- Chimera-users - RBVI Mailing Lists

defining planes and axes based on existing ones
by ChuHui Fu 25 Oct '18

25 Oct '18

Hello, I am trying to define planes and axes that are orthogonal to the planes and axes that I have previously defined. I have an alpha helix, and I only managed to define one plane and two orthogonal axes around the helix. Is it possible to define the rest of the axes and planes? Thanks! -- ChuHui Fu B.S.Candidate in Chemistry Haverford College, Class of 2019 cfu(a)haverford.edu

5 9

Saving a moved PDB only moved in a new session
by Marta Perez Illana 25 Oct '18

25 Oct '18

Hi all I am working with chimera, and I have a map and a pdb. 1) I have split the pdb into several fragments in order to fit them into the map 2) I have successfully moved the PDBs and fitted them into the map 3) I have "write each PDB" "relative to the map, which seems to make sense :) 4) In the current session I keep the map and the moved PDB open ...plus I open the just saved "wrote PDB" (intended to be on the same position I moved it). To me both, the opened PDB (which I have moved) and the just saved PDB, might be in the same position, fitting into the map... But... the just save-written PDB is clearly somewhere else... :( 5) But... If I make a NEW session, opening the map and the "wrote PDB", everything make sense, and the PDB is where I in fact moved to keep it fitted... Why is that that in the current session the written-PDB is not where it was "moved"; but when a new session is opened it is displayed where it was moved? It seems that everything works fine, it is just a bit confusing to me. Thanks in advanced! Marta

2 1

Help SASA
by Andrea Yimena Cardona Barreto 25 Oct '18

25 Oct '18

Good afternoon, my name is Andrea Cardona and I´m a student of a magister in Human Genetics at Universidad Nacional de Colombia. In my thesis I´m interested in obtain the surface accessible solvent area of a homotetrameric protein (fumarate hydratase) but I have some troubles with Chimera. Can you give some help? -- Andrea Yimena Cardona Barreto Maestría en Genética Humana Universidad Nacional de Colombia

2 3

Accessible surface area and ASA per residue
by anastasia＠campus.technion.ac.il 25 Oct '18

25 Oct '18

Dear User, I'll appreciate your help. I've worked with Chimera previously, but have not used it recently. Now I try to repeat some of the analysis I've done, but I don't see the option ,solvent accessible surface, in the software (I guess I've installed a newer version). I would like to color all the exposed (to the solvent) residues like in the image below and export a table with these values per atom and residue. [cid:7c648fa9-c7cf-4dab-bf40-f0b4a95b8f47] What I tried to do this time is : 1. Show a molecular surface.. 2. Depiction --> render by attr , when attr is set to areaSAS on residues [cid:f46b071c-36ab-4792-bfc2-31eb50fc2be3] The result I got was: [cid:6b44e796-b2c2-42f8-aac8-1ab725121d38] Am I doing it right? how can export the calculated areaSAS per atom and residue from chimera? How the SAS values calculated in Chimera? Does the higher value means that this residue is more exposed? Thank you for your help, Anastasia

2 2

Chimera bug report submission
by Anas 23 Oct '18

23 Oct '18

The following bug report has been submitted: Platform: osx_x11 Chimera Version: (None given) Description Hello, I am trying to superpose a .pdb file on a density map (.mrc), and save it as .pdb. Chimera saves the file, but when I open it it doesn’t display any density map. Just the pub file which was superposed. I am doing it to start model building, but I am stuck at this. Kindly help.

2 1

MacOS Mojave
by Eric Pettersen 22 Oct '18

22 Oct '18

Hi all, A fix for the non-showing buttons problem on MacOS Mojave (10.14) is now in the Chimera daily build and the 1.13.1 release candidate. If you encounter any problems with the new version please use Chimera’s Help→Report A Bug to let us know about them. Note that the fixed version only runs on Mac OS 10.10 or later, whereas the previous version also ran on 10.8 and 10.9. —Eric Eric Pettersen UCSF Computer Graphics Lab

