- Chimera-users - RBVI Mailing Lists

Getting the analysis of the side chains that are not in the density map
by Dmitry Semchonok 13 Mar '20

13 Mar '20

Dear colleagues, I have a map with the fitted model inside. Some of the side chains are out for the density map. I want to have a get a file where the side chains that are not in the density map are listed. Does anyone know how to do that? Thank you! Sincerely, Dmitry

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Help please
by Dr Musa Said 11 Mar '20

11 Mar '20

Dear there I am training myself in Chrimera software. The first example shows the ligand is on one side and 1HOM is on another side. Where did I g wrong, please. Please see the attachment. Regards Musa

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Re: [Chimera-users] how to create a sphere in Chimera
by Elaine Meng 11 Mar '20

11 Mar '20

Hi Sc Ke, Chimera doesn't do that projection calculation; you would have to do it yourself. I think you could select all the nitrogens within the sphere and then write out their coordinates, but any other steps after that would require your own processing. You don't even need the sphere (it may just be for display purposes) since you already have an atom at the center of it to define the radius for finding nitrogens. I think you could select the nitrogens, for example, by just selecting the center atom (Ctrl-click on it, you may need to hide the sphere first if it's covering the atom), and then using a command something like: select N & sel za<8.5 ... where instead of 8.5 you would put the radius of the sphere. It means select element N and also within 8.5 angstroms of current selection, which is the center atom you selected first. You can hide the sphere by un-checking its S (Shown) checkbox in the Model Panel (show by choosing Model Panel from the Favorites menu). Then you could get the coordinates of the selected nitrogens, for example with command getcrd sel ... and then look in the Reply Log for the list of coordinates (show by choosing Reply Log from the Favorites menu). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 10, 2020, at 6:05 PM, Ke Shyue-Chu <ke(a)gms.ndhu.edu.tw> wrote: > > Hi, Elaine, > Thank you for the detailed instruction. I got the sphere. > > May I ask one more question: > How do I define an equator plane of that sphere and project all nitrogen atoms within that sphere onto the equator plane; i.e. the polar coordinates of the nitrogen atoms within a sphere are what I would like to have? > Thank you very much. > sc > > -----Original Message----- > From: Elaine Meng [mailto:meng@cgl.ucsf.edu] > Sent: Thursday, March 05, 2020 12:46 AM > To: Ke Shyue-Chu <ke(a)gms.ndhu.edu.tw> > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] how to create a sphere in Chimera > > Hi Sc Ke, > There is more than one way. Say you have already selected the single atom. Then, > > (A) to put a marker (essentially a fake atom) at that position, command “measure center”, for example: > > measure center sel mark true radius 4.0 color pink model #8 transparency 50 #8 > > see manual for command options > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#center> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/transparency.html> > > (B) to put a spherical surface model at that position, command “shape sphere”, for example: > > shape sphere radius 8.5 center sel color orange modelid #8 transparency 60 #8 > > see command options > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html#sphere> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Mar 4, 2020, at 2:40 AM, Ke Shyue-Chu <ke(a)gms.ndhu.edu.tw> wrote: >> >> Hi, >> I would like to know how to create a sphere of certain radius around a selected atom, for visualization purpose. >> Thank you. >> Sc Ke >> Professor >> Department of Physics >> National Dong Hua University >> Hualien, Taiwan > > > -- > 此電子郵件已由 AVG 檢查病毒。 > http://www.avg.com > >

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Change default pseudobond color?
by Oliver Clarke 10 Mar '20

10 Mar '20

Hi, Is it possible to change the default pseudobond color? The current default is yellow, which is unreadable on a white background (but fine on a black background). Orange is readable on both black and white backgrounds - would it be possible to change the default color for distances to orange? Cheers Oli

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Numbers(markers) inside/on the map
by Dmitry A. Semchonok 10 Mar '20

10 Mar '20

Dear colleagues, I would like to place the numbers (markers) inside/on our map. Could you please prompt how to do that ? Thank you. Sincerely, Dmitry

