '15

Dear Chimera User List Members, EMDataBank/Unified Data Resource for 3DEM is pleased to announce the 2015 Map Challenge. All members of the Scientific Community--at all levels of experience--are invited to participate as Challengers, and/or as Assessors. Seven benchmark raw image datasets have been selected for the challenge. Six are selected from recently described single 3D electron microscopy single particle structure determinations with image data collected as multi-frame movies; one is based on simulated (in silico) images. Challengers are sought to create single particle reconstructions from the targets, and then to upload their results with associated details. Assessors are sought to participate in evaluating submitted reconstructions. Registration is now open for all interested participants. Challengers may submit maps between August and December. Before submissions open, all are encouraged to provide feedback on submission requirements. An open assessment period will commence in early 2016. To learn more about this challenge and to register, please visit http://challenges.emdatabank.org and click on "MAP CHALLENGE" in the menu bar. The map challenge is the first of two community-wide challenges being sponsored by EMDataBank this year to critically evaluate 3DEM methods that are coming into use, with the ultimate goal of developing validation criteria associated with every 3DEM map and map-derived model. The second challenge, focused on creating coordinate models from 3DEM maps, will be announced later this year. Sincerely, Cathy Lawson on behalf of the EMDataBank Team and the Map Challenge Committee emdatabank.org www.facebook.com/emdatabank3dem

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Mac-Book Pro
by Bobby Barnett 22 Jul '15

22 Jul '15

I have some students who have mac's, so I tried to download and install chimera on my Mac-Book Pro 17" . I get the following message. I downloaded chimera-1.10.1-mac64.dmg from your site. I am the only user on my computer. Any suggestions? Should I try and downloading it again? Bobby Barnett “Chimera” can’t be opened because the identity of the developer cannot be confirmed.

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PB lines visualization
by Sana Saeed 22 Jul '15

22 Jul '15

is it possible to visualize periodic boundary lines (solvated box) in chimera.

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