- Chimera-users - RBVI Mailing Lists

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

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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.

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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

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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.

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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

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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.

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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.

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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

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Calculating surface for modified pdb file
by 김민재 29 Sep '18

29 Sep '18

Hi y'all, I've been trying to calculate the surface area of a modified pdb file. It is an extracted part from 3hgn. Although the file seems pretty small and simple, I keep getting a miscalculation-due-to-huge-chain error message from Chimera. I think it's because of the "WARNING: treat_rs_edge: third atom not found for edge 7 9" lines that get recorded on the reply log.I'm new to Chimera and using pdb files, so I would really appreciate advice on how to solve this issue. I took everything in a screen shot below. I can send anyone the actual files if they want to take a closer look. Thanks.

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Model color won't change
by Ahmad Khalifa 28 Sep '18

28 Sep '18

I have a structure with a biological unit. When I select the structure, click biological unit, it shows a surface. By selecting the surface I can show ribbon and then I have the entire biological unit fitted in my density. The original structure has the color #beb7beb7beb7. the biological unit geenrated from it has the color #beb8beb8beb8. In ribbon view, the structures look the same, but the chain trace shows a darker colored original structure (see the picture). None of them would allow me to change to the same color code #beb7beb7beb7 or #beb8beb8beb8. I want all of them to have the same color in chain trace view. How can I fix it?

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Displaying chain trace without atoms
by Ahmad Khalifa 28 Sep '18

28 Sep '18

I have some structures in chain trace view, I hid them via the command line ~disp, but when I reshow them with disp, all the atoms are present. How to show chain trace while hiding the atoms?

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Chimera morph colors with morph conformations
by Ahmad Khalifa 28 Sep '18

28 Sep '18

Hello, I'm trying to create a movie with morph conformations. I wonder if it's possible to morph the colors, or change colors midway through, going from one conformation into the other. Please feel free to contribute any ideas or thoughts on how to make my movie clearer and more visually aesthetic. Thanks.

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Loading multiple ligand mol2 files for AV
by Leif Peterson 26 Sep '18

26 Sep '18

Is it possible to load multiple mol2 files, and add H, equlibrate charges, then energy minimize all if the ligands in batch mode, then save all of them to pdbqt files? Then, loop through all of the ligands using AV on each to get sorted docking results. Reason I ask is because almost all resources available on multiple ligand use with AD and AV seem outdated, developers moved on, and am hitting dead ends and pages not found.

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Query
by Vani Pande 26 Sep '18

26 Sep '18

Hi, I am new to chimera. I want to superimpose a domain for the two protein molecules and get the rmsd for the non superimposed protein parts. How should i do it. Ihave superimposed domain of interest for my protein using match, but now i am not getting how to proceed further. Thanks Vani Pande Int PhD Biological sciences IISER Pune 20162013

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Command line equivalent to hide
by Ahmad Khalifa 26 Sep '18

26 Sep '18

While the command line equivalent to show is "modeldisplay #modelnumber", what is the equivalent for hide? Regards.

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Re: [Chimera-users] Chimera-users Digest, Vol 185, Issue 16
by Vani Pande 26 Sep '18

26 Sep '18

Hello, I did not receive a reply to the message I sent. Could you kindly help me out. Thankyou Vani Pande Int PhD Biological sciences IISER Pune 20162013 On Wed, Sep 26, 2018 at 5:50 PM <chimera-users-request(a)cgl.ucsf.edu> wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Fitmap: correlation about the mean for global search > (Michele Lunelli) > 2. Re: Fitmap: correlation about the mean for global search > (Tom Goddard) > 3. Command line equivalent to hide (Ahmad Khalifa) > 4. Re: Command line equivalent to hide (Elaine Meng) > 5. Re: [chimera-dev] Auto set threshold boundaries and colors > (Benjamin Looker) > 6. Query (Vani Pande) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 25 Sep 2018 18:02:38 +0200 > From: Michele Lunelli <michlun23(a)gmail.com> > To: chimera-users(a)cgl.ucsf.edu > Subject: [Chimera-users] Fitmap: correlation about the mean for global > search > Message-ID: > < > CADZjtDT0D2srWpLg3LDbeoPvReaO2mDAnqqCJisUuAKrBMZOwQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear people, > > I want to do a global search of an atomic model into an EM map, using the > correlation about the mean (cam) as metric. I use a command like this: > fitmap #0 #1 resolution 6 metric cam search 100 radius 150 > > However, only the correlation about zero is reported in the final fit list > (and used to rank the solutions). Where can I find the cam values for all > the fits? > > Thank you > Michele >

