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Interpretation of fitmap translation vector
by Benjamin Basanta 21 Jul '20

21 Jul '20

Hi, I am trying to implement a python script that takes a rotation matrix and a translation vector from Chimeras' fitmap output, and applies those rotations and translations to particle 2D projections from electron micrographs. I have successfully applied the reverse rotation, getting 3D reconstructions that are almost aligned, except for the translation. I am having problems interpreting the values of the translation vector (4th column from fitmap output matrix). According to information I found online the units of this vector are angstroms, but the length of the translation vector output by fitmap would put my density near the edge of the particle box. My interpretation of the tranlation vector is the following: original_position + trans_vec = new_position. For example, I have two densities (box size 264^3, angpix correctly set to 1.15Å), both near the center of the box, fitmap aligns them with what is clearly a small translation after rotation, yet I get the following fitmap output, with a translation vector of length >180Å: > fitmap #1 #0 search 50 Found 34 unique fits from 50 random placements having fraction of points inside contour >= 0.100 (50 of 50). Correlations and times found: 0.9847 (1), 0.9722 (5), 0.9523 (3), 0.9044 (2), 0.8574 (2), 0.8567 (2), 0.8534 (1), 0.8503 (2), 0.849 (2), 0.832 (2), 0.8317 (2), 0.8274 (1), 0.8225 (3), 0.8205 (1), 0.8184 (1), 0.8062 (1), 0.8058 (1), 0.8043 (2), 0.8017 (1), 0.8007 (1), 0.7977 (1), 0.7809 (1), 0.78 (1), 0.7761 (1), 0.7566 (1), 0.7557 (1), 0.7555 (1), 0.7467 (1), 0.7431 (1), 0.7145 (1), 0.7062 (1), 0.6922 (1), 0.6049 (1), 0.6015 (1) Best fit found: Fit map run_it025_class003.mrc in map run_it025_class002.mrc using 70798 points correlation = 0.9847, correlation about mean = 0.6976, overlap = 38.71 steps = 448, shift = 52.7, angle = 48.4 degrees Position of run_it025_class003.mrc (#1) relative to run_it025_class002.mrc (#0) coordinates: Matrix rotation and translation 0.98449497 -0.14831781 0.09365615 14.82575334 0.15479139 0.48339849 -0.86160636 179.12850738 0.08251833 0.86274430 0.49886170 -54.91381047 Axis 0.98487954 0.00636148 0.17312375 Axis point 0.00000000 137.68459847 125.30174028 Rotation angle (degrees) 61.09376942 Shift along axis 6.23421857 Disallowing fitmap shift outputs an even larger translation, which I find odd: > fitmap #1 #0 search 50 shift false Found 35 unique fits from 50 random placements having fraction of points inside contour >= 0.100 (35 of 50). Correlations and times found: 0.8342 (1), 0.8038 (1), 0.7294 (1), 0.699 (1), 0.6862 (1), 0.685 (1), 0.6602 (1), 0.6548 (1), 0.6403 (1), 0.6318 (1), 0.629 (1), 0.6281 (1), 0.6145 (1), 0.6072 (1), 0.601 (1), 0.582 (1), 0.5695 (1), 0.5682 (1), 0.5529 (1), 0.544 (1), 0.5386 (1), 0.5317 (1), 0.5225 (1), 0.5152 (1), 0.5049 (1), 0.4984 (1), 0.4933 (1), 0.4718 (1), 0.4715 (1), 0.4698 (1), 0.4515 (1), 0.44 (1), 0.4243 (1), 0.4102 (1), 0.3598 (1) Best fit found: Fit map run_it025_class003.mrc in map run_it025_class002.mrc using 70798 points correlation = 0.8342, correlation about mean = 0.1402, overlap = 24.51 steps = 224, shift = 3.75e-13, angle = 59.1 degrees Position of run_it025_class003.mrc (#1) relative to run_it025_class002.mrc (#0) coordinates: Matrix rotation and translation -0.99670235 -0.06634245 -0.04672373 320.71861709 -0.08010133 0.71238040 0.69720724 -47.18870041 -0.01296937 0.69865073 -0.71534534 162.45334925 Axis 0.03956990 -0.92529900 -0.37716838 Axis point 158.55880471 0.00000000 92.42576286 Rotation angle (degrees) 178.95488392 Shift along axis -4.91780500 I am clearly missing something, how should I interpret the translation vector output by fitmap? Thank you for your help, Benjamin

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Issues using chimera
by Anna V. Bachmann 21 Jul '20

21 Jul '20

Hello, I am a new user of chimera on MacBook Pro and have been working through the tutorials. In a few sections of the tutorials, it says to ctrl-doubleclick an atom/bond/etc. to get a context menu. I am able to ctrl-click to select as well as shift-ctrl-click to select additional items, but when I attempt to ctrl-doubleclick with my trackpad it behaves the same way as a ctrl-click. Because of this I’ve been unable to complete some of the tutorials. I have not been able to find a solution to this online or in the mouse preferences of chimera. Is there a setting I can change to allow double-clicking on chimera, or is there another way I can show the context menu? Thank you Anna Bachmann Anna Bachmann anna.bachmann(a)centre.edu<mailto:anna.bachmann@centre.edu> Centre College ‘21

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Question about missing segments/pseudobonds
by OLMAN JOSE GOMEZ ESPINOZA 20 Jul '20

20 Jul '20

Dear colleagues, hope your fine well. I have a question about the pseudobonds/missing segments, what those missing segments really mean?. After I performed some docking analysis (using auto dock vina), I used ViewDock to evaluate the results, but I noticed some dotted lines between some atoms in the molecule, so I went to PseudoBond Panel and realized that this dotted lines are missing segments. So I did not understand if this missing segments are a truly chemical bond, or what are they? What would be its importance or relevance for my structure? Thanks in advance for your help Olman Gomez E. --

