- Chimera-users - RBVI Mailing Lists

3D Viewing Collaboration
by Provance, Jeremy 30 Jun '16

30 Jun '16

Hello, My name is Jeremy and I work at the University of Missouri—Kansas City School of Medicine. To cut to the chase, we’re doing R&D work with Microsoft HoloLens as it applies to medicine in both macroscopic (telemedicine) and molecular (pharmaceutical compound visualization and manipulation) applications. I’ve been using Chimera for some time in my academic explorations and wanted to contact you all to start a conversation about how we might collaborate to make molecular manipulation in 3D a reality. I’m imagining importing a protein and coloring areas of polarity and hydrophobicity, real-time, as the protein floats in the space of a classroom, as the proof of concept. Let me know if this is something you all would be interested in working together on. Jeremy ----- Jeremy Provance<https://twitter.com/jeremyprovance> | Software Analyst, Center for Health Insights<http://chi.umkc.edu> 2411 Holmes Street, Kansas City, MO 64108 | MG-204A (816) 235-1938 | provancej(a)umkc.edu<mailto:provancej@umkc.edu>

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Re: [Chimera-users] [Chimera] #14773: Connectivity problems with CIF file
by Eric Pettersen 30 Jun '16

30 Jun '16

Hi Clarisse, While it is theoretically possible to add methyl groups as donors in Chimera, it is by no means easy. Firstly, you’d have to come up with geometric criteria as per the source Chimera uses: Three-dimensional hydrogen-bond geometry and probability information from a crystal survey. <http://www.ncbi.nlm.nih.gov/pubmed/9007693> Mills JE, Dean PM. J Comput Aided Mol Des. 1996 Dec;10(6):607-22. Then you would have to modify the FindHBond module to add methyl donors and their geometry criteria. The learning curve would be steep. Since you have explicit hydrogens on your structures, a simpler alternative that may be good enough is to use the Find Clashes/Contacts tool to find “contacts” between methyl hydrogens and hydroxyl oxygens. Just run the tool, select methyl hydrogens (e.g. “sel methyl & H”), designate them as a set to check, select the hydroxyl oxygens (“sel hydroxyl & O”), designate them as the second set, set checking to be between the two sets, then perhaps check contacts using the default parameters, or whatever parameters you felt were appropriate. BTW, you have to get tomorrow’s build to have the “methyl & H” thing work, because there was a bug where “methyl” only selected the methyl carbon. —Eric Eric Pettersen UCSF Computer Graphics Lab

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about "adjust angle" command
by Jiying Jia 30 Jun '16

30 Jun '16

Hi, I'm trying to use chimera to adjust angles in my polymer. First: Probably I found a bug: when I typed "adjust angle 90 #0:4@C #0:5@C #0:6@C" in the command line, it reported that "the degree should be a number". After I changed line 488 in /Chimera/share/Midas/midas_text.py to "degrees, spec = args.split(None,1)", the command works. Second: still about "adjust angle", if the polymer is a straight line, the command doesn't work, while it works for a random distributed polymer. For the line polymer, type "adjust angle 90 #0:4@C #0:5@C #0:6@C" and then "angle #0:4@C #0:5@C #0:6@C", it returns 180 degree. Below is the pdb example: line polymer: ATOM 1 C DA 1 0.000 0.000 0.000 1.00 0.00 C ATOM 2 C DA 2 1.000 0.000 0.000 1.00 0.00 C ATOM 3 C DA 3 2.000 0.000 0.000 1.00 0.00 C ATOM 4 C DA 4 3.000 0.000 0.000 1.00 0.00 C ATOM 5 C DA 5 4.000 0.000 0.000 1.00 0.00 C ATOM 6 C DA 6 5.000 0.000 0.000 1.00 0.00 C ATOM 7 C DA 7 6.000 0.000 0.000 1.00 0.00 C ATOM 8 C DA 8 7.000 0.000 0.000 1.00 0.00 C ATOM 9 C DA 9 8.000 0.000 0.000 1.00 0.00 C ATOM 10 C DA 10 9.000 0.000 0.000 1.00 0.00 C ATOM 11 C DA 11 10.000 0.000 0.000 1.00 0.00 C ATOM 12 C DA 12 11.000 0.000 0.000 1.00 0.00 C ATOM 13 C DA 13 12.000 0.000 0.000 1.00 0.00 C ATOM 14 C DA 14 13.000 0.000 0.000 1.00 0.00 C ATOM 15 C DA 15 14.000 0.000 0.000 1.00 0.00 C ATOM 16 C DA 16 15.000 0.000 0.000 1.00 0.00 C ATOM 17 C DA 17 16.000 0.000 0.000 1.00 0.00 C ATOM 18 C DA 18 17.000 0.000 0.000 1.00 0.00 C ATOM 19 C DA 19 18.000 0.000 0.000 1.00 0.00 C ATOM 20 C DA 20 19.000 0.000 0.000 1.00 0.00 C CONECT 1 2 CONECT 2 1 3 CONECT 3 2 4 CONECT 4 3 5 CONECT 5 4 6 CONECT 6 5 7 CONECT 7 6 8 CONECT 8 7 9 CONECT 9 8 10 CONECT 10 9 11 CONECT 11 10 12 CONECT 12 11 13 CONECT 13 12 14 CONECT 14 13 15 CONECT 15 14 16 CONECT 16 15 17 CONECT 17 16 18 CONECT 18 17 19 CONECT 19 18 20 CONECT 20 19 END random polymer: ATOM 1 C DA 1 -7.600 -3.500 -1.800 1.00 0.00 C ATOM 2 C DA 2 -6.600 -4.500 0.200 1.00 0.00 C ATOM 3 C DA 3 -3.600 -2.500 -0.800 1.00 0.00 C ATOM 4 C DA 4 -3.600 -2.500 -1.800 1.00 0.00 C ATOM 5 C DA 5 -3.600 -2.500 -2.800 1.00 0.00 C ATOM 6 C DA 6 -3.600 -2.500 -3.800 1.00 0.00 C ATOM 7 C DA 7 -3.600 -2.500 -4.800 1.00 0.00 C ATOM 8 C DA 8 -1.600 3.500 -2.800 1.00 0.00 C ATOM 9 C DA 9 0.400 3.500 -3.800 1.00 0.00 C ATOM 10 C DA 10 -0.600 0.500 -3.800 1.00 0.00 C ATOM 11 C DA 11 -1.600 1.500 -1.800 1.00 0.00 C ATOM 12 C DA 12 -0.600 0.500 0.200 1.00 0.00 C ATOM 13 C DA 13 -1.600 2.500 2.200 1.00 0.00 C ATOM 14 C DA 14 1.400 2.500 2.200 1.00 0.00 C ATOM 15 C DA 15 2.400 0.500 4.200 1.00 0.00 C ATOM 16 C DA 16 5.400 0.500 4.200 1.00 0.00 C ATOM 17 C DA 17 6.400 1.500 2.200 1.00 0.00 C ATOM 18 C DA 18 7.400 -1.500 2.200 1.00 0.00 C ATOM 19 C DA 19 7.400 -1.500 5.200 1.00 0.00 C ATOM 20 C DA 20 9.400 -0.500 6.200 1.00 0.00 C CONECT 1 2 CONECT 2 1 3 CONECT 3 2 4 CONECT 4 3 5 CONECT 5 4 6 CONECT 6 5 7 CONECT 7 6 8 CONECT 8 7 9 CONECT 9 8 10 CONECT 10 9 11 CONECT 11 10 12 CONECT 12 11 13 CONECT 13 12 14 CONECT 14 13 15 CONECT 15 14 16 CONECT 16 15 17 CONECT 17 16 18 CONECT 18 17 19 CONECT 19 18 20 CONECT 20 19 END ------------------ Best Wishes! Jiying Jia