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Re: [Chimera-users] [chimera-dev] Auto set threshold boundaries and colors
by Elaine Meng 25 Sep '18

25 Sep '18

Hi Benjamin, This only refers to intiial display. You can of course change the threshold (isosurface level) to whatever is appropriate for the specific data, by dragging the vertical bar in the Volume Viewer histogram or by using the “volume” command. It is not a preference, but you could create an alias that would be listed in the menu so that you could reapply it easily. For example, command: alias ^orbitals volume all level 0.05 color pink style surface … or there could be multiple levels and colors specified in the same command. Then your alias “orbitals” (or whatever you named it) would be listed in a top-level Aliases menu for easy reapplication to later datasets. I.e., choosing menu: Aliases… orbitals or typing the command “orbitals” would run it. Aliases are saved in the preferences: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html> The volume command has many options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html> The 1% initial display (rather than a specific threshold value) was most useful for the wide variety of volume data where people often do not know what threshold will be best for viewing. It is surely adjustable by changing the code but others would have to advise on that matter. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 23, 2018, at 10:18 AM, Benjamin Looker <bgl44(a)cornell.edu> wrote: > > Hello! > > My name is Benjamin Looker, and I have recently become acquainted with your software for visualization of molecular orbital calculations that my group does with some regularity. I was wondering whether the statement on this page refers to a specific preferences file in the Chimera program files. : > > (http://www.rbvi.ucsf.edu/chimera/1.8/docs/ContributedSoftware/volumeviewer/…) > > "For unsigned data types, an initial threshold is set so that 1% of voxels" > > The reason I ask is because it would be much simpler, given a known color code and level, to standardize the import of files into Chimera for any sort of publication, especially in the event that many molecular orbitals needed to be visualized at once for a project. > > Best, > > -- > Benjamin G. Looker > Graduate Student > Lancaster Group

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Fitmap: correlation about the mean for global search
by Michele Lunelli 25 Sep '18

25 Sep '18

Dear people, I want to do a global search of an atomic model into an EM map, using the correlation about the mean (cam) as metric. I use a command like this: fitmap #0 #1 resolution 6 metric cam search 100 radius 150 However, only the correlation about zero is reported in the final fit list (and used to rank the solutions). Where can I find the cam values for all the fits? Thank you Michele

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MatchMaker
by Ward, Miriam L. (CDC/OID/NCIRD) 24 Sep '18

24 Sep '18

Hello, I used MatchMaker to superimpose a couple of models. Now when I open any .pdb files, they automatically superimpose. How can I "turn off" MatchMaker so it doesn't automatically superimpose everything? Thanks, Leanne M. Leanne Ward, MEd. Microbiologist II Cherokee Nation Assurance contractor Rotavirus Surveillance and Molecular Epidemiology Team Gastroenteritis Viruses Branch Division of Viral Diseases, NCIRD, CDC Mailstop G04 1600 Clifton Rd. N.E. Atlanta, Georgia 30329 U.S.A. Phone: (404) 639-3265 Email: mrw0(a)cdc.gov<mailto:mrw0@cdc.gov>

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Hiding AutoDock Vina Search Volume (frame)
by leifepeterson＠sbcglobal.net 24 Sep '18

24 Sep '18

Using Select-->Chains-->(no ID), I can select the AutoDock Vina Search Volume structure after performing a docking, but once it's selected (highlighted in green), I can't seem to remove it from the molecular plot. What is the recommend way to remove the square frame?

