- 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

2 1

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

2 2

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

2 3

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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Creating maps from models for map/model FSC calculations
by Ardan Patwardhan 03 Jun '16

03 Jun '16

Dear all We are using Chimera to align PDB models to maps, then creating maps from the models using the following command (as an example): molmap #0 5 gridSpacing 1.3 This should create a map with the voxel spacing of 1.3A and a gaussian atom spread function with the width related to 5A resolution (https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html) Our problem is a) the map that is created can have an arbitrary size - we need it to be cubic and have the same (known) dimensions as the second map against which it will be compared b) we have tried padding it in other programs like bsoft but then we sometimes run into problems of centring the model. I was wondering if there was a way to get a centred map of a certain size from a model directly from Chimera? Perhaps there are certain parameters that can be used in molmap? You thoughts and advice on this issue are much appreciated! Many thanks and best wishes Ardan Patwardhan Coordinator - cellular structure & PDBe production Protein Data Bank in Europe (PDBe) European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD Tel: +44 1223 492649

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mask
by Dougherty, Matthew T 02 Jun '16

02 Jun '16

I have a volume whose density values are -127 thru 127. Zero is a valid density & approximately the peak of the Guassian distribution. I would like to use the command mask. It sets the unmasked density values to zero. How can I set the unmasked density values to -128 using the mask command? Will I need to hack the code? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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finding residues with large effects on local electrostatic potential
by Elaine Meng 01 Jun '16

01 Jun '16

Hi Deniz, No need to apologize, that’s why we have an address for questions. :-) I am guessing you were coloring by electrostatic potential and want to figure out which residues are having large effects in some places. The question is not that simple because electrostatic interactions are long-range, meaning that the potential at a point is based on many atoms in many residues, including those farther away. However, the largest contributions at a surface point will generally be from the residues with net positive or negative charges that are not too far away. In other words, if you see a blue patch, you could then try to figure out positively charged residues are near it, or if a red patch, which negatively charged residues are near it. The problem in Chimera that you may be having is that when you put the mouse over the surface, the surface is blocking the atoms, so it does not tell you what residue is under that surface. One way to try to figure it out is to temporarily hide the surface (Favorites… Model Panel, uncheck the “Shown” button for the surface), then click back into the main window *without moving the structure* and put the mouse over the same area to see what residues are there, using the pop-up balloons with residue information. You would probably want to show all the sidechain atoms first (e.g. command: display protein), and maybe select residues that are known to be positive (or negative) to help guide yourself to the right place. Command: select :lys,arg,his (… the ones likely to contribute to positive patches…) Command: select :asp,glu (… the ones likely to contribute to negative patches…) You can keep turning the surface on and off with the checkbox in the Model panel. This is interactive guessing and may not be that easy. Just keep in mind that you can’t say that some patch is all from one or two residues, only that they have significant contributions. 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 1, 2016, at 3:44 PM, Deniz Simsek Buck <simsekd(a)stanford.edu> wrote: > Hi Elaine, > I am sorry for bothering you. But, I need urgent help. > If I tell chimera to find the surface charge, negative and positive, and if I want to know which residues are responsible for this charge, what do I do? > > thank you so much, > deniz

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How to build symmetry in Chimera
by Ana Ramos 01 Jun '16

01 Jun '16

To whom it may concern, I am working with a protein with P61 symmetry, and I would like to build symmetry mates; however in the pdb, the symmetry is not stated. How can I build in chimera symmetry mates with a P61 symmetry? Best, Ana

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Chimera 1.11 - Combining Transparancies of Ribbon and Surface
by Falko Jähnert 01 Jun '16

01 Jun '16

To whom it may concern, since I'm using Chimera a lot lately I enjoy the usage of this program and can't await the release of Chimera X. Now I like to ask if it is possible to combine the transparency of the ribbon and the surface representation using Chimera so that you can visualize both parts in varying transparency levels. My problem with this is if I use "transparency 80,r [Tag]" the part of my protein gets transparent (as requested) whilst activating the transparency function of the surface results in complete hiding of the previously chosen amino acids. Is there a workaround available? Thanks in advance for your help. Best regards, Falko Jähnert. _____ Martin-Luther-University Halle-Wittenberg Institute for Biochemistry and Biotechnology Departement for Naturstoffbiochemie Kurt-Mothes-Str. 3 D-06110 Halle/Saale _____ Tel. +49 (0)345 - 55 24812 Mail. <mailto:falko.jaehnert@biochemtech.uni-halle.de> falko.jaehnert(a)biochemtech.uni-halle.de

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Re: [Chimera-users] Analysis of the contact maps from the MARTINI MD trajectory
by James Starlight 01 Jun '16