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Problem opening .py files
by Luca Pellegrini 30 Jun '16

30 Jun '16

Hi, When I try to open a chimera session file, Chimera asks me to identify the file type, and then stops with the error message below. Can you please advice? I am using MacOSX 10.11.3. Best regards, Luca *** You are now running Chimera version 1.11 (build 41141). Your previous version was 1.10.1 (build 40415). Check the release notes for new features and other info. (To access the release notes, use the Help menu to bring up the User's Guide. Then click the 'Documentation index' link and you will then see a link for the release notes.) Registration file "/Users/lp212/.chimera/registration" has expired. Error while sourcing SsoCdc45.py, line 0: "import cPickle, base64" Unrecognized command: "import" Error while sourcing SsoCdc45.py, line 0: "import cPickle, base64" Unrecognized command: "import" Error while sourcing SsoCdc45.py, line 0: "import cPickle, base64" Unrecognized command: "import" Model 0 (Cdc45_depo.pdb) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 4 minimum strand length 3 Use command 'help ksdssp' for more information. Luca Pellegrini, PhD Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA UK Email: lp212(a)cam.ac.uk Phone: 0044-1223-760469

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Re: [Chimera-users] vector from atom
by fglaser＠techunix.technion.ac.il 29 Jun '16

29 Jun '16

Hi Elaine, Thanks a lot for your detailed answer, I think I did not explain myself good enough, I just want to find a water molecule far away from tunnel exit, which I can easily identify, and use that water to pull the ion from the tunnel towards it. I would prefer to avoid dummy atoms into the simulation if possible. So the only thing I want from chimera is to visualize a vector from the ion inside the tunnel (the ion is present in the Pdb) towards the exit (which I can easily identify) and in that way to identify a water molecule in the path of that vector to use as a kind of dummy atom (it will not move during simulation). That is it. So is there a way to draw or visualize a vector from an atom in chimera to a certain direction? In this way I will be able to find my water molecule far from the tunnel entrance. Thanks a lot, Fabian -- Sent from myMail app for Android Wednesday, 29 June 2016, 08:52PM +03:00 from Elaine Meng meng(a)cgl.ucsf.edu : >Hi Fabian, >Not sure I understand the exact problem, but I’m guessing the MD program takes as input some vector to apply force, and you are trying to figure out what to use as that vector. > >Chimera won’t figure out where the exit tunnel is, so first you would need to know yourself which direction that is. Then, maybe you could open a structure that is just two fake atoms several angstroms apart connected by one fake bond (I attach a PDB file of such a model). Then, you can move that long “stick” separately from the original structure to manually position it in the direction of the exit tunnel (with the “Active models” checkboxes below the Command Lne or the “A” checkboxes in the Model Panel, you can activate/deactivate models for movement with the mouse, so that they can be moved separately. Command Line or Model Panel can be shown using the Favorites menu). >< http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef > > >If the stick is too short or long, you can select it and change its length in the Adjust Bonds panel of Build Structure (in menu under Tools… Structure Editing). > >Then save the simple stick model to a PDB file (menu: File… Save PDB), making sure to save it “relative to” the other structure. In the resulting PDB file, the coordinates of the two fake atoms will define the vector, i.e. subtract x,y,z of one fake atom from the other to get vector x,y,z. Which you subtract from which depends on the direction of the vector. You can label the simple stick model in Chimera to see which atom is on which end. > >This might be a crazy idea or too much work, though. >Best, >Elaine >----- >Elaine C. Meng, Ph.D. >UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >Department of Pharmaceutical Chemistry >University of California, San Francisco > > > >On Jun 29, 2016, at 7:26 AM, Fabian gmail < fabian.glaser(a)gmail.com > wrote: > >> Hi, >> I have an ion in a membrane transporter which I am simulating in MD, now, I need in order to pull the ion outside the transporter to use a vector to identify a water molecule which is exactly in the direction of the exit tunnel. For that purpose I need to draw such a vector or to at least identify a water molecule in the right direction. Can Chimera help me with that? >> >> I mean is there a way to identify which water is on the exact pathway of the ion exit? >> How can I do it? >> Thanks a lot in advance, >> Fabian >

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Selection of residues and superposition
by Alessandra Gastaldello 29 Jun '16

29 Jun '16

Hi, I am trying to use Chimera to do superposition of multiple 3D structures. What I would really like to do is: 1. to select some residues for each of the structure and then 2. to superimpose the structures telling to chimera that the residues I selected have necessarily to be superimposed. To align "only" the protein sequences in a similar way for example I use COBALT that allows to specify the position of residues that have to be aligned necessarily together. Can I do this in chimera with 3D structures? thank so much for any help! -- Alessandra Gastaldello SIB | Swiss Institute of Bioinformatics CMU - 1, rue Michel Servet - 1211 Geneva 4 t: +41 22 379 50 50 - f: ... Alessandra.Gastaldello(a)sib.swiss - http://www.sib.swiss

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vector from atom
by Fabian gmail 29 Jun '16

29 Jun '16

Hi, I have an ion in a membrane transporter which I am simulating in MD, now, I need in order to pull the ion outside the transporter to use a vector to identify a water molecule which is exactly in the direction of the exit tunnel. For that purpose I need to draw such a vector or to at least identify a water molecule in the right direction. Can Chimera help me with that? I mean is there a way to identify which water is on the exact pathway of the ion exit? How can I do it? Thanks a lot in advance, Fabian Fabian Glaser Head of the Structural Bioinformatics section Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa 32000, ISRAEL fglaser at technion dot ac dot il Tel: +972 4 8293701 http://bku.technion.ac.il

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Transfer of the selection from reference to the ensemble
by James Starlight 29 Jun '16