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Re: [Chimera-users] Placing Autodock Vina Pocket around AA residues from RaptorX
by Leif Peterson 20 Sep '18

20 Sep '18

Hi Elaine, Thanks for the tip on the center command, and looking up the Swiss-Prot method. Leif Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Placing Autodock Vina Pocket around AA residues from RaptorX
by leifepeterson＠sbcglobal.net 20 Sep '18

20 Sep '18

Couple newbie questions: 1. I don't know if any users have run RaptorX (U-Chicago) for ligand-residue pocket prediction, but the results simply tell you the specific AA residues are which are close to the pocket For example the locations could simply be e.g. the residues K252, Q256, and K260 in the input PDB file. So my question in terms of AA annotation in Chimera is, how could I center Autodock Vina's pocket box around residues something like K252, Q256, and K260? I looked through the select options and didn't see where numbered residues could be selected. 2. For 3D modeling when x-ray crystallography results are not available in PDB, I commonly will submit a protein's FASTA sequence to SWISS-MODEL, and then download the PDB and go through dock prep for the receptor and minimization of the ligand(and adding e.e. hydrogens, etc.) Isn't the SWISS-MODEL approach an alternative for using the MODELLER add-on for homology modeling. The MODELLER run I just went through was really using a lot of core resources, and the BLAST template results were complexes between receptors and ligands, and sometimes DNA. So isn't there an advantage to inputting a FASTA from Uniprot into SWISS-MODEL to obtain the predicted 3D structure, when compared with the BLAST results required during MODELLER runs?

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chimerax mesh commands doesn't work
by Yehuda Halfon 20 Sep '18

20 Sep '18

Hi all, I wanted to use chimeraX to use some commands on mesh display. Some works like meshLightning but others like lineThickness doesn't I use volume #1 lineThickness 10 (or any other integer) but nothing seems to change. What am I doing wrong? Yehuda Halfon

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change the center of a pdb model
by C.J. 19 Sep '18

19 Sep '18

Dear specialists, When I opened two pdb files of icosahedral model(two structures of the same virus), I found both center didn't overlap. My question is how to change the origin of a pdb model to overlap both. Thank you! -- Best regards! Jianhao Cao

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How to show ligand pocket as wireframe mesh
by leifepeterson＠sbcglobal.net 19 Sep '18

19 Sep '18

I ran a ligand-receptor prediction for a protein at Site-hound, and downloaded all the files. Is there a Chimera tutorial which shows how to display the volume a selected cluster inside the protein as a wireframe mesh? My guess is that the volume will be between all the AA residues in the given cluster(?) Once I can show the mesh, I will then go through the Autodock Vina run using ligands in a mol2 file, to sort their energies.

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FW: Question for using Chimera 1.8
by Williams, Joanne 17 Sep '18

17 Sep '18

From: Shabnam Nadjafi <shabnam.nadjafi(a)gmail.com> Date: Monday, September 17, 2018 at 12:29 AM To: "chimera(a)cgl.ucsf.edu" <chimera(a)cgl.ucsf.edu> Subject: Question for using Chimera 1.8 Dear Manager I am a pharmacologist and I decide to publish a book about drugs and some biochemicals by in silico evaluation of the chemical structures with biologic targets. I have to use the impressive software "Chimera 1.8". Would you please give me some information about this? Is it enough to cite "Chimera 1.8" in "Foreword" or "Preface" sections of the book? Is it free to use "Chimera 1.8" for publishing a book? Sincerely Yours Shabnam Nadjafi M.D. PhD of Pharmacology Neuroscience Research Center, Iran University of Medical Sciences, Tehran, Iran

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Add to discussion group
by Ayala Carl 17 Sep '18

17 Sep '18

To whom this may concern, I am a chimera user and have been having some difficulty opening structural measurement file. I would like to join the discussion group to post a question regarding this topic. Thanks, Ayala

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Atom specifiers for selected atoms
by BuddySphinx 16 Sep '18

16 Sep '18

Dear Chimera users, I have a simple question, if I have selected some atoms from my coordinates using mouse and draw a square. How do I know which atoms I have selected? Is there any way to show the atom specifier? Best, Yangqi Sent from Mail for Windows 10