01 Jun '16

Yep thanks so much Eric! In my case the contacts have been started to be recognized both from only after choosing the vdw cutoff > -4.0 A and decreasing statistical (weight discard edge threshold) factor to 0.3 (here I am analyzing big trajectory consisted of 7 independent MD trajectories for the same system merged together where both proteins are present both in bound and unbound states during the progression of simulation). Eventually I obtained LYS 25.A vdw SER 712.C 0.39322 CYS 14.A vdw TRP 1586.I 0.427119 HIS 33.A vdw ions 0.335593 HIS 33.A vdw LYS 1577.I 0.444068 LYS 27.A vdw TRP 1586.I 0.369492 GLU 838.C vdw PHE 46.A 0.444068 GLN 12.A vdw TRP 1586.I 0.501695 ASP 1580.I vdw LYS 7.A 0.318644 PHE 46.A vdw TRP 1586.I 0.491525 GLU 732.C vdw LYS 79.A 0.372881 PHE 46.A vdw solvent 0.501695 CYS 1584.I vdw HIS 26.A 0.616949 HIS 26.A vdw SER 712.C 0.423729 ASP 1580.I vdw LYS 8.A 0.305085 TYR 1542.I vdw VAL 11.A 0.311864 LYS 27.A vdw solvent 0.40678 THR 28.A vdw TYR 731.C 0.379661 PHE 46.A vdw TYR 1587.I 0.484746 Also may I ask within this output the first column should correspond to first selection, right? here the contacts was defined as between atoms from chain A which is the smaller protein and the rest of the system consisted of atoms of receptor. Thanks again! Gleb 2016-05-17 22:37 GMT+02:00 Eric Pettersen <pett(a)cgl.ucsf.edu>: > Well, if I were you I would go to a trajectory frame that I think should have contacts, and then bring up the Find Clashes/Contacts tool (in the Structure Analysis category of Tools) and play around with the criteria to see what yields contacts. You might also change the atoms to sphere mode (Actions->Atoms/Bonds->sphere) to see if they have any VDW overlap or are close. You might also measure some distances (control-click an atom, then control-shift-double-click a second atom and then pick “Show Distance” from the popup menu). Without actual access to your data, I can’t offer any more specific suggestions. > > —Eric > >> On May 17, 2016, at 2:08 AM, James Starlight <jmsstarlight(a)gmail.com> wrote: >> >> Thanks Eric! >> >> it quite strange that no interactions are found- because in my >> trajectory the complex between both proteins are emerged very soon >> after beginning of the simulation and is quite stable until ed of it. >> Seems like the Chimera does not recognize martini's CG atoms properly. >> Are there any suggestions to fix it e.g by the variations using any of >> options - e.g vdw settings etc? >> >> Gleb >> >> 2016-05-17 1:32 GMT+02:00 Eric Pettersen <pett(a)cgl.ucsf.edu>: >>> The clustering is based on least-squares-fit RMSDs between corresponding atoms, and therefore global translations and rotations are irrelevant. >>> >>> —Eric >>> >>>> On May 16, 2016, at 9:08 AM, James Starlight <jmsstarlight(a)gmail.com> wrote: >>>> >>>> update :-) >>>> >>>> in addition to the previous question which is still actual I am >>>> interesting in the clusterization of binding interfaces established >>>> during MD e.g based on the position of one protein regarding another. >>>> >>>> For my case I have performed such clusterization from MD movie plugin >>>> (which was based on current selection which was the atoms of smaller >>>> protein) obtaining alot of overlapped clusters in case of smallest >>>> step size and afew clusters increasing step size twisly. Is it >>>> possible here to increase accuracy of the clusterization and to remove >>>> some degrees of freedom which are not important for my case ? E.g to >>>> pre-process trajectory using PCA before clusterization to discard >>>> rotation translation of the system will be good option? >>>> >>>> >>>> >>>> James >>>> >>>> 2016-05-16 15:20 GMT+02:00 James Starlight <jmsstarlight(a)gmail.com>: >>>>> update : >>>>> >>>>> already playing with the plugin MD movie and "residue iteration >>>>> network within the trajectory" tool >>>>> just selecting atoms from the chain A as 1st selection >>>>> and other atoms from other chains as 2nd selection >>>>> >>>>> running calculation (trying to varry cut-off corresponded to vdw overlap radii) >>>>> >>>>> obtained error >>>>> AttributeError: 'ResInteractionDialog' object has no attribute 'markers' >>>>> >>>>> File "/opt/UCSF/Chimera64-1.10.2/share/Movie/ResInteraction.py", >>>>> line 535, in Apply >>>>> markerSettings = [(m['xy'], m['rgba']) for m in self.markers] >>>>> >>>>> See reply log for Python traceback. >>>>> >>>>> Does it means that somethig special should be specified for the >>>>> MARTINI CG atoms? >>>>> >>>>> Thanks ! >>>>> >>>>> Gleb >>>>> >>>>> 2016-05-16 12:13 GMT+02:00 James Starlight <jmsstarlight(a)gmail.com>: >>>>>> something relevant in my model: >>>>>> >>>>>> this