29 Jun '16

Dear Pymol Users! Within the Pymol session I have 2 loaded superimposed objects: 1) one experimental pdb consisted of protein with co-factors (ligand and metals); 2) ensemble of 20 MD snapshots of the same protein (superimposed on each others) without any cofactors; For my particular task I need 1) to copy the selection (which include metals and ligand atoms) from the reference structure to each model of the MD ensemble (via Pymol), 2) make quick geometrical optimization of side-chains (I guess it better to do it using Chimera) within the active side of each model from MD ensemble 3) perform post-processing - analysis of the distances between cofactors and optimized side-chains of each MD conformers to obtain statistical distribution of averaged distances (I guess it better to do it via some MD software like Gromacs). I will be very thankful for any suggestions for practical realization of those steps! James

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Highlighting the H bonds during simulation
by Natesh Singh 28 Jun '16

28 Jun '16

Dear Sir, How could I highlight the formation and breakdown of Hbonds with the ligand to that of residues during the md simulation. I tried using the script (per-frame commands) chain @ca ~disp solvent hb line 2 color yellow reveal true Using this command, highlights all Hbonds in the system during the simulation, but I would like to see only Hbond interactions with ligand to that of nearby residues. How could I do this? what would be the appropriate per-frame script? Looking forward for the guidance. Best regards, Natesh Uni.Wien

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tmp files for MAC OS
by James Starlight 27 Jun '16

27 Jun '16

Dear Chimera Users! I am interesting where actually Chimera saves various tmp files produced by various analysis and post-processing tools on my MAC X OS? For instance I made calculations of residue contacts using network method from MD ensemble tool and would like to obtain txt files of residue pair contacts (on Linux it usually saved in tmp folder). Thanks for help! Gleb

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opening large xyz file
by Michał Kadlof 27 Jun '16

27 Jun '16

Hello, I'm trying to open a xyz file that contain ~66000 entries (1.7 MB). Chimera hangs and rapidly allocates huge amounts of RAM (more than 60 GB) which is close to limits of my PC, is it normal? Is there any "rescue mode opening" that wouldn't search for bonds to render and/or would show particles as dots or 2D disks instead of ball? My system is spatially small and probably Chimera is trying to search all-to-all particles to render bonds between them, but I do not need this. Is there any way to prevent this behaviour? -- best Michał

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(no subject)
by Nicole Mckinney 27 Jun '16

27 Jun '16

Hi I was wondering if you can tell me why my cell phone has chimera modules installed into the internal storage if I did not download and put them there

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Chimera question
by Smart Biology 24 Jun '16

24 Jun '16

Hello, I understand Chimera is for non-commercial use only. We would like to use this program simply to open a .map file and export as .obj for use in another 3D modelling program, for commercial use. Would this be allowed, or do we need to obtain a licence for commercial use? We have been looking throughout the web for the past few days and your program is the only way we have come across to convert .map to .obj. Thank you, Andrew -- Andrew Catalano, PhD Science and Animations Director Smart Biology www.smart-biology.com <https://www.smart-biology.com/> email: info(a)smart-biology.com <https://www.linkedin.com/company/smart-biology?trk=top_nav_home> Linkedin-Email-Signature

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Solvent Accessibility of Amino Acids
by Eric Berg 24 Jun '16

24 Jun '16

Hello, I've been spending some time trying to determine solvent accessibility for certain regions of protein complexes. I need something that is precise enough to determine the solvent accessibility of individual amino acids within a selected region (or the entire complex). There are a few tools online, but so far I haven't found something that does this. Does Chimera currently have a tool for measuring solvent accessibility of individual amino acids? Eric Berg

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default directory for opening files
by Dougherty, Matthew T 24 Jun '16

24 Jun '16

Starting chimera without a session file, I would like to use the open pulldown menu. The default directory is at root "/". If I use a 'cd somedirectory' command and open with the gui, it still defaults to the root. Is there a command that will set the open/save directory for the gui? If not, a way in python? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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Module import error
by Subha Kalyaanamoorthy 23 Jun '16

23 Jun '16

Hi There, I am trying to call a script with Chimera commands(saved as sample.py file) in another python program using os.system("chimera --nogui --nostats sample.py") and I get an module load error as below, import chimera ImportError: No module named chimera However, if I call the script with chimera it works, for eg., chimera --nogui --nostats sample.py typed directly in terminal is working. Can anybody help fix this error? Thanks in advance, Best Regards, Subha

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Displaying Labels without displaying Atoms
by Nicholas Hyman 23 Jun '16

23 Jun '16

Hello, I have been working with labeling EPR restraints on a protein model through chimera. I would like to show a label of the distance between two residues and color it to show how well the model fulfills the restraint. I worked with the distance function, but I could not figure out how to change the color of the label through the command line, as there are quite a few restraints. I was able to achieve the desired result by writing a python script that makes a pseudo bond file. My issue is that in order for the labels to be shown, atoms must also be displayed. This creates a lot of complexity and makes the labels difficult to read. I was wondering if there is any way to keep only the ribbon display but add the labels in still? Please let me know what you think. Thanks, Nicholas Hyman *________________* *Nicholas Hyman* Vanderbilt University, Computer Science and Chemistry, Class of 2018 (770) 314-9270 | nicholas.j.hyman(a)vanderbilt.edu

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assistance
by A G Szabo 23 Jun '16

23 Jun '16

Two things, can't seem to figure out how to: 1. Offset a residue label 2. In stick mode enlarge the stick or thicken it. Thanks A G Szabo

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Re: [Chimera-users] A question about subunit chain-letter ID.
by Elaine Meng 23 Jun '16

23 Jun '16

On Jun 22, 2016, at 1:14 PM, T-I <ignatiou(a)gmail.com> wrote: > Dear Elaine, > I'm a student from London and I have a quick question for you. > > I have a single pdb file consisting of 7 separate subunit chains (with TER between each chain). > > I would like to know how to assign an identifying chain letter to each of those subunit chains (i.e, from A to G).without having to manually copy and paste columns of chain letters into the pdb text file. > > This way when i scroll over each pdb chain in Chimera i will be able to see the chain letter too. > > Can this chain letter ID assignment be done directly in Chimera?..... and if so, how and which tool do i need to use.? > Thank you for your assistance. > Ti > Dear Ti, I think you can use the “Change Chain IDs” tool (in menu under Tools… Structure Editing). If I recall correctly, even though you don’t already have chain IDs, the parts separated by TER will be listed separately in the dialog and you can specify a new ID for each. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/changecha…> There is also a “changechains” to do basically the same thing, but it only handles chains that already have IDs that are different from each other. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/changechains.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco P.S. we generally recommend sending questions to the chimera-users list, CC’d here

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volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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Re: [Chimera-users] Chimera-users Digest, Vol 158, Issue 30
by Jaime Rodríguez-Guerra Pedregal 21 Jun '16

