July 2020 - Chimera-users - RBVI Mailing Lists

Setting a unique torsion to a specified value
by Jerry Tanoury 29 Jul '20

29 Jul '20

Dear forum, I am new to chimera. I have been building and modifying several structures using command-line, and have been successful except for setting a specific torsion to a specified angle. The torsion is not phi, psi, etc. I thought I could define the torsion as a specific attribute using an attribute assignment file and defattr. In my model, the torsion is ":1.A@O3 :1.A@S1 :1.B@O2 :1.B@S2", and I would like to set it to a value of 15. So, my assignment file would be (?): attribute: MyTors match mode: any recipient: atoms :1.A@O3 :1.A@S1 :1.B@O2 :1.B@S2 15 Then from command-line I would use: defattr MyTors Is this correct? Thank you for the help, Jerry

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Re: [Chimera-users] [chimerax-users] [External] Re: Clip surface but not atoms
by Pufall, Miles A 27 Jul '20

27 Jul '20

That is very nice - particularly is you can make the cap translucent (so you can see what the ligand might be interacting with. M On Jul 27, 2020, at 3:15 PM, Elaine Meng <meng(a)cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> wrote: Another thing users might not know is that one can also color the planar surface cap by the MLP, e.g. by saving the lipophilicity map and then using a separate command to recolor the surface including the cap. E.g. adding the following commands to my previous example: mlp map true color sample #1.1 map #2 palette lipophilicity range -20,20 This is not to say it would make a better figure... just giving options. :-) Best, Elaine <mlpclip.png> On Jul 27, 2020, at 12:16 PM, Pufall, Miles A <miles-pufall(a)uiowa.edu<mailto:miles-pufall@uiowa.edu>> wrote: Thanks Elaine! I’ll save the full string of commands you sent. Tom’s guidance helped a lot - the figure came out just how I wanted it. <699C644F-6A5E-47A1-9559-30329A1B5105.png> Thanks again - M On Jul 27, 2020, at 2:14 PM, Elaine Meng <meng(a)cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> wrote: Hi Miles, In case it's useful, here's a little example that works in the current daily build. This protein has oleic acid (residue name OLA) in a buried pocket. The example turns off clipping for the parent model #1 (the atomic model, which includes any ribbon and atom/bond displays) but leaves it on for the molecular surface model #1.1. open 1g74 surface clip front 0 position :ola clip model #!1 false hide ~:ola target ar style :ola ball Probably you'd want to use the Right Mouse modes to translate and rotate the clipping plane interactively since it's hard to get the position you want with commands only. Elaine On Jul 25, 2020, at 7:12 AM, Pufall, Miles A <miles-pufall(a)uiowa.edu<mailto:miles-pufall@uiowa.edu>> wrote: Cool - thanks! Downloading now - will let you know if all is well. Miles On Jul 24, 2020, at 10:32 PM, Tom Goddard <goddard(a)sonic.net<mailto:goddard@sonic.net>> wrote: Hi Miles, I added the ability to turn off clipping for specific models, in tonight's ChimeraX builds. It only effects clip planes that rotate with the models, not the near / far camera clip planes: clip model #!1 off The molecular surface of atomic model #1 is a submodel #1.1. So I use "#!1" in this command instead of #1 so the command acts on only model #1 and not its child models #1.1, 1.2,... You also will want to turn of surface caps surface cap false so that the hole left in the clipped surface is not covered by a cap. Tom On Jul 24, 2020, at 11:35 AM, Elaine Meng <meng(a)cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> wrote: Hi Miles! I remember meeting you at UCSF years ago. I hope you are well. This unfortunately is one of the features often needed for figures but that is not yet available in ChimeraX, the ability to clip one model (e.g. the surface) without clipping the other (e.g. the ligand atoms). I've listed it in the Missing Features section of the ChimeraX download page as "per-model clipping." It is one of the things on the To-Do list and is a ticket in our database. I will add your e-mail address to the notification list for that ticket. For now, you would still need to use Chimera for per-model clipping. Sorry about that, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 24, 2020, at 10:32 AM, Pufall, Miles A <miles-pufall(a)uiowa.edu<mailto:miles-pufall@uiowa.edu>> wrote: Hi! I’ve used Chimera for years (though not recently) and am switching to ChimeraX. I’m looking to display the ligand binding pocket with the ligand, and the tutorial you have is great. I generated this picture, which is really close to what I want. It shows the ligand, and the pocket, and I’m able to slice it with the interactive side view tool to get to this point. However, the left side of the ligand is slightly clipped. I’ve played with rotation and with moving the slice plane, but can’t find an orientation that shows the pocket so nicely (without any surface in the foreground) and not ligand clipping. My question is: is there a way to tell ChimeraX to clip the surface but not the ligand? Thanks! Miles <DAC_binding_pocket.png> _______________________________________________ ChimeraX-users mailing list ChimeraX-users(a)cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________ _______________________________________________ ChimeraX-users mailing list ChimeraX-users(a)cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. _______________________________________________ ChimeraX-users mailing list ChimeraX-users(a)cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________

