- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Where is the 2D Labels gui?
by Elaine Meng 31 Jul '20

31 Jul '20

> On Jul 31, 2020, at 4:58 AM, Chin-Bow, Stephen <stephen.chin-bow(a)yale.edu> wrote: > > Hi Elaine, > I just searched for: > > chimera 2D labels +gui > > but I did not find it. > Is it possible that the 2D Labels GUI was added for ChimeraX users? > Many thanks! > Stephen Hi Stephen, Chimera's 2D Labels tool is in the menu under Tools... Utilities, and also under Tools... Depiction. In general every command manual page also has a crossreference link to its tool, so you could just look at the "2dlabels" command manual page to find out about the tool. We generally just call the graphical interface dialogs "tools" so you wouldn't see the jargon "gui" very often in the documentation or find it in a search. If you just searched for "2d labels" you would find it. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels…> The 2D Labels tool is also mentioned in the "tips on preparing images" and used in many of the image-making tutorials. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#tips> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/convergent.html> Another way to find out about the tool is to look at the Tools index in the User Guide. Each tool's individual manual page says what tool category it is in (which is the submenu under Tools in which it appears). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecontrib.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels…> ChimeraX does not have a 2D Labels GUI (tool dialog) yet, only a 2dlabels command. We changed the syntax of this command between the two programs, to simplify/improve it in ChimeraX. Regarding your other message, we had envisioned new users finding out about Chimera features in these ways: (1) tutorials: numerous in the User Guide and additional ones on our website (2) using menu Help... Search Documentation to search for terms of interest (3) browsing the User Guide (included with download, menu Help... User's Guidef), scanning through tools index, commands index, basic functions outline for topics of interest (e.g. "tips on preparing images") and then following the links to read more details. (4) website feature highlights, image gallery, and animation gallery This does not address learning the programming (python) side of things. Chimera includes a Programmers Guide, but information for programmers is much less detailed than for users. <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/index.html> ChimeraX has much more emphasis than Chimera on supporting programmers (APIs, programmer documentation, ...), as well as a Toolshed online repository for plugins (similar to the Cytoscape App store). I hope this clarifies things. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Is there a way to determine the "screen" window coordinates (x, y) of an "atom-spec"
by Chin-Bow, Stephen 30 Jul '20

30 Jul '20

Hello, It has been only a few weeks since I first started learning Chimera 1.14 (build 42094) on a Linux64 system with X11. I hope my experiences will help you improve both Chimera and ChimeraX. Earlier today, I reported a situation which results in an unexpected handling of a "divide by zero" bug. I am using the experience to also learn some Python. I am sure there are better ways, but I edited your playmorph.py code to record an animation with a morphing sequence played in reverse. I admit that I still do not understand the different coordinate systems used in Chimera. I have a question which can simply be answered using a ruler, but I am hoping there is another more elegant solution. "2D Labels" arrow ends are specified as a percentage of the screen width and screen height (range 0.0 to 1.0). I would like to draw an arrow whose end (x,y) is specified with precision. After I can specify the windowsize Is there a way to request the "window-screen" coordinates of a specific atom-spec? This is useful, because if I have set the windowsize then I can simply divide the coordinates by the window dimensions to get the desired end for the arrow. Many thanks, Stephen

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ViewDock problem
by Krivic, Denis 30 Jul '20

30 Jul '20

Hello, Does anybody know why the viewdock calculates Hbonds, but doesn't want to show them (in some cases-picture, not always)? Kind regards, Denis

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The 2D labels keeps on moving away. Inb
by Shinjini Ghosh 29 Jul '20

29 Jul '20

Whenever I am trying to label the structure with 2D labels and after that when I am trying to save it as a POV ray image, the labelling keeps on moving away from the original position. What should I do to keep the labelling in the original place? I have attached the normal jpeg picture and the POV ray picture saved as PNG. -- Shinjini Ghosh. Student of Master of Science, Biophysics and Molecular Biology' Rajabazar Science College, University of Calcutta. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> 07/29/20, 10:19:50 AM

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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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