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Calculating surface area
by Yangqi Gu 14 Sep '18

14 Sep '18

Dear Chimera users, I am trying to visualize the interface surface of my two monomers. Is there anyway to show the interacting surface from Chimera by using the EM map? Or should I do it from PDB coordinates? Best, Yangqi -- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus

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Morph colors
by Rajan Prabu 14 Sep '18

14 Sep '18

Hello again, Following another old thread, http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-September/012743.html I could morph/play the coordinates and Volume at the same time. The script is given below. ---------------------------------------------------- # Open maps and set threshold open 1.mrc open 2.mrc open start_full.pdb open end_full.pdb vol #0,1 level .025 # Create a marker for coloring measure center #2 mark true radius 20 color red ~display #4 # Create morph volume vop morph #0,1 frames 0 model #5 # Create morph models model #6 morph start #2 frames 200 morph interpolate #3 frames 200 morph movie # marker on morph measure center #6 mark true radius 20 color red # Color near marker scolor #5 zone #6 range 50 coordset #6 1,100; vop morph #0,1 start 0 playstep 0.01 frames 100 model #6 ---------------------------------------------------- Still the color is at centre of of the first Frame of morph. If I understand correct I have to measure the centre for each Frame and add marker and color it. But I still can't make it. Any help/directions in this regard would be very helpful. Thanks in advance for your time and help. best regards Rajan

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Open Structural Measurement table
by Ayala Carl 13 Sep '18

13 Sep '18

Hi, I have been having difficulty opening a previously saved table of measured distances. I cannot open in as any file type listed by chimera and unfortunately I did not save the session that I measured the distances. If I open my models is there a way to impose the distances saved to the opened models? Thanks in advance

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Morph colors
by Rajan Prabu 13 Sep '18

13 Sep '18

Hello all, First please accept my apologies for to open a topic which is discussed already, but I couldn't get it working. I would like to morph a volume and colour its subregions. I made the following script ( adopting old messages in this forum ) open 1.mrc open 2.mrc open start_full.pdb open end_full.pdb vol #0,1 level .025 # Create a marker for coloring measure center #2 mark true radius 20 color red ~display #4 # Create morph vop morph #0,1 frames 0 model #5 # Color near marker scolor #5 zone #4 range 50 #Play morph vop morph #0,1 model #5 frames 200 interpolateColors false In the above script everything works, but color stays at place. Unfortunately for my morphing the marker has to move along with the morph. But I dont know how to do that. Any help in this regard would be very helpful. best regards Rajan

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Errors applying AddCharge to PDB files with non-Chimera protonation
by Matthias Bal 12 Sep '18

12 Sep '18

Hi, I have a large amount of PDB files which need explicit hydrogens for MD and quantum calculations. To go beyond Chimera's AddH function, I've tried using the Protoss tool among others. Trying to add charges (AMBER ff14SB) using Chimera to PDB files protonated in this way leads to errors regarding non-standard atom names in standard residues. For example, the protonated PDB case 1amw gives the following errors in the Reply Log: > Non-standard atom names: > ALA H (ALA 2.A H) > Total charge for #0: -12.939 > The following residues had non-integral charges: > ALA 2.A 0.4009 > LYS 102.A 0.66 > Correct charges are unknown for 1 non-standard atom names in otherwise standard residues > Charges of 0.0 were assigned to the unknown atoms I know the suggestion of the help page on AddCharge is to remove the hydrogens and re-add them using AddH since they are often the problem, but that's not really an option in this case. Is there an overview somewhere of all the different PDB hydrogen naming conventions (like a more recent version of https://www.ics.uci.edu/~dock/pdb2pqr/programmerguide.html) and how they relate to what Chimera/Amber is using? And is there a way to script the conversion to treat files in batches? Thanks a lot, Matthias

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Unix download
by KEITH MUNSON 10 Sep '18

10 Sep '18

Hi Chimera, I downloaded chimera-1.13-linux_x86_64.bin <http://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=linux_x8…> into my Dell desktop Downloads dir but there was no chimera-installer.bin included in the download. Where do I get the installer? Thanks, Keith Munson

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Writing models in PDB only working via model panel, not via drop-down menu (UCSF Chimera 1.3)
by Jun Ha Song 10 Sep '18

10 Sep '18

Dear RBVI, I noticed that I could not write .cmm marker sets in UCSF Chimera as PDB file via drop down menu from main window, but that I could write it as PDB via Model Panel's side menu. Is this a bug? Best, Junha Song.