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Regarding Structure minimize
by Yash Bahl 08 Mar '20

08 Mar '20

To do structure minmization, what is the adequate values? Steepest descent should be changed to 75 from 100. What else? Should intervals be also changed to 25? Thanks

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visualizing potential with volume data
by Christos Deligkaris 06 Mar '20

06 Mar '20

dear all, I have obtained a cube file from NWChem with the electrostatic potential around a molecule. I visualized the molecular surface using Actions->Surface->Show and then colored it using the volume data (followed instructions https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecontrib.html in tools->surface color (electrostatic surface coloring)) . Since I do not have my data stored in a potential file, can I still do the surface offset? The chimera tool webpage discusses why that is preferred than showing the potential on the solvent excluded surface and it seems to me that option to not be available with volume data. Also, my surface does not look like the electrostatic potential surface shown here: https://www.cgl.ucsf.edu/chimera/data/tutorials/maps08/volume-basics.html . The molecular surface we get with Action->Surface->Show seems to be constructed with greater atomic radii than the one shown in that image. I am not sure how important that is though. Is there a way to ask Chimera to visualize the electrostatic potential volume data with the same options Chimera would use if it was reading a Delphi, PBS file? Best wishes, Christos Deligkaris, PhD Assistant Professor of Physics

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move labels
by Dieter Blaas 06 Mar '20

06 Mar '20

Hi, I once knew but forgot and spent hours not finding it: How do I select a label by clicking and then move it with the mouse? Thank you very much, bw Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Choosing Help->Search Documentation causes seg fault
by Hua tiger 05 Mar '20

05 Mar '20

Hello, First of all thank you for your good work and assistance. Core dump trace is attached and a snippet follows. Choosing Help->Search Documentation causes seg fault. The remaining help menu items work fine. Please see below. Thank you so much. John ------------------------------------------------------------------- huatiger@huatiger:debug$ coredumpctl debug PID: 23503 (python2.7) UID: 1000 (huatiger) GID: 1000 (huatiger) Signal: 11 (SEGV) Timestamp: Sat 2020-02-29 14:35:13 EST (1min 8s ago) Command Line: /opt/UCSF/Chimera64-1.14/bin/python2.7 /opt/UCSF/Chimera64-1.14/share/__main__.py --debug Executable: /opt/UCSF/Chimera64-1.14/bin/python2.7 ... Core was generated by `/opt/UCSF/Chimera64-1.14/bin/python2.7 /opt/UCSF/Chimera64-1.14/share/__main__.'. Program terminated with signal SIGSEGV, Segmentation fault. #0 0x00007fe3a31c51f8 in uncompress2 () from /lib/x86_64-linux-gnu/libz.so.1 ---------------------------------------------------------------------------------------- huatiger@huatiger:Downloads$ cat /etc/os-release NAME="Ubuntu" VERSION="19.10 (Eoan Ermine)" ID=ubuntu ID_LIKE=debian PRETTY_NAME="Ubuntu 19.10" VERSION_ID="19.10" HOME_URL="https://www.ubuntu.com/" SUPPORT_URL="https://help.ubuntu.com/" BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/" PRIVACY_POLICY_URL=" https://www.ubuntu.com/legal/terms-and-policies/privacy-policy" VERSION_CODENAME=eoan UBUNTU_CODENAME=eoan huatiger@huatiger:Downloads$ uname -a Linux huatiger 5.3.0-40-generic #32-Ubu

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LINK record not honoured in Chimera?
by Kate Kim 04 Mar '20

04 Mar '20

Hello, I would like to visualize a thioester bond between a CYS residue of my protein and a carbonyl carbon of ligand (DCR) in my model. I have a LINK record for the DCR-CYS thioester bond created from Jligand and inserted in the PDB right before the CRYST1 line. However, when I open this PDB in Chimera, the thioester linkage is not drawn. The distance between the C1 of DCR and SG of CYS is 1.79 angstrom. Does Chimera need something else other than the LINK record in the PDB to display the bond? Thank you, Kate

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