21 Jun '16

Hi, I am the developer of the PyChimera wrapper! Glad to know someone besides me is actually trying to use it! If you installed pychimera with pip or conda, you should have an executable called 'pychimera'. With it you can run the script directly with pychimera, like 'pychimera myscript.py'. Also, a bare PyChimera command ('pychimera') should bring up a Python interpreter where you can do "import chimera" just fine. Let me know if you are able to make it work! Jaime Rodríguez-Guerra Pedregal Molecular modeling of transition metal systems group Department of Chemistry, Faculty of Sciences Universitat Autònoma de Barcelona Edif. C · C7/153 Campus de la UAB · 08193 Bellaterra (Cerdanyola del Vallès) · Barcelona · Spain +34 93 581 28 57 www.uab.cat<http://www.uab.cat/> [http://www.uab.cat/vcard/Logo_ORCID_0.png] <http://orcid.org/0000-0001-8974-1566> [http://www.uab.cat/vcard/Logo_LinkedIn_0.png] <https://www.linkedin.com/in/jaimergp> This message may contain private or confidential information, and is addressed exclusively to its intended recipient. If you have received it in error, please notify the sender and delete it. Please bear in mind that you are not authorized to use it for any purposes. Please consider the environment before printing this email. ________________________________ De: chimera-users-bounces(a)cgl.ucsf.edu <chimera-users-bounces(a)cgl.ucsf.edu> en nombre de chimera-users-request(a)cgl.ucsf.edu <chimera-users-request(a)cgl.ucsf.edu> Enviado: martes, 21 de junio de 2016 21:00:02 Para: chimera-users(a)cgl.ucsf.edu Asunto: Chimera-users Digest, Vol 158, Issue 30 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. Re: Module import error (Subha Kalyaanamoorthy) 2. Re: Module import error (Greg Couch) ---------------------------------------------------------------------- Message: 1 Date: Mon, 20 Jun 2016 16:27:14 -0600 From: Subha Kalyaanamoorthy <kalyaana(a)ualberta.ca> To: Chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Module import error Message-ID: <CAFuN1V=PtjK=nBd6+-_4Tir1T+xc8JebJvx0frzbeoyqEUq1og(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Greg, Thanks for the kind reply. Sorry about the typo. The environment variables of the system seem fine to me. I also tried calling Chimera from the same directory as the script and its working fine. However, calling the chimera script using "python sample.py" doesn't work and using absolute path to chimera didn't help too. I tried installing pychimera, but end up with the same kind of error when I try pychimera -i import pychimera ImportError: No module named pychimera Couldn't understand what's going on with these import modules. I would greatly appreciate any suggestions to solve this. Thanks, Subha On Mon, Jun 20, 2016 at 4:05 PM, Greg Couch <gregc(a)cgl.ucsf.edu> wrote: > (I assume you meant --nostatus) > > For me the simple test of a file with: > > import os > os.system("chimera --nogui --nostatus") > > works just fine. So it's probably something about your particular setup > that is tickling this bug. > > It might be the directory that you're running the script in, it might have > python modules/packages that conflict with chimera's. Or it might > something in the environment. Chimera tries to protect its python from the > user's environment, but maybe we missed something. Also double check that > the chimera you're invoking is the one you're expecting -- try using an > absolute path to chimera while you're debugging this. > > HTH, > > Greg > > > On 06/20/2016 01:18 PM, Subha Kalyaanamoorthy wrote: > > Hi There, > > I am trying to call a script with Chimera commands(saved as sample.py > file) in another python program using os.system("chimera --nogui --nostats > sample.py") and I get an module load error as below, > > import chimera > > ImportError: No module named chimera > > > However, if I call the script with chimera it works, for eg., chimera > --nogui --nostats sample.py typed directly in terminal is working. > > > Can anybody help fix this error? > > > Thanks in advance, > > Best Regards, > > Subha > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > -- Dr. Subha Kalyaanamoorthy Post Doctoral Fellow Faculty of Pharmacy and Pharmaceutical Sciences University of Alberta Edmonton, Canada.

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Add Charges failure (libquadmath)
by Subha Kalyaanamoorthy 20 Jun '16

20 Jun '16

Hi There, I am trying to run charge calculation using Antechamber in chimera, but getting an error related to library not found. _______________________ Running ANTECHAMBER command: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/antechamber -ek qm_theory='AM1', -i /var/folders/pq/d4fvmdj542gcnqqjbfm554hr0000gt/T/tmpJCy8sw/ante.in.mol2 -fi mol2 -o /var/folders/pq/d4fvmdj542gcnqqjbfm554hr0000gt/T/tmpJCy8sw/ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 (UNK) (UNK) dyld: Library not loaded: /usr/local/lib/libquadmath.0.dylib (UNK) Referenced from: /Applications/Chimera.app/Contents/Resources/lib/libgfortran.3.dylib (UNK) Reason: image not found (UNK) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac (UNK) (UNK) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (UNK) Total number of electrons: 302; net charge: 1 (UNK) (UNK) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out (UNK) Error: cannot run "/Applications/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 UNK Check reply log for details ----------------------- FYI, I am running on OS X EI Capitan version 10.11.5 Thanks, Subha

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Chimera - Saving multiple files
by Elza Sofia Fonseca 20 Jun '16

20 Jun '16

Dear all, I am Elza Fonseca, a PhD student of the University of Porto and I am now learning to do dockings. I am using Chimera for open the results from SwissDock and I would like to save it like a multiple file. However I always get the same error message: "You must provide a file name that contains either $name or $number, which will be changed to the model name or model number (respectively) in the final saved file name". I don't understand what "$name or $number" means... May you please help me solving it? I apologize for my ignorance. Best regards, -- Elza Fonseca 00351 966 199 802 PhD student CIIMAR – AGE/EDEC http://www.ciimar.up.pt/researchgroup.php?id=AGE

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Chimera - Saving multiples files
by Elza Sofia Fonseca 19 Jun '16

19 Jun '16

Dear all, I am Elza Fonseca, a PhD student of the University of Porto and I am now learning to do dockings. I am using Chimera for open the results from SwissDock and I would like to save it like a multiple file. However I always get the same error message: "You must provide a file name that contains either $name or $number, which will be changed to the model name or model number (respectively) in the final saved file name". I don't understand what "$name or $number" means... I want to save the protein - target.pdb (#0) - and the model (#1.1), so I selected these ones and in the name I wrote docking1.1.pdb, but it didn't work. May you please help me solving it? I apologize for my ignorance. Best regards, -- *Elza Fonseca* 00351 966 199 802 PhD student *CIIMAR – AGE/EDEC* http://www.ciimar.up.pt/researchgroup.php?id=AGE

