- Chimera-users - RBVI Mailing Lists

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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