1 0

Re: [Chimera-users] Chimera problems
by Elaine Meng 20 Oct '18

20 Oct '18

> On Oct 19, 2018, at 8:41 PM, Shriwas, Pratik <ps774614(a)ohio.edu> wrote: > > Hi, > I am trying to use USCF chimera for studying docking between my compound and the receptor called GLUT1 (PDB - 4pyp or 1SUK). My concerns are: > > • I find different scores everytime I use the same compound and receptor Hi Pratik, Sounds like you are using the Autodock Vina interface of Chimera. Chimera does not calculate the docking, it just sends/receives data from an outside web service that is running the Autodock Vina program. It may be that the docking process uses some random numbers, and because the web service does not allow a high amount of sampling, it cannot always find the same top score(s). However, I do not know the details of Autodock Vina and you would have to look at its website <http://vina.scripps.edu/> and/or paper to learn about that. I’m guessing you are using Chimera’s Autodock Vina GUI to enter inputs, not the “vina” command. However, if you are using the command make sure you get a recent version of Chimera, because some problems with the command were fixed. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> > • I am not able to show my hydorgen bonds between compound snd receptor in GUI. Although I can see them in the list box. Maybe the atoms are not shown (for example, if the sidechain is not shown, the H-bond to the sidechain won’t be shown). To make sure the H-bonding atoms are shown, in the H-bond parameters dialog turn on the option “If endpoint atom hidden, show endpoint residue.” However, if that is not the problem, then maybe the graphics on your computer has trouble showing lines. You could try updating your graphics driver, or try showing the H-bonds as sticks instead of lines with command: setattr p drawMode 1. Or maybe it can draw lines but they are too thin for you to see. In that case, in the H-bond parameters dialog increase the “Line width” value. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbo…> > • I am not able to find exact binding energy. This is the central problem of docking! Firstly docking scores are not binding energies, only approximations, and secondly, one has to do a lot of conformational and positional sampling to find the most accurate position. The Autodock Vina website does not allow a high amount of sampling, as it is a shared resource provided for free. If you want to do more intensive docking you can download Autodock Vina (or some other docking progam like DOCK, Gold, ...) and run it directly. > • My ligand is not on pubchem/NIH servers. What is best way to find its smiles string. Different websites have different smiles string and I get different interactions. Usually there are multiple ways of writing the SMILES string for the same compound. As long as the compound looks right to you (has the correct covalent structure, the right elements connected in the right way) then the results should be equally valid even though the coordinates might be slightly different (e.g. rotated or translated or different conformation). Any slight change in inputs will change docking outputs, since sampling is not exhaustive, but the change does not mean one answer is “wrong” and the other is “right". > > Regards, > Pratik Shriwas > Phd Candidate, > Molecular and Cellular Biology program, > Edison Biotechnology Institute, > Ohio University. For future reference, Chimera questions should be sent to chimera-users(a)cgl.ucsf.edu (CC’d here). For Autodock Vina questions, see <http://vina.scripps.edu/questions.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Finding files my session is showing
by David Sáez 19 Oct '18

19 Oct '18

Hello everyone. I saved some sessions time ago. Now I found the .py files, and they work fine, but I do not remember what files I am opening when I restore the session. In the .py file I could not find any information about loaded topologies or pdb files. Can these data be recovered from a session? Thanks in advance

3 4

Saving PDBs
by Elliott, Jabari 17 Oct '18

17 Oct '18

When attempting to save PDBs of multiple models into one file, I end up with a pdb file with no data (0-600 bytes). When attempting to open files in pymol, they are blank. Please advise. Thank you.

2 2

Alias commands for volume pieces
by Benjamin Looker 17 Oct '18

17 Oct '18

Hello! I have recently received emails from Tom Goddard and Elaine Meng on this subject, but I believe it can be further clarified. The research group I am a part of routinely generates Gaussian cube files for molecular orbitals using the DFT program ORCA, we then manually use Chimera to change the level and color of the two phases of the resulting wave function, *which appear in Chimera as two **surface pieces* belonging to the same surface. In the volume viewer menu Data, *and* in the Model Panel, there is no way to see a #0.1 #0.2 model subnumber, and Group/Ungroup returns the error "Cannot group a single molecule." Is there a way to refer to volume pieces in the command line? Such that an alias can be written to do this formatting in a more efficient manner? Best, -- Benjamin G. Looker Graduate Student Lancaster Group

2 1

Re: [Chimera-users] [chimera-dev] Chimera orbitals alias question
by Elaine Meng 16 Oct '18