2 1

change default application for pdb files
by Cygler, Miroslaw 15 Jun '16

15 Jun '16

Hi, Since I have installed chimera on my mac laptop, it established itself as a default program to open pdf files. When I try to change the default to another software, it works only for one file at the time. Trying to make the change for all files with the .pdb extension by clicking “change all” button on the file info page strangely reverts back to chimera. This should not be happening according to Apple, as this is the standard way to change the default program to open specific file types. Any idea what is happening? Mirek

2 1

Analysis of NMR-like ensembles in CHIMERA
by James Starlight 15 Jun '16

15 Jun '16

Dear Chimera Users! I have loaded 2 NMR ensembles each of which is consisted of several models as 2 different object and now would like to do: 1 - becasue actually two esembles made from the conformers of the same protein (one from experiment (NMR) and another one from MD simulation) with totally equal sequence - I would like to copy from the first ensemble the chain information to the second one where such information is absent but the order of residues and atoms are the same. 2- Is it possible to set visualization mode as split view to see on the screen both ensembles in the adjacent positions with the posibility to easily browes separate models within each of them (like pymol style)? Thanks for help ! Gleb

2 7

Chimera is featured on LabWorm this week!
by Alon V 15 Jun '16

15 Jun '16

Dear people of Chimera, I'm Alon, a co-founder of LabWorm.com , a discovery platform that exposes top research tools with the goal of promoting a more open, collaborative and cutting edge science. Our community members have recently submitted Chimera to LabWorm. Since we thought our community could greatly benefit from getting to know a resource for powerful molecular visualization such as Chimera, we decided to feature it on our main feed under “New this week” here . Featured tools are voted on by the community and the top 5 voted tools appear in our weekly newsletter. I invite you to join our community. Once you register an account(s), I'll also be able to designate that account(s) as official creator/representative of Chimera , just reply to this e-mail with your account(s) name(s). Feel free to contact me with any thoughts or questions. Best wishes, Alon Vitenshtein Co-founder | LabWorm.com | @TheLabWorm

1 0

RR distance plot export
by Toshiki Nakashige 14 Jun '16

14 Jun '16

Hello, I am creating distance difference plots and was interested in exporting the plots. I want to generate two plots comparing different chains, and since the maximum and minimum difference values are different for each plot, I'm not able to have both plots on the same color scale. Is there a way to export the figure as a table of numbers such that I can create a color scale in a different program? I only see the icon to save the figure as an image and am not sure if there is an export as table option. Thank you, Toshiki

2 1

Paper viruses
by David Bhella 14 Jun '16

14 Jun '16

Hi, I have been trying to recreate the paper viruses shown on ViperDB and on your own site here: http://www.cgl.ucsf.edu/chimera/data/kids-day-apr2008/papervirus.html How did you keep the structure within the confines of the triangular facets? Is this possible within the flatten-icosahedron command, or was there some additional manual processing involved? Thanks, Dr David Bhella MRC-University of Glasgow Centre for Virus Research Sir Michael Stoker Building Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK) Telephone: 0141-330-3685 Skype: d.bhella Virus structure group on Facebook: https://www.facebook.com/CVRstructure Molecular Machines - Images from Virus Research: http://www.molecularmachines.org.uk CVR website: http://www.cvr.ac.uk CVR on Facebook: https://www.facebook.com/centreforvirusresearch

2 1

How to check flexibility of a protein
by shazia sabir 14 Jun '16

14 Jun '16

Can we check flexibility of a protein in chimera? Can we see if protein is affected after a mutation of only single amino acid? Are there some parameters that shows protein become more rigid or flexible after mutation? Regards, Shazia. Sent from my iPhone

2 1

Re: [Chimera-users] Save bond-distance label-position
by Eric Pettersen 13 Jun '16

13 Jun '16

Hi Maarten, I hope you wound up having something better to do on Sunday, because the code I committed wasn’t quite right. I’ve corrected the code and committed it to the release candidate as well now. —Eric Eric Pettersen UCSF Computer Graphics Lab > On Jun 10, 2016, at 10:17 AM, Maarten Schledorn <m.schledorn(a)gmail.com> wrote: > > Dear Eric, > It is not urgent. I knew in advance that they would not be saved so today I just positioned them and exported my images and video without closing the session. I'm happy to hear that they should be saveable soon! I'll give it a try on Sunday (: > Thanks again, > Maarten > > > On Friday, 10 June 2016, Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: > Hi Maarten, > This is a bug. Label offsets are being saved for bonds, but not pseudobonds (e.g. distances). I have committed changes to the code to save/restore the offsets, but as I'm working from home today it's awkward for me to test the changes. If you are feeling brave you can try tomorrow's daily build and see if the changes work. Otherwise I will test them myself Monday and ensure they work, and then add them to the release candidate as well. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > On Jun 10, 2016, at 4:28 AM, Maarten Schledorn wrote: > > > Dear reader, > > > > The distance measurement tool outputs a distance 'label' that by default is on the center of the line connecting the two atoms involved. In my structure I have about twenty of these, and I have manually dragged all distance values to empty spots in the image. However, if I save and re-open the session, the labels are back at their default position. I have tried <savepos>, and also <scene save>, but to no avail. Is there a way to save the bond-distance label-positions? > > > > Many thanks in advance, > > with kind regards, > > Maarten > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <javascript:;> > > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >

1 0

configuring stereoscopic view in RHEL-7.x
by abhisek Mondal 13 Jun '16

13 Jun '16

Hi, I'm using Chimera - 1.10 on a RHEL-7.x operating system (64-bit) with 128 GB of DDR3 RAM, 2.3 GHz Intel Xeon processor, Nvidia Quadro K5200, ASUS VG278 monitor (3D compatible). I have successfully configured Coot to run in stereoscopic view in the same machine but Chimera is giving me a hard time regarding the same. Any suggestions regarding this issue will be highly appreciated. Thank you. -- Abhisek Mondal *Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA*

2 1

Re: [Chimera-users] Splitting an pdb with multiple proteins
by Eric Pettersen 13 Jun '16

