- ChimeraX-users - RBVI Mailing Lists

Drawing objects in ChimeraX?
by de Miranda Seabra, Gustavo 23 Feb '22

23 Feb '22

Hi, I was wondering if it is possible to draw objects in ChimeraX. More specifically, I'd like to show the gridbox used for docking calculations, so it would be nice if I could draw a cube, and even better if it can be drawn as a surface that could have color, transparency, etc. How to do this in ChimeraX? Thanks a lot! -- Gustavo Seabra Research Associate Professor Center for Natural Products, Drug Discovery, and Development (CNPD3) Department of Medicinal Chemistry College of Pharmacy University of Florida, Gainesville, FL, USA

3 4

Re: [chimerax-users] Regarding generating volume surface in ChimeraX for large maps
by Tom Goddard 22 Feb '22

22 Feb '22

Hi Rakesh, ChimeraX displays just a single plane when you open a map file larger than 256 Mvoxels -- often the situation for electron microscopy tomograms, for example a 2048 by 2048 by 100 map (400 Mvoxels), but also for large electron microscopy single particle reconstructions, e.g. 800 x 800 x 800 (512 Mvoxels). Maps larger than 16 Mvoxels will not be shown at full resolution (step 1), instead the step size will be chosen to only display at most 16 Mvoxels when the map is first opened, again to improve load speed for common interactive use cases. So if you are writing a script and need the full map shown always include a volume command to assure it is shown how you want, for example to show all planes, volume #1 region all style surface or to assure it is shown at full resolution volume #1 step 1 region all style surface and to make sure the threshold level is what you want you can specify it too volume #1 level 4.5 step 1 region all style surface There are volume command options that set the 256 MVoxel limit for planes (option name "voxelLimitForPlane") and 16 MVoxel full resolution limit (option name "voxelLimit") that you can use to change the default for the current session, but unfortunately ChimeraX currently does not offer a way to save new default values. These are all documented https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#sampling Tom > On Feb 18, 2022, at 12:47 PM, Rakesh Ramachandran <rakeshramachandran10(a)gmail.com> wrote: > > Hi Tom, > > I am trying to segment volume using 'volume splitbyzone' in ChimeraX for a large number of maps. But what I observed is that some of the maps are displayed as planes instead of surfaces and this affects the volume splitbyzone command. > > I tried using 'volume style surface' but it doesn't seem to work unless I manually set it in the GUI. What option do I use to generate surfaces for map volumes automatically from the command line in such cases? > > -- > Regards > Rakesh Ramachandran > Postdoctoral Scholar > Department of Bioengineering and Therapeutic Sciences > University of California, San Francisco > Byers Hall Room 501 > 1700 4th Street > San Francisco, CA 94143, USA

2 2

Editing preset for initial colors
by Niels Bradshaw 22 Feb '22

22 Feb '22

Hi Elaine, Is there a way in chimera X to change the initial colors preset for new models? I’m not into the default tan color, so I end up changing the color immediately every time I open a new model. In previous versions of Chimera, I had disabled color by model and set all new models to open with grey. In pymol, I defined the colors for the first 10 models I open in the startup script, which is even more convenient. Having the option to have the default to color by chain could also be nice if that is possible. I tried some workarounds like redefining the tan color, but it appears that is not allowed. Thanks, Niels

4 3

Re: [chimerax-users] Mailman privacy alert
by Ralph Loring 22 Feb '22

22 Feb '22

Hi, I keep getting these notifications that ChimeraX on both my laptop and my office computer is not registered and I need to register them again. I think between the two computers, I've registered the program four times in the past two months. What's up with this? Ralph Loring Ralph H. Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring(a)northeastern.edu On Thu, Feb 17, 2022 at 8:32 PM <chimerax-users-bounces(a)cgl.ucsf.edu> wrote: > An attempt was made to subscribe your address to the mailing list > chimerax-users(a)cgl.ucsf.edu. You are already subscribed to this mailing > list. > > Note that the list membership is not public, so it is possible that a bad > person was trying to probe the list for its membership. This would be a > privacy violation if we let them do this, but we didn't. > > If you submitted the subscription request and forgot that you were already > subscribed to the list, then you can ignore this message. If you suspect > that > an attempt is being made to covertly discover whether you are a member of > this > list, and you are worried about your privacy, then feel free to send a > message > to the list administrator at chimerax-users-owner(a)cgl.ucsf.edu. >