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max density value using a script
by Tamas Hegedus 07 Sep '18

07 Sep '18

Hi, I subtract two electron density maps and I would like to get the min and max density values of the resulted map. I can see these values in the GUI, but I would like to get them running chimera without a gui using a python script. (Without saving the final map into an .mrc file and reading the header of that file.) Thanks for your help, Tamas -- Tamas Hegedus, PhD Senior Research Fellow Department of Biophysics and Radiation Biology Semmelweis University | phone: (36) 1-459 1500/60233 Tuzolto utca 37-47 | mailto:tamas@hegelab.org Budapest, 1094, Hungary | http://www.hegelab.org

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calculate density from an AA model
by Tamas Hegedus 06 Sep '18

06 Sep '18

Hi, Is there an option (command, tool) in Chimera to calculate the theoretical electrondensity map for an all atom protein model? Similar to the MDFF tool in VMD. https://www.ks.uiuc.edu/Training/Tutorials/science/mdff/tutorial_mdff-html/… Thanks, Tamas -- Tamas Hegedus, PhD Senior Research Fellow Department of Biophysics and Radiation Biology Semmelweis University | phone: (36) 1-459 1500/60233 Tuzolto utca 37-47 | mailto:tamas@hegelab.org Budapest, 1094, Hungary | http://www.hegelab.org

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Visualizing major and minor axes of inertia
by Felipe Vasquez 05 Sep '18

05 Sep '18

Dear all, I am interested in visualizing the major and minor axes of inertia of a ligand in a PDB structure by using UCSF Chimera. Once I calculate the axis of inertia by entering in command line: measure inertia sel I obtained the following info (in reply log): v1 = 0.985 -0.173 -0.013 a = 6.079 r1 = 2.103 v2 = -0.086 -0.553 0.829 b = 4.564 r2 = 2.765 v3 = -0.150 -0.815 -0.559 c = 1.127 r3 = 3.400 center = 38.682 56.595 62.547 However, I do not still know: 1- What are the major and minor axes of inertia? This info is given by the "a/b/c" or "r1/r2/r3" values? 2-How can I visualize the major and minor axes of inertia as planes (or arrows)? Thanks in advances for your help. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* PhD candidate in Chemical Engineering Universidad de los Andes Bogotá, D.C., Colombia Carrera 1 #18A-12, Of. ML-754(26) +57 1 3394949 Ext. 1747

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ChimeraX and crosslinks visualization
by Pascal Albanese 04 Sep '18

04 Sep '18

Dear Support Staff, first of all many thanks for developing Chimera! I'm using ChimeraX to integrate CryoEM and crosslinking MS data.I think that some features might be further implemented (or maybe are already there but i don't know how to use them): - Is it possible to load different sets of distances/crosslinks (like with different IDs)? - is it possible to color code the distances with a cutoff (like red if >30 for instance)? - The histogram and network is a nice feature, but it would be nice if there were some grouping based on the distances (i.e.: 1 to 5 A; 5 to 10 A, 10 to 15 A... etc), and then you can click on the column representing your distances class to select them (so you can make a subgroup, or delete them, or edit them etc...) that's it, maybe something can be done writing the code but unfortunately it's not my job. Thanks a lot and looking forward to hear from you, Cheers, Pascal -- Pascal Albanese, PhD *Post-doc*, Politecnico di Torino Dipartimento DISAT, BioSolar Lab@Environment Park Via Livorno 60 10144 Torino e-mail: pascal.albanese(a)polito.it Phone number: +39 011 2257655 <+39%20011%20225%207655>