13 Jun '16

Hi Jochen, Support for chain descriptions coming from mmCIF files (rather than PDB files) was only added after the 1.10.2 release. Please try the current 1.11 release candidate and see how that works. --Eric Eric Pettersen UCSF Computer Graphics Lab On Jun 10, 2016, at 1:36 AM, Jochen Baßler wrote: > Dear Elaine, Eric, > > Thanks a lot for your fast replay. > I imported 3jct and 5hau to test your suggestions, but the reply log just contained : > > [MMLIB:WARNING] monomer description not found in zipfile for '4SU' > [MMLIB:WARNING] monomer description not found in zipfile for '5MC' > > How can I activate the status message? > With the mouse I can see the chain number near the mouse pointer, but there is no information below at the main window. > > (I am running chimera version 1.10.2) > > Best wishes > > Jochen > > > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Date: Friday, 10June, 2016 1:51 AM > To: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Cc: J B <jochen.bassler(a)bzh.uni-heidelberg.de> > Subject: Re: [Chimera-users] Splitting an pdb with multiple proteins > > It is also listed in the reply log as the structure is opened. > > —Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > >> On Jun 9, 2016, at 4:49 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >> Hi Jochen, >> This information is already imported, and when you mouse over the chain, it is shown in the “status message” area across the bottom of the Chimera window. >> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/chimerawindow.html> >> >> I tested just now, and the information is retained and can be shown in the same way after “split” is used. However, it is not automatically used as the model names. >> I hope this helps, >> Elaine >> ---------- >> Elaine C. Meng, Ph.D. >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> >>> On Jun 9, 2016, at 4:05 AM, Jochen Baßler <jochen.bassler(a)bzh.uni-heidelberg.de> wrote: >>> >>> Hi, >>> >>> I´m frequently looking at pdb´s that contain multiple chains, like ribosomes or preribosomes (e.g. Pdb 3JCT). >>> Is there a way to import the information from the pdb database, which tells you the name of the chains? >>> Chain A = rpl2 >>> Chain B = Rpl4 etc. >>> Cool would be to split the pdb into multiple models that have the name from the pdb database. >>> (It is quite annoying to have a pdb with nearly 60 different chains and you have to spend half a day to rename the chains or to create individual models, before analyzing the structure) >>> >>> Thanks for suggestions and solutions >>> >>> Best wishes >>> >>> Jochen >>> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >

2 4

pdb coordinates and their fonts in article
by Vasantha Kumar 10 Jun '16

10 Jun '16

Dear Chimera users I have a trivial question related to pdb coordinates in text format. For a small molecule I would like to report pdb coordinates (12 column) in an article. Regular .text (to pdf and illustrator ) file fonts are horrible, Is there is way to keep same space between columns and change the fonts size and style that respects pdb format. Therefore I want know is there any additional option in chimera to export coordinates? in a nice way so that if someone copy these coordinates from the article they should be open in chimera with out further editing. Have a good weekend!! thanks in advance.. Vince

2 2

Save bond-distance label-position
by Maarten Schledorn 10 Jun '16

10 Jun '16

Dear reader, The distance measurement tool outputs a distance 'label' that by default is on the center of the line connecting the two atoms involved. In my structure I have about twenty of these, and I have manually dragged all distance values to empty spots in the image. However, if I save and re-open the session, the labels are back at their default position. I have tried <savepos>, and also <scene save>, but to no avail. Is there a way to save the bond-distance label-positions? Many thanks in advance, with kind regards, Maarten

2 1

Splitting an pdb with multiple proteins
by Jochen Baßler 09 Jun '16

09 Jun '16

Hi, I´m frequently looking at pdb´s that contain multiple chains, like ribosomes or preribosomes (e.g. Pdb 3JCT). Is there a way to import the information from the pdb database, which tells you the name of the chains? Chain A = rpl2 Chain B = Rpl4 etc. Cool would be to split the pdb into multiple models that have the name from the pdb database. (It is quite annoying to have a pdb with nearly 60 different chains and you have to spend half a day to rename the chains or to create individual models, before analyzing the structure) Thanks for suggestions and solutions Best wishes Jochen

3 2

query regarding volume viewer
by Nidhi Batra 09 Jun '16

09 Jun '16

Dear Sir/Madam I have carried out MD simulations on a set of proteins belonging to a protein family. Further, I computed the water density around the protein and have the output in .dx format. I want to use Chimera to visualize the water density around the protein within 4 A. For this, I loaded the protein and the .dx file in volume viewer, selecting the protein and changing the zone to 4 and generating results. I want to have a comparison of water density across all proteins. I am unable to understand how to normalise the settings so that the results are comparable. What I understand is to keep the step same. Additionally, all the .dx files have different ranges which is obvious, what should be the value of level so that I can compare the water density across different proteins? Should it be kept at a median value of the range or something else? Please help. If I keep everything default, the results are misleading. Thanking you Yours sincerely -- Nidhi Batra DBT-Research Associate Institute of Genomics and Integrative Biology (IGIB), Mathura Road, Sukhdev Vihar New Delhi, INDIA 110020

2 4

renumbering missing residues
by Charles, Fiorella 08 Jun '16

08 Jun '16

Dear sir or madam, I am working with structure 1p22 and want to renumber the residues of chain A so they match Uniprot Q9Y297, but when I tried to it does not work for the 2 missing structures on the pdb file, and it continues the numbering as if they were not there. Is there a way to number this part correctly? with kind regards Fiorella

2 2

deleting entries from rapid access list (plain text format)
by Oliver Clarke 07 Jun '16

07 Jun '16

Sort of related to this - would be great to have a way to filter the rapid access list by filetype or pattern match - maybe have a box one could type in up the top of the list to filter what is displayed? Oli. > Very useful for clearing the Rapid Access list entirely. FYI, since that original message an “Edit” button has been added below the list so that you can selectively delete items. > > —Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > > >* On Jun 2, 2016, at 6:53 AM, Jaime Rodríguez-Guerra Pedregal <Jaime.RodriguezGuerra at uab.cat <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>> wrote: > *> >* Hi, > *> >* I was searching for a Chimera function that did this very same thing, but found nothing, so I created a little script to do that from the terminal. I know this is old, but maybe somebody finds it useful after all! > *> >* Get it here https://gist.github.com/jaimergp/8c2efd34fb2c7eba8054eeec791bf768 <https://gist.github.com/jaimergp/8c2efd34fb2c7eba8054eeec791bf768> <https://gist.github.com/jaimergp/8c2efd34fb2c7eba8054eeec791bf768 <https://gist.github.com/jaimergp/8c2efd34fb2c7eba8054eeec791bf768>> > *> >* Jaime Rodríguez-Guerra Pedregal > *>* Molecular modeling of transition metal systems group > *>* Department of Chemistry, Faculty of Sciences > *> >* Edif. C · C7/153 > *>* Campus de la UAB · 08193 Bellaterra > *>* (Cerdanyola del Vallès) · Barcelona · Spain > *> >* +34 93 581 28 57 > *>* www.uab.cat <http://www.uab.cat> <http://www.uab.cat/ <http://www.uab.cat/>> > *> >* <http://orcid.org/0000-0001-8974-1566 <http://orcid.org/0000-0001-8974-1566>> <https://www.linkedin.com/in/jaimergp <https://www.linkedin.com/in/jaimergp>> > *>* This message may contain private or confidential information, and is addressed exclusively to its intended recipient. If you have received it in error, please notify the sender and delete it. Please bear in mind that you are not authorized to use it for any purposes. > *> >* Please consider the environment before printing this email. > *>* _______________________________________________ > *>* Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> <mailto:Chimera-users at cgl.ucsf.edu <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>> > *>* Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>> > *