is martini CG model consisted of big membrane protein and small >>>>>> water soluble protein. In my particular trajectory I have only atoms >>>>>> of both proteins recognized by chimera as individual chains (e.g small >>>>>> protein is chain A and the biggest is consisted of chains B-N). >>>>>> >>>>>> Gleb >>>>>> >>>>>> 2016-05-16 11:58 GMT+02:00 James Starlight <jmsstarlight(a)gmail.com>: >>>>>>> update: >>>>>>> >>>>>>> with the up-to-date chimera Trajectory is loaded fine >>>>>>> now the question is related to the analysis of the binding interface. >>>>>>> is it possible to make contact maps plots based on the 2 selections >>>>>>> from the input trajectory assuming that I am using martini CG model? >>>>>>> >>>>>>> Gleb >>>>>>> >>>>>>> 2016-05-16 10:39 GMT+02:00 James Starlight <jmsstarlight(a)gmail.com>: >>>>>>>> OK will try to update Chimera today ! >>>>>>>> >>>>>>>> What chimera's tools could be useful for the contact map based >>>>>>>> analysis of md trajectories related to my case ? E.g to determine >>>>>>>> binding interface between 2 proteins from long md simulation. >>>>>>>> >>>>>>>> Gleb >>>>>>>> >>>>>>>> 2016-05-13 19:52 GMT+02:00 Eric Pettersen <pett(a)cgl.ucsf.edu>: >>>>>>>>> Hi Gleb, >>>>>>>>> If you are using Gromacs 5 trajectories, you have to be using at least >>>>>>>>> version 1.10.2 of Chimera. If you are using that version (or later), please >>>>>>>>> use “Report a Bug” in Chimera’s Help menu to file a bug report and attach >>>>>>>>> your topology file to the bug report. Thanks! >>>>>>>>> >>>>>>>>> —Eric >>>>>>>>> >>>>>>>>> Eric Pettersen >>>>>>>>> UCSF Computer Graphics Lab >>>>>>>>> >>>>>>>>> >>>>>>>>> On May 13, 2016, at 1:46 AM, James Starlight <jmsstarlight(a)gmail.com> wrote: >>>>>>>>> >>>>>>>>> Dear Chimera users! >>>>>>>>> >>>>>>>>> >>>>>>>>> I am in charge with the analysis of protein-protein association during >>>>>>>>> long molecular dynamic simulation where my system was parametrized >>>>>>>>> using MARTINI CG force field. In particularly I am interesting to >>>>>>>>> find residues on one of the protein which are crustal for the binding >>>>>>>>> interface established during this MD. >>>>>>>>> For that purpose I am trying to use Chimera to load trajectory and >>>>>>>>> corresponded tpr file using MD movie plugin and than to >>>>>>>>> map contact maps produced by Gromacs onto the 3D structure using Chimera. >>>>>>>>> The problem that Chimera does not recognize properly the trajectory >>>>>>>>> and topology. Briefly I have removed all solvent from both files >>>>>>>>> before loading them to the Chimera using editconf and gmx convert-tpr >>>>>>>>> obtaining eventually trajectory and topology with the same number of >>>>>>>>> atoms. >>>>>>>>> >>>>>>>>> >>>>>>>>> Than when I load it to Chimera that is the error which MD movie sent me: >>>>>>>>> >>>>>>>>> VERSION 5.0.2 >>>>>>>>> using floats >>>>>>>>> version 100, generation 26 >>>>>>>>> 8 atoms >>>>>>>>> Traceback (most recent call last): >>>>>>>>> File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", >>>>>>>>> line 1747, in __call__ >>>>>>>>> File "CHIMERA/share/chimera/baseDialog.py", line 328, in command >>>>>>>>> File "CHIMERA/share/chimera/baseDialog.py", line 543, in OK >>>>>>>>> File "CHIMERA/share/Trajectory/EnsembleLoader.py", line 92, in Apply >>>>>>>>> File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line >>>>>>>>> 56, in loadEnsemble >>>>>>>>> File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line >>>>>>>>> 67, in loadEnsemble >>>>>>>>> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 25, >>>>>>>>> in __init__ >>>>>>>>> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 86, >>>>>>>>> in __init__ >>>>>>>>> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line >>>>>>>>> 345, in _readTopology >>>>>>>>> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line >>>>>>>>> 338, in _readString >>>>>>>>> File "CHIMERA/lib/python2.5/xdrlib.py", line 197, in unpack_fstring >>>>>>>>> raise EOFError >>>>>>>>> EOFError >>>>>>>>> EOFError >>>>>>>>> >>>>>>>>> File "CHIMERA/lib/python2.5/xdrlib.py", line 197, in unpack_fstring >>>>>>>>> raise EOFError >>>>>>>>> >>>>>>>>> See reply log for Python traceback. >>>>>>>>> >>>>>>>>> Will be thankful for any suggestions! >>>>>>>>> >>>>>>>>> Gleb >>>>>>>>> _______________________________________________ >>>>>>>>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >>>>>>>>> Manage subscription: >>>>>>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>>>>>>> >>>>>>>>> >>>> >>>> _______________________________________________ >>>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >>>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>> >>> >> >