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Re: [Chimera-users] Mirror image proteins
by Chu Ji 04 Sep '18

04 Sep '18

Hi Eric, I was trying to get a mirror image of a PDB model and came across your thread. I know that you are typing in m = chimera.openModels.list()[0] for a in m.atoms: crd = a.coord() crd.z = 0 - crd.z a.setCoord(crd) in the Gen Control>IDLE section, but I also read on GitHub that I should change the [0] in openModels.list()[0]to the model specifier. What does that mean exactly? I tried to type in the PDB ID to replace the 0 but nothing happened…Could you show me an example? What if I want to flip Chain B of a certain model or just the entire model? Thank you so much for your help! Looking forward to hearing from you. Best, Nancy Sent from Mail for Windows 10

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Chimera: Amber to PDB
by Boris TOUZEAU 04 Sep '18

04 Sep '18

Hi, I am Boris TOUZEAU, actually a PhD student at the National Taiwanese University (NTU) based in Taipei. I had a question about chimera; Is it possible to output pdb files having amber residues naming convention instead of pdb residues naming convention ? I saw it was possible to do it for the atoms (ligands) but I would be more interested to do it for residues. Best wishes, Boris TOUZEAU

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chimera error during AddCharge for MD preparation
by Waterbury, Amanda 04 Sep '18

04 Sep '18

Hi, I am attempting to perform MD stimulations with a protein containing an FAD cofactor, however, I keep receiving the following error message: Charge model: AMBER ff14SB Assigning partial charges to residue FAD (net charge -2) with am1-bcc method Running ANTECHAMBER command: /Users/alwaterbury/Desktop/Chimera.app/Contents/Resources/bin/amber14/bin/antechamber -ek qm_theory='AM1', -i /var/folders/wd/pdz6gvr12ybbxtfs6m6mn1y80000gn/T/tmpUR9bIs/ante.in.mol2 -fi mol2 -o /var/folders/wd/pdz6gvr12ybbxtfs6m6mn1y80000gn/T/tmpUR9bIs/ante.out.mol2 -fo mol2 -c bcc -nc -2 -j 5 -s 2 (FAD) (FAD) dyld: Library not loaded: /usr/local/lib/libquadmath.0.dylib (FAD) Referenced from: /Users/alwaterbury/Desktop/Chimera.app/Contents/Resources/lib/libgfortran.3.dylib (FAD) Reason: image not found (FAD) Running: /Users/alwaterbury/Desktop/Chimera.app/Contents/Resources/bin/amber14/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac (FAD) (FAD) Running: /Users/alwaterbury/Desktop/Chimera.app/Contents/Resources/bin/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (FAD) Total number of electrons: 408; net charge: -2 (FAD) (FAD) Running: /Users/alwaterbury/Desktop/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out (FAD) Error: cannot run "/Users/alwaterbury/Desktop/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit Failure running ANTECHAMBER for residue FAD Check reply log for details Any help/suggestions would be much appreciate! Best, Amanda

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Depicting entropy and mobility in pdb files
by George Tzotzos 27 Aug '18

27 Aug '18

Hi everybody, I’ve generated two pdb files which are of identical coordinates. Their only difference is that the b-factor column has been replaced with data indicating residue conservation (structure 1) and residue intrinsic mobility from normal mode analysis (structure 2). Below are indicative atomic coordinates. Structure 1 ATOM 24 NH1 ARG A 5 5.258 -15.260 -22.393 1.00 2.87 N ATOM 25 NH2 ARG A 5 6.717 -16.030 -20.793 1.00 2.87 N ATOM 26 N ARG A 6 3.934 -11.168 -16.245 1.00 2.84 N ATOM 27 CA ARG A 6 5.160 -10.666 -15.652 1.00 2.84 C Structure 2 ATOM 24 NH1 ARG A 5 5.258 -15.260 -22.393 1.00 1.35 N ATOM 25 NH2 ARG A 5 6.717 -16.030 -20.793 1.00 1.35 N ATOM 26 N ARG A 6 3.934 -11.168 -16.245 1.00 1.73 N ATOM 27 CA ARG A 6 5.160 -10.666 -15.652 1.00 1.73 C Is there a way to visualise these differences (e.g. by different thickness of ribbons or any other means e.g. colour of spheres). Thank in advance for any suggestions George