2 1

Trouble starting Chimera
by Janet Iwasa 07 Jun '16

07 Jun '16

Hello, I recently upgraded to a new workstation, and am running into trouble with installing Chimera. The error (with an exit code of 2) I'm getting is: Error initializing OpenGL: couldn't set pixel format Couldn't configure togl widget My workstation is 64 bit, running Windows 7, with a NVIDIA Quadro M4000 graphics card. I've tried installing the latest NVIDIA driver, which didn't seem to help. I've reinstalled Chimera several times, trying both 32 and 64 bit. My tech support also tried changing permissions on various files, to no avail. The weird thing is that my tech support folks got Chimera to open a few times successfully when they were logged in, which makes me wonder whether it might be a permissions issue, but they aren't able to get it to open consistently, either. Any ideas/advice would be welcome! thank you! Janet Iwasa

2 1

mtz file of an mrc map and its model open correctly in coot but not in chimera
by Oliver Clarke 07 Jun '16

07 Jun '16

Dear Shabih, I haven't used mrc2mtz.sh, but have had no problems with Coot/chimera compatibility using phenix.map_to_structure_factors for the same purpose, ( http://www.phenix-online.org/documentation/reference/map_to_structure_facto…) perhaps you might try that? Cheers, Oliver, > Dear All, > > > I converted an mrc map to mtz (using mrc2mtz.sh from CCP4EM) in order to do model building and model refinement in coot. However when I open the model in chimera along with its corresponding mrc map they do not open in same place. How can I rectify it? > > > Any help will be appreciate. > > > Regards, > > Shabih > >

1 0

mtz file of an mrc map and its model open correctly in coot but not in chimera
by Shakeel, Shabih 07 Jun '16

07 Jun '16

Dear All, I converted an mrc map to mtz (using mrc2mtz.sh from CCP4EM) in order to do model building and model refinement in coot. However when I open the model in chimera along with its corresponding mrc map they do not open in same place. How can I rectify it? Any help will be appreciate. Regards, Shabih

2 1

box size limit
by Franken, L.E. 07 Jun '16

07 Jun '16

Dear chimera users, I am running into troubles displaying a map of a 650x650x650 volume and I was wondering if there is a box size limit to chimera or what else could be the problem. The way it displays the 3D .mrc file is as a single slice rather than a volume. It will also go straight to solid display rather than surface, did anyone encounter such a problem before? I can open the map in coot and relion (slices), so I do not think that the map is corrupt. Thank you for your time. Best wishes, Linda On Mon, Jun 6, 2016 at 11:14 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. Re: coloring by RMSD (conformational variability) (Elaine Meng) > 2. Re: Chimera-win10-install (Greg Couch) > 3. Re: coloring by RMSD (conformational variability) (George Tzotzos) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 6 Jun 2016 12:55:52 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > To: George Tzotzos <gtzotzos(a)me.com> > Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] coloring by RMSD (conformational > variability) > Message-ID: <5242FA3C-E185-453E-93DD-BEF75F495BBC(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=utf-8 > > Hi George, > I?m not really sure how you got those flat ribbons, but I think you can > just use the transparency command. It takes a percentage transparency, so > for 75% transparent, a command something like: > > transp 75,r :1-10,124-125 > > ? where the ?,r? part does NOT have any space before it, and ?r? stands > for ribbons. > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > On Jun 6, 2016, at 11:36 AM, George Tzotzos <gtzotzos(a)me.com> wrote: > > > > Following PC analysis, I have obtained pseudo trajectories for each of > the first 3 principal components. I used Chimera to colour the regions > exhibiting the largest structural variations as per instructions of Elain > Meng, which I attach for easy reference. > > > > I have placed side by side, say the 1st PC, of two independent pseudo > trajectories (see attached image). As the structure is disordered between > residues 1-10 and 124-125, I?d like to render these ranges of residues > semitransparent. I?ve tried to do this with the transparency command but > this applies to ribbons only (I think). > > > > I?d appreciate any suggestions as to how this can be done. > > > > Thank you in advance > > > > George > > > > <dimer_deet2015_6MH2016.tif> > > From: Elaine Meng <meng(a)cgl.ucsf.edu> > > Subject: coloring by RMSD (conformational variability) > > Date: 25 March 2014 at 19:32:47 GMT+1 > > To: George Tzotzos <gtzotzos(a)me.com> > > Cc: chimera List <chimera-users(a)cgl.ucsf.edu> > > Reply-To: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > > > > Hi George, > > Sure, you can do it by having Chimera calculate the CA-RMSD at each > position and then mapping that value to color. The file is a little > strange in that it has only CA atoms and all the residues are ALA, but it > will still work: > > > > (1) show the sequence (menu: Favorites? Sequence). Just choose any one > of the 34 -- it doesn't matter which one, since they all have the same > sequence. > > > > (2) associate all 34 copies of the structure with the one sequence: in > the sequence window menu, choose Structure? Associations. In that dialog, > change all the "none" to the same sequence, then click OK. This is > somewhat tedious, but I just did it, so you can too! Now, all of the > structures will be connected to that one sequence. > > > > (3) tell Chimera to calculate the RMSD at each position: in the sequence > window menu, choose Headers? RMSD. Now the sequence window will have an > RMSD histogram above the sequence. It may almost look like a line because > most of the bars in the histogram (the RMSD values) are very low. > > > > (4) color the structures by the RMSD values with Render by Attribute (in > main Chimera menu under Tools? Depiction). In that tool, choose attributes > of "residues" and attribute name "mavRMSD" (the "mav" part stands for > Multalign Viewer, which is showing the sequence). It will show a histogram > of the values with some vertical colored bars. You use those bars to > define how the values are mapped to color. The bars can be dragged left > and right, and you can delete bars or add more bars with Ctrl-click. You > can change the color of each bar by clicking it and then clicking the > "Color" square below the histogram and using the Color Editor, or you can > just use one of the Palette options below that. You can keep clicking > Apply and then adjusting the coloring until it is how you like it. For > example, I show coloring by RMSD from blue->red->yellow (and then menu: > Presets? Publication 1) in the attached image. > > > > I hope this helps, > > Elaine > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > > Manage subscription: > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > ------------------------------ > > Message: 2 > Date: Mon, 6 Jun 2016 14:01:18 -0700 > From: Greg Couch <gregc(a)cgl.ucsf.edu> > To: Mitja Ogrizek <ogrizek.mitja(a)gmail.com>, > chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] Chimera-win10-install > Message-ID: <5755E49E.7070006(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="windows-1252"; Format="flowed" > > Hello Mitja, > > I was able to get the Windows installer to fail in one situation -- I > hope this is the same problem you're having. > > If you download the installer as a non-administrative user and then try > to run it, it fails because it can't install Chimera in the default > location even though you've typed in an administrative password. My > workaround was to use the file browser to locate the installer on the > disk, do a right-mouse click on the installer, and then "Run as > Administrator". I expect that it would also work if you installed > Chimera to a non-system directory. > > HTH, > > Greg > > On 06/04/2016 05:46 AM, Mitja Ogrizek wrote: > > Dear all, > > > > I tried to install a new version of chimera on my laptop with win10, > > but it doesn't want to load and start the setup. > > Has anybody else reported or had the same troubles? > > > > Kind regards, > > Mitja Ogrizek > > > > > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > > Manage subscription: > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

