- Chimera-users - RBVI Mailing Lists

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 21 Sep '18

21 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 18 Sep '18

18 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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