16 Oct '18

> On Oct 13, 2018, at 2:34 PM, Benjamin Looker <bgl44(a)cornell.edu> wrote: > > Hello! > My name is Benjamin Looker, I am a chemistry graduate student at Cornell University, and our group often uses Chimera to visualize the orbitals output from the DFT software ORCA. > > When these .cube files are opened in Chimera, the two phases of the wavefunction surface are given different colors and bars in the volume viewer. > > My question is, when using an alias command, how would one set the level and color of only one of these phases, ie: to perform actions on only one of the bars and colors, instead of homogenizing the whole function? > > An alias such as: > alias ^orbitals volume all level 0.05 color #2d2d00000b0b style surface > > Is great, but that pesky "all" undermines the point of the operation. I have tried referencing model numbers, such as #0, #1, and #2 instead of "all," but Chimera returns an error. I do not know the label of the object that I am trying to affect. > > Any help would be greatly appreciated! > Best, > -- > Benjamin G. Looker > Graduate Student > Lancaster Group Hi Benjamin, I don't have an example cube file to test with, but from your description I'm guessing it has signed data and that is why Chimera automatically shows two isosurfaces when you open a single file. The levels are the same magnitude, just the opposite signs. How the initial display values are set is described in the “surface and mesh display” section of the Volume Viewer documentation: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/fram…> "For unsigned data types, an initial threshold is set so that 1% of voxels (1% of the volume encompassed by the data region) lie above it; for signed data types, positive and negative thresholds are placed symmetrically about zero." In that case, there is no way to specify in the command line changing only one isosurface and not the other. You can see in the Model Panel (open from Favorites) that the entire dataset is listed as one model. Although you could open the data twice and use your volume command on only one copy (specified by the model number as shown in the Model Panel) that would still leave both the isosurfaces on the other copy as initially shown. However, there is nothing magical about the initial display setting other than it is meant to be easily viewable. There is no knowledge used about the type of data (i.e. it doesn’t care or know that orbitals are what you’re showing) so you may want to go ahead and set all the isosurfaces using your values rather than relying on initial display. You can specify level and color multiple times in the volume command for multiple isosurfaces, e.g. volume #0 style mesh level 0.8 color red level 1.2 color 0,.5,.8 This is one of the examples in the “volume” command manpage <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. for future reference, the chimera-dev list is mainly for programming questions. General usage questions are better sent to chimera-users(a)cgl.ucsf.edu CC’d here

2 1

Visualize 3-10 helix
by BuddySphinx 15 Oct '18

15 Oct '18

Dear Chimera users, I am wondering if there is a quick way in Chimera to visualize 3-10 helix? Or showing the dihedral angle of the peptide bonds? Best, Yangqi Sent from Mail for Windows 10

3 2

problem with autodock vina page
by ammad aslam 13 Oct '18

13 Oct '18

I wonder, is there any problem with autodock vina website vina.scripps.edu/download.html ? I and my friends here cannot open it. Can anyone update me about the real problem. Regards, Ammad

2 1

Morphing code
by Minh Le 12 Oct '18

12 Oct '18

Hello there, I'm currently having trouble with the morphing code in chimera and I don't know how to use Python to make the morph.py. Is there any way you can help me with this? Thank you, Minh

2 3

MD movie metafile
by Matthias Fellner 12 Oct '18

12 Oct '18

Good day I successfully loaded NAMD psf/dcd files into chimera (version 1.13.1) using the tools MD movie interface. As I have many runs and each has multiple dcd files I wanted to use a script to load the different runs, instead of manually picking all the files through the interface each time. I tried to follow the limited instructions of the MD Movie homepage but failed to get anywhere. I tried some versions of this command: md: D:\script.txt or movie: D:\script.txt The command md appears to try to start MDA (MultiDomain Assembler), the command movie wants some other unrelated inputs. I am also not sure if the script command would even work like this: namd(psf/dcd) D:\structure.psf structure_MD001.dcd - D:\ Any advice is appreciated Thank you Matthias Fellner

3 3

Generating symmetry mates
by Vani Pande 10 Oct '18

10 Oct '18

Hello, I wanted to generate symmetry mates for the protein, I am not finding a way to do so in chimera.The protein is a monomer in an asymmetric unit. Thanks Vani Pande Int PhD Biological sciences IISER Pune 20162013

2 2

C-N peptide bond within one peptide
by Emily Xu 08 Oct '18

08 Oct '18

Hello, Is there a way to join two ends of a peptide in Chimera? I am trying the create a peptide bond linking the C and N termini in a singular peptide to form a cyclotide. Is this possible in Chimera?