2 2

Re: [Chimera-users] deleting entries from rapid access list (plain text format)
by Jaime Rodríguez-Guerra Pedregal 06 Jun '16

06 Jun '16

Hi, I was searching for a Chimera function that did this very same thing, but found nothing, so I created a little script to do that from the terminal. I know this is old, but maybe somebody finds it useful after all! Get it here https://gist.github.com/jaimergp/8c2efd34fb2c7eba8054eeec791bf768 Jaime Rodríguez-Guerra Pedregal Molecular modeling of transition metal systems group Department of Chemistry, Faculty of Sciences Edif. C · C7/153 Campus de la UAB · 08193 Bellaterra (Cerdanyola del Vallès) · Barcelona · Spain +34 93 581 28 57 www.uab.cat<http://www.uab.cat/> [http://www.uab.cat/vcard/Logo_ORCID_0.png] <http://orcid.org/0000-0001-8974-1566> [http://www.uab.cat/vcard/Logo_LinkedIn_0.png] <https://www.linkedin.com/in/jaimergp> This message may contain private or confidential information, and is addressed exclusively to its intended recipient. If you have received it in error, please notify the sender and delete it. Please bear in mind that you are not authorized to use it for any purposes. Please consider the environment before printing this email.

2 1

coloring by RMSD (conformational variability)
by George Tzotzos 06 Jun '16

06 Jun '16

Following PC analysis, I have obtained pseudo trajectories for each of the first 3 principal components. I used Chimera to colour the regions exhibiting the largest structural variations as per instructions of Elain Meng, which I attach for easy reference. I have placed side by side, say the 1st PC, of two independent pseudo trajectories (see attached image). As the structure is disordered between residues 1-10 and 124-125, I’d like to render these ranges of residues semitransparent. I’ve tried to do this with the transparency command but this applies to ribbons only (I think). I’d appreciate any suggestions as to how this can be done. Thank you in advance George From: Elaine Meng <meng(a)cgl.ucsf.edu> Subject: coloring by RMSD (conformational variability) Date: 25 March 2014 at 19:32:47 GMT+1 To: George Tzotzos <gtzotzos(a)me.com> Cc: chimera List <chimera-users(a)cgl.ucsf.edu> Reply-To: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> Hi George, Sure, you can do it by having Chimera calculate the CA-RMSD at each position and then mapping that value to color. The file is a little strange in that it has only CA atoms and all the residues are ALA, but it will still work: (1) show the sequence (menu: Favorites… Sequence). Just choose any one of the 34 -- it doesn't matter which one, since they all have the same sequence. (2) associate all 34 copies of the structure with the one sequence: in the sequence window menu, choose Structure… Associations. In that dialog, change all the "none" to the same sequence, then click OK. This is somewhat tedious, but I just did it, so you can too! Now, all of the structures will be connected to that one sequence. (3) tell Chimera to calculate the RMSD at each position: in the sequence window menu, choose Headers… RMSD. Now the sequence window will have an RMSD histogram above the sequence. It may almost look like a line because most of the bars in the histogram (the RMSD values) are very low. (4) color the structures by the RMSD values with Render by Attribute (in main Chimera menu under Tools… Depiction). In that tool, choose attributes of "residues" and attribute name "mavRMSD" (the "mav" part stands for Multalign Viewer, which is showing the sequence). It will show a histogram of the values with some vertical colored bars. You use those bars to define how the values are mapped to color. The bars can be dragged left and right, and you can delete bars or add more bars with Ctrl-click. You can change the color of each bar by clicking it and then clicking the "Color" square below the histogram and using the Color Editor, or you can just use one of the Palette options below that. You can keep clicking Apply and then adjusting the coloring until it is how you like it. For example, I show coloring by RMSD from blue->red->yellow (and then menu: Presets… Publication 1) in the attached image. I hope this helps, Elaine

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Chimera-win10-install
by Mitja Ogrizek 06 Jun '16

06 Jun '16

Dear all, I tried to install a new version of chimera on my laptop with win10, but it doesn't want to load and start the setup. Has anybody else reported or had the same troubles? Kind regards, Mitja Ogrizek

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Cap color precedence when global clip planes slice through multiple volumes?
by Oliver Clarke 06 Jun '16

06 Jun '16

Hi, When slicing through multiple superimposed volumes with caps shown, the color of the resulting cap seems to be a bit of a patchwork - sometimes dominated by one volume, sometimes by another, sometimes a mix of the two It would be good if there were a way to control the precedence of the caps, to make a cleaner and more interpretable picture - it is often good to be able to see the outline of both overlayed volumes. I know there is one way to do this, by using per model clipping planes and changing the offsets such that one per model clip plane is just slightly in front of the other, but it might be helpful in ChimeraX to have more granular control over this. Cheers, Oli

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Cut asymmetric unit from volume
by Morris, Kyle 03 Jun '16

03 Jun '16

Hi Chimera team and users, Is there a way to extract the asymmetric unit from a volume which has been 'symmetrised’ from, say for instance, Relion? In this case what are the conventions used by chimera to define the bounds of the sub-volume to extract? Thanks for your help! Best wishes, Kyle

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Request for support
by Mendoza Wilson, Ana Maria 03 Jun '16

03 Jun '16

Hello, How I can select an isodensity value in the Chimera software (1.11rc) for calculating molecular surface and molecular volume from one cube data file or fchk file previously generated in Gaussian 09? Thanks in advance -- Dra. Ana María Mendoza Wilson Investigador Titular Centro de Investigación en Alimentación y Desarrollo, A.C. Coordinación de Tecnología de Alimentos de Origen Vegetal Carretera a La Victoria Km. 0.6 Hermosillo, Sonora, México C.P. 83000 Tel +52 (662) 289 24 00 Ext. 354

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FW: Chimera Log File
by Williams, Joanne 03 Jun '16

03 Jun '16

From: Erin Coppola <erincoppola8(a)gmail.com<mailto:erincoppola8@gmail.com>> Date: Friday, June 3, 2016 8:10 AM To: "chimera(a)cgl.ucsf.edu<mailto:chimera@cgl.ucsf.edu>" <chimera(a)cgl.ucsf.edu<mailto:chimera@cgl.ucsf.edu>> Subject: Chimera Log File Hi, When using Chimera, is there a way of tracking the script command versions of GUI actions performed?

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