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Re: [Chimera-users] UCSF Chimera Ribbon Question
by Elaine Meng 25 Aug '18

25 Aug '18

Hi Alex, The problem is not the ribbon style (and you don’t need supersmooth, simply smooth will do) but the “subdivision” graphics quality, which has apparently gotten set to some abnormally low value. Your ion isn’t particularly spherical in the image either, because this parameter also affects atom and bond display. See Tools… Viewing Controls… Effects, “subdivision” in the lower right area of the dialog. The factory default is 1.5 whereas your image looks something like 0.1. You can also control this value with the “set” command. This is discussed in the “Image Tips” under smoothness <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#tips> …as well as the Effects and “set” documentation <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/sideview.html#effects> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html#subdivision> For future reference, we recommend sending questions to chimera-users(a)cgl.ucsf.edu (CC’d here) to better ensure that you get an answer. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 24, 2018, at 6:41 PM, Alex Yorn <alexyorn(a)yahoo.com> wrote: > > Elaine, > I'm having a little difficulty viewing ribbon models. I'm not sure what I did exactly, but I every time I open up Chimera, the default setting is this (see attached photo). This looks like a flat representation of the ribbon, but it's actually the supersmooth representation. I've tried double-checking the Cross Section in the Ribbon Style Editor, but everything looks normal (see attached photo). Can you help me with this? > Sincerely, > Alex Yorn

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Tetramer using Chimera
by Bárbara Abrahim Vieira 24 Aug '18

24 Aug '18

Dear all, We wish apply in our research the Chimera system. Initially, we build our model (monomer) using ab initio and then, we will investigate the active site using docking. However, it is known that the protein is a tetramer. Then, we need to create a tetramer, without any pdb homologous, is it possible? Thanks for your time, ________________________________ Bárbara Abrahim-Vieira Modelagem Molecular ModMolQSAR Faculty of Pharmacy Federal University of Rio de Janeiro

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some issues with download Chimera
by Zhu, Daming (NIH/NIAID) [E] 23 Aug '18

23 Aug '18

Hello, I have some issues with downloading Chimera. I can download and install it onto my computer, but it messed up my screens-I have two computer screens but only one works (with a terrible looking), and the other one cannot be connected. If I want both Chimera and my two computer screens working, what is the basic requirement for a computer? Thank you for your help. Best regards, Daming Zhu Daming Zhu Laboratory of Malaria Immunology and Vaccinology NIAID/NIH Twinbrook I, Room 1118 5640 Fishers Lane Rockville, MD 20852 Phone: 301-761-3993

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Dropdown list of models in groups
by Yasser Almeida Hernández 23 Aug '18

23 Aug '18

Hello, I am working with groups of models, and I wonder if there is a way to make a group, with a defined name, and then inspect each models independently without lose the group. Currently, if I make a group, and then ungroup, I lose the definition, notes ans any other action on it. If there is no possibility, I would suggest the developers to consider the option to make groups with dropdown list of models. Best Yasser

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Getting measure distance value
by al.kupczyk 22 Aug '18

22 Aug '18

Hi, I'm struggling with getting a value from runCommand in Chimera. I need to measure distance between an atom and a density map and keep it in a variable, so I'm trying to get a value from "measure distance" command in Python, but unfortunately with no results. Is there any way to somehow get it into a variable? Yours sincerely, Alicja

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Changing chain ID for ligands
by Ahmad Khalifa 20 Aug '18

20 Aug '18

Is there a way to do it in chimera? Regards.

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Chimera download
by Fengbiao Guo 17 Aug '18

17 Aug '18

Hello, My name is Fengbiao Guo, I work on Mercer University School of Medicine Savannah campus. I want to download the Chimera software, but I can’t open the page, so I want to ask how could I do can download this? Best regards, Fengbiao Guo

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