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Error while doing docking
by Reshu Kunche 27 Jul '20

27 Jul '20

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HOW TO USE YOUR SOFTWARE
by HEWARTH ALBERTO MERCADO LOPEZ 25 Jul '20

25 Jul '20

HAVE A GOOD DAY ON MY PART. MY WRITING IS TO REQUEST FORMALLY THE USE OF YOUR CHIMERA SOFTWARE FOR ACADEMIC USE I AM A STUDENT OF CHEMISTRY AT A UNIVERSITY OF SOUTH AMERICA EXPERIENCED IN COLOMBIA TODAY, COLLEGES WOULD HAVE A WEBINAR ON THE USE OF THEIR SOFTWARE IN INVESTIGATION YOUR GRADE PROJECTS. I WANTED TO BE ABLE TO ACCESS THE SOFTWARE, THEY COULD TELL ME HOW TO DOWNLOAD IT SINCE THE AUTOMATIC DOWNLOAD METHOD IS NOT GIVEN TO ME UNA RAZON MIL OPORTUNIDADES

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Error
by Reshu Kunche 25 Jul '20

25 Jul '20

While opening the file showing error while opening it what the reason

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Electrostatic Potential Calculations Using Coulomb's Law
by Arth Patel 24 Jul '20

24 Jul '20

Hello Everyone, I have a .pqr file generated using the APBS website and I want to calculate the electrostatic potential for each atom of the proteins using this. I did this using the surface analysis --> Coulombic Surface on Chimera. As part of my current research I am supposed to write a code on python for the same but when I compare the results, I am getting different results. Can someone please explain how to calculate the atom electrostatic potentials from a .pqr file theoretically? Thanks, Arth

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Crystallographic Map Expansion
by Jessica Bruhn 24 Jul '20

24 Jul '20

Hi, I am trying to open a map generated by microED. I generated a SigmaA map in coot based on an fcf file generated by SHELXL (see attached). I can open it in Chimera and things look reasonable. I am wondering if it is possible to expand the density map beyond the boundaries of the available box using the crystallographic symmetry? Additionally, I am a bit confused by the size of the box. I would have expected it to have the dimensions of the unit cell or the asymmetric unit, but it does not appear to be either of those. The map does appear to be scaled properly. Any help would be greatly appreciated. Thanks, Jessica -- Jessica Bruhn, Ph.D Principal Scientist NanoImaging Services, Inc. 4940 Carroll Canyon Road, Suite 115 San Diego, CA 92121 Phone #: (888) 675-8261 www.nanoimagingservices.com

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How to avoid ”designate file type“ while opening a file
by Gong, Zhen 23 Jul '20

23 Jul '20

Hi, When I click on “file”, then “open”, no matter what types of files I am opening, there would be a window asking me to “designate file type”. This window came up very recently on my Chimera 1.13. Then I updated to Chimera 1.14 but still have this problem. Does anyone know how to avoid this? Many many thanks. Best, Zhen

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Large scale drug screening with chimera
by 최근호 22 Jul '20

22 Jul '20

Dear officer, I am geunho choi from korea. I am doing a docking simulation through chimera. My work is done in the order of dock prep -> autodock vina. If I need to docking 1 protein and 500 drugs, is there a way to docking it all at once? I really appreciate it if you help me. regards, geunho choi

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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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