2 1

error opening .cif file
by Francesco Pietra 07 Oct '18

07 Oct '18

Hi With my /opt/UCSF/Chimera64-1.11.2/bin/chimera, I notice a mistake in opening 4i4t.cif.gz (as 4i4t.cif), i.e., residue 43 and 44 in chain D are mis-numbered 44 and 45, giving the wrong impression that residues 43 and 44 are missing. I have not checked anything else. cheers francesco pietra

2 4

Recording movie at 720p
by Ahmad Khalifa 05 Oct '18

05 Oct '18

I'm recording a movie in the command line using: movie record movie stop movie encode output ~/ I tried to include the option preset dvd for movie encode, I recieved the following error: "Error reading paper_movie.txt: AttributeError: 'module' object has no attribute 'standard_formats' File "/opt/UCSF/Chimera64-1.12/share/MovieRecorder/moviecmd.py", line 124, in encode_op settings = RG.standard_formats.get(preset) See reply log for Python traceback." What am I doing wrong and how can I record my movie at 720p? Regards.

2 1

Maps/models display/activate checkboxes? [Feature suggestion]
by Oliver Clarke 04 Oct '18

04 Oct '18

Hi, It would be very helpful to have a way to undisplay all maps, or all models, at once. This would be particularly handy when inspecting the fit of a model in a map, as the residue tooltips don’t work when there is a surface in front of the atoms. Would it be possible to add two checkboxes in addition to the model specific checkboxes and the “all” checkbox that controls whether models, maps, or both are displayed? I would envision both the model and map checkboxes working as toggles, checked by default, but one could uncheck either to temporarily undisplay all maps/models, and then check the box again to return to the previous state. I know most effort is going into ChimeraX, so please disregard if this is difficult to implement. Cheers OIi

2 1

Chimera pdb error
by 김민재 03 Oct '18

03 Oct '18

Hi! Thanks for all of your help, but I got another problem... I uploaded a picture of the Chimera error. The HG hydrogen atoms are not being shown in Chimera. When I extract just the CG and HG pdb lines and input them, Chimera works fine and can even calculate the surface. But, when I run it with the pdb file that I have right now, it keeps returning that error. I thought that maybe Chimera could only calculate the surface for atoms which are connected, and that the program was looking for mandatory bond between the atoms. I was wondering if there was a settings change I could make to fix this, or if there was any other way to go about straightening things out to calculate the solvent excluded area of this pdb file.

2 1

MacOS Mojave
by Eric Pettersen 01 Oct '18

01 Oct '18

Hi all, MacOS Mojave will be released this Monday, Sept. 24. On Mojave, Chimera buttons and popup menus are not shown until the window containing them is resized. Therefore we advise against upgrading to Mojave until we come up with a fix for this issue — which we will announce on this list as soon as it is available. —Eric Eric Pettersen UCSF Computer Graphics Lab

1 1

Hiding models one by one?
by Ahmad Khalifa 01 Oct '18

01 Oct '18

I'm trying to hide a range of models using ~modeldisplay #16-60. For display purposes, I want to to make them disappear one by one or in groups. I can of course write down a bunch of ~modeldisplay #16; wait 5; ~modeldisplay #17; wait 5;...etc. Is there a way to for loop that process in the command line or do it in a better way? Regards.

2 1

Calculating surface area of a single atom
by 김민재 01 Oct '18

01 Oct '18

Hey everyone! I've been trying to calculate the solvent excluded surface area of a single hydrogen atom, but Chimera keeps returning an error "miscalc code 5" message whenever I run the "surface probeRadius" command. I would really appreciate anyone's help.

2 1

FW: Contributing to ChimeraX ?
by Williams, Joanne 01 Oct '18

01 Oct '18

From: Nicholas Yue <yue.nicholas(a)gmail.com> Date: Sunday, September 30, 2018 at 3:40 AM To: "chimerax(a)cgl.ucsf.edu" <chimerax(a)cgl.ucsf.edu> Subject: Contributing to ChimeraX ? Hi, I took ChimeraX for a spin and when I save out to OBJ, the geometries looks connected up wrongly. I was hoping I can take a look at the source code to attempt to fix it myself. I see git being mentioned in the documentation. Is there a git repo I can clone and contribute to? If I need to sign any documents before contributing, let me know :-) I have other geometry format I'd like to write out to and also I am hoping to write out quads rather than triangles for use with OpenSubdiv in rendering software like RenderMan, Arnold, Mantra etc. Cheers -- Nicholas Yue Graphics - Arnold, Alembic, RenderMan, OpenGL, HDF5 Custom Dev - C++ porting, OSX, Linux, Windows http://au.linkedin.com/in/nicholasyue https://vimeo.com/channels/naiadtools

1 0