2 1

Re: [chimerax-users] Bundle dependency
by Anthony James Schaefer 21 Feb '22

21 Feb '22

Katie, I'm not sure. I tried adding pdb-objects to one of my bundle's dependencies, and it was installed. I'm testing this on a ChimeraX 1.4 daily build. My bundle_info.xml has this: <Dependencies> <Dependency name="ChimeraX-Core" version=">=1.2.dev"/> <Dependency name="pdb-objects"/> </Dependencies> and my log has this after installing (along with a bunch of other stuff): Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing c:\users\normn\documents\github\chimerax_themes\dist\chimerax_themes-0.3.1-py3-none-any.whl Requirement already satisfied: ChimeraX-Core>=1.2.dev in e:\chimerax 1.4.dev202202010639\bin\lib\site-packages (from ChimeraX-themes==0.3.1) (1.4.dev202202010639) Collecting pdb-objects Using cached pdb_objects-0.1.3-py3-none-any.whl (6.6 kB) Installing collected packages: pdb-objects, ChimeraX-themes Successfully installed ChimeraX-themes-0.3.1 pdb-objects-0.1.3 --- Successfully installed ChimeraX-themes-0.3.1 pdb-objects-0.1.3 Installed ChimeraX-themes (0.3.1) Towards the bottom, it says it installed pdb-objects and my bundle. I can then go into the shell and import pdb_objects without error. Best, Tony ________________________________ From: Zeng, Katie <jingrou.zeng18(a)imperial.ac.uk> Sent: Monday, February 21, 2022 2:59 PM To: Anthony James Schaefer <tony.schaefer(a)uga.edu> Subject: Re: Bundle dependency [EXTERNAL SENDER - PROCEED CAUTIOUSLY] Hi Tony, Thanks for pointing that out. I've now changed the dependency to pdb-objects, but I still get the same error when I try to use the bundle in ChimeraX. Have you got any idea why it's giving this error? Best Regards, Katie ________________________________ From: Anthony James Schaefer <tony.schaefer(a)uga.edu> Sent: 21 February 2022 17:57 To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu>; Zeng, Katie <jingrou.zeng18(a)imperial.ac.uk> Subject: Re: Bundle dependency This email from tony.schaefer(a)uga.edu originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping for this address. Katie, It looks like PDB objects on PyPI is called pdb-objects, not pdb_objects. For dependencies, ChimeraX looks for the package name and not the import name. Best, Tony ________________________________ From: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu> on behalf of Zeng, Katie via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> Sent: Monday, February 21, 2022 11:50 AM To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Subject: [chimerax-users] Bundle dependency [EXTERNAL SENDER - PROCEED CAUTIOUSLY] Hi, I'm currently working on building a membrane builder bundle and it requires the use of a python library called 'pdb_objects'. Following the tutorial on the website, I'm adding the following line to my bundle_info.xml file under the dependencies tag: <Dependency name="pdb_objects"/> It still gives me an error of <No module named 'pdb_objects'> when I load my bundle in ChimeraX. How can I allow the use of this library in my bundle? Thanks for your help! Best Regards, Katie

1 0

Bundle dependency
by Zeng, Katie 21 Feb '22

21 Feb '22

Hi, I'm currently working on building a membrane builder bundle and it requires the use of a python library called 'pdb_objects'. Following the tutorial on the website, I'm adding the following line to my bundle_info.xml file under the dependencies tag: <Dependency name="pdb_objects"/> It still gives me an error of <No module named 'pdb_objects'> when I load my bundle in ChimeraX. How can I allow the use of this library in my bundle? Thanks for your help! Best Regards, Katie

2 1

Re: [chimerax-users] No suitable models found for viewDockX
by Rangarajan, Amith 21 Feb '22

21 Feb '22

hello chimeraX, I am trying to open a glide docking result using viewdockx and i am getting this error message ('no suitable models found"). I tried opening the file as .mae file ( protein and ligand are both in same model )and a pv.mae file ( protein and ligand are in diff models). I am still getting the same error. I am using chimerax ver 1.3 please help me see what i am missing. thanks amith

2 1

Question about Coulombic electrostatic potential
by Sunisa Yoodee 21 Feb '22

21 Feb '22

Dear UCSF ChimeraX We used the ChimeraX program to calculate electrostatic potential. By using the coulombic command, a molecular surface was generated and colored. However, we also need the electrostatic potential value (kcal/(mol*e))of the protein. Could you please give some advices how to get this value? Best Regards, Sunisa Yoodee -- *Sunisa Yoodee*, Ph.D Medical Proteomics Unit, Faculty of Medicine Siriraj Hospital, Mahidol University, 6th Floor SiMR Building, 2 Wanglang Road, Bangkoknoi, Bangkok 10700, THAILAND Tel: 66-8-06691102 e-mail: yd.sunisa(a)gmail.com

3 3

Define axis tool missing?
by James Hodgkinson-Bean 20 Feb '22

20 Feb '22

Hi I am currently doing some geometric analysis of a protein complex, and was wanting to define certain axis normal to planes I have defined; on the online chimerax documentation there seems to be an option “define axis”, however in my actual chimeraX program, this command doesn’t work, and is not listed under the “help define” command which shows how to define planes and centroids. I am running ChimeraX version 1.3 (2021-12-08), which I downloaded recently. Any assistant would be much appreciated 😊 P.S I absolutely love chimeraX!! It is one of the best pieces of software I’ve ever used. Cheers, James.

2 1

The ChimeraX-Modeller interface
by Ralph Loring 18 Feb '22

18 Feb '22

Hi, The intracellular domain (ICD) of Alpha7 nicotinic receptors, like almost all eukaryotic Cys-loop receptors, is not resolved using X-ray crystallography or cryo-EM. Last week the PDB for an ensemble of NMR ICD structures for the receptor was released (PDB 7RPM). I've been unsuccessfully trying to use ChimeraX and Modeller to make a model of a subunit that includes the ICD. The 7RPM models include all 4 transmembrane domains and the ICD (but lacks the extracellular domain), so there is considerable overlap with the 7KOO PDB fo a7. I started by deleting all but one of the identical subunits in the 7KOO pdb and loaded one of the 7RPM models and tried to use Modeller to make a construct that includes both the extracellular domain and the ICD. Unfortunately, even though both 7KOO and the single 7RPM are in the sequence alignments window, the ChimeraX-Modeller combination ignores the structure that is not chosen as the target (e.g. if 7RPM is the target, there is no extracellular domain, but if 7KOO is the target, there is either no ICD or the ICD that is shown bears no relevance to the structure in 7RPM). I can align the two structures well with a low RMSD using Matchmaker because of the TMDs overlapping. I just want to fill in the missing parts. Is there a special trick to get Modeller to fill in the missing parts using ChimeraX as the interface? I'm not that experienced using Modeller. Thanks, Ralph H. Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring(a)northeastern.edu

3 10