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detergent subtraction
by Dmitry A. Semchonok 17 Jul '20

17 Jul '20

Dear colleagues, Is there a way to subtract the detergent shell from the cryo-em map in chimera? Thank you Sincerely, Dmitry

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Re: [Chimera-users] difference electron density maps
by Elaine Meng 17 Jul '20

17 Jul '20

Hi Agata, Yes, I was describing using Ctrl-click to add a contour level at a negative level, using the Volume Viewer GUI, in addition to the one at the positive level that was already shown. You can have multiple contours at different levels at the same time, as shown by multiple vertical bars on the histogram. You can also do it in a single command, e.g. volume #1 sdlevel 3.5 sdlevel -3.5 Or via alias alias ^map_sig volume $1 sdlevel $2 sdlevel -$2 map_sig #1 3.5 I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 17, 2020, at 9:13 AM, Butryn, Agata (DLSLtd,RAL,LSCI) <agata.butryn(a)diamond.ac.uk> wrote: > > Hello Elaine, > > Thanks a lot for your advice, it is not quite obvious when the map is displayed in a surface mode.. I wanted to display both positive and negative peaks at a certain level simultaneously (like in Coot). If you type > > alias ^map_sig volume $1 sdlevel $2 > map_sig #1 3.5 > > only positive values at 3.5 sigma are displayed. By adding > > map_sig #1 -3.5 > > and unclicking 'cap high values at box faces' everything works perfectly. Many thanks again! > > Best wishes, > Agata > > > On 17/07/2020, 16:23, "Elaine Meng" <meng(a)cgl.ucsf.edu> wrote: > > Hi Agata, > I guess you mean that the map has both positive and negative values, but when it first displays there is only one isosurface at a positive value. > > In the Volume Viewer dialog there is a histogram of the map values with a vertical bar marking the isosurface level. You just Ctrl-click on the histogram to add another one. You can drag the vertical bars (thresholds) horizontally on the histogram to whatever contour levels you want, positive and/or negative, change their colors, etc. > > This is explained in the section about surface display with Volume Viewer: > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/fram…> > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volu…> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Jul 17, 2020, at 3:13 AM, Butryn, Agata (DLSLtd,RAL,LSCI) <agata.butryn(a)diamond.ac.uk> wrote: >> >> Hello, >> I have been trying to display a difference electron density map in Chimera. The map was exported from Coot in a ccp4 format and contains both positive and negative peaks. When I load the map in Chimera only the positive peaks are displayed. Is there a way to display the negative peaks? >> Many thanks and best wishes, >> Agata >> >

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difference electron density maps
by Butryn, Agata (DLSLtd,RAL,LSCI) 17 Jul '20

17 Jul '20

Hello, I have been trying to display a difference electron density map in Chimera. The map was exported from Coot in a ccp4 format and contains both positive and negative peaks. When I load the map in Chimera only the positive peaks are displayed. Is there a way to display the negative peaks? Many thanks and best wishes, Agata ~~~ Agata Butryn Postdoctoral Research Associate, XFEL Hub Diamond Light Source Ltd. Harwell Science & Innovation Campus Didcot, Oxfordshire, OX11 0DE United Kingdom +44 (0) 1235 778 788 agata.butryn(a)diamond.ac.uk<mailto:agata.butryn@diamond.ac.uk> -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Rama Plot generation for PDB with multiple Models
by Samuel Himes 16 Jul '20

16 Jul '20

Hello! I am working with PDBs with up to 100 models I want to generate one Rama Plot for the entire PDB. However, when I use the “Ramachandran Plot” in the model panel it creates a single plot for each model. Meaning 100 separate windows open. Is there a good way generate one Rama Plot for multiple models? Thanks -Sam Himes

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H-Bond Parameters
by Luke Kurfman-Student 16 Jul '20

16 Jul '20

Hello Sr./Ms., I'm using UCSF Chimera to analyze the hydrogen bonding of some structures of mine, in this case a system of three sulfuric acids. When I attempt to analyze this structure by changing the "Relax constraints by:" :[cid:d0a4e474-33c9-4d74-84c4-5b6b7101e390] The bond on the left gets eliminated before the bond on the right, even though by calculating the angle with the Angles/Torsion tool, between the O--H-------O of each hydrogen bond, I get an angle of 146.337 for the bond on the left, whereas for the angle on the right I get an angle of 144.189. It should not logically cut off the hydrogen bond on the left before the one on the right since the left hydrogen bond is shorter and straighter. Thus, I'm wondering why is chimera cutting the left angle off, and also is there a way for it to automatically display what chimera finds is the bond angle without using the angle/torsion tool? I've also tried different combinations of 3-4 atoms to get different bond angles, but no success in determining this difference. By adjusting the H-bond constraints by trial and error, the bond angle difference appears to be about 1.603 degrees according to what chimera automatically finds: [cid:d86dc3ee-58f1-4911-8cc2-a92268240a94] Any help is appreciated, Luke

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how can i cluster the result in .dcd file using chimera on a superomputer?
by Ibrahim Mohamed 16 Jul '20

16 Jul '20

Greeting sir, i want to use chimera (V 1.14) on a super computer to cluster the results from NAMD .dcd file but i found that it can be used only through the GUI. Is there a way to cluster the results from .dcd file using a script? if it is possible please send me the script thanks

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crop map command
by Hernando J Sosa 15 Jul '20

15 Jul '20

Dear Chimera, I there a chimera command equivalent to Features -> subregion selection -> crop in the Volume viewer menu? Thanks Hernando

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