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suggest improvements/group viz
by Dougherty, Matthew T 31 May '16

31 May '16

1) in a group viz it would be desirable to have two cursors. A regular cursor that would operate as expected under the OS, and a second cursor that would be restricted to the view window overlay. The first cursor would be controlled by the viz operator used to adjust parameters. The second cursor would be controlled by the group through a gamepad etc, that could be used as a pointer. Possibly the volume eraser might be a quick work around. 2) volume eraser when erasing sets the density to zero. Need to be able to set the value. Zero is a valid density value, usually in the middle of the density histogram, which causes problems for volume rendering. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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Rotamers in Chimera
by Lew Jacobson 31 May '16

31 May '16

I am using Chmiera 1.10 build 40304 on a Mac. (I am a leftover Midas user!) So far as I can tell, this version is still using the Dunbrack 2002 rotamer library. Is any subsequent version using the improved 2011 Dunbrack library? If not, can you instruct me how to incorporate that newer library into Chimera? thanks, Lew Jacobson -- Dr. Lewis Jacobson Professor of Biological Sciences Univ. of Pittsburgh Pittsburgh PA 15260 412-624-4647 Fax 412-624-4759 LJAC(a)pitt.edu

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Can I use wait command over Rest service?
by Mungo Carstairs (Staff) 31 May '16

31 May '16

Hi, I am trying to devise a way to highlight locations on a structure in Chimera while mousing over the sequence in Jalview. My latest attempt tries to 'flash' the side-chain display at the residue position i.e. - hide then show atoms (if currently displayed e.g. display is in atom mode) - or show then hide atoms (if currently not displayed e.g. display is in ribbon mode) I'm sending a command like display #0:30.A;wait 20;~display #0:30.A to the Rest service. However while this seems to do what I want when used at the Chimera command line, via the Rest service it ignores the wait command, with the result that the action is too quick to see. Any suggestions please for how to get this to work, or a better alternative? Thanks, Mungo Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK. www.jalview.org<http://www.jalview.org/> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/> The University of Dundee is a registered Scottish Charity, No: SC015096

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broken lines
by shazia sabir 29 May '16

29 May '16

Hi dear All, Why chimera is showing broken lines (region encircled in red at one area). What can we predict from structure. I attached sequence of structure that shows amino acid is there(gey region in sequence). Regards, shazia.

2 1

Modeller awareness of other proteins
by Eiros Zamora, Juan 26 May '16

26 May '16

Dear Chimera experts, I’ve got a system of three interacting proteins, and each of them is missing some linker regions in the crystal structure. I’ve succesfully used the Modeller interface in Chimera to add these regions, but the problem I’m facing now is that it adds the residues without considering that other atoms from another protein of the system are in the way. Is there a way to tell Modeller to be sensitive to other structures nearby? Thanks for any comments, [Imperial College London] <http://www.icb-cdt.co.uk/> Juan Eiros Zamora / PhD Student je714(a)ic.ac.uk<mailto:je714@ic.ac.uk> / +44 (0) 7783018326 Imperial College London Imperial College Road SW7 2AZ | UK http://www.icb-cdt.co.uk/

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Evolutional-based analysis in Chimera
by James Starlight 25 May '16

25 May '16

Dear Chimera Users! For my particular analysis I have 2 homologue membrane proteins (one is bacterial, and another one- mammalian cytocrome-C oxydase) each bound to same smaller (ligand) protein called for simplicity "the_guy". For that particular case the conservation in sequence of both protein is quite low however 1) the overall fold of both proteins especially within the membrane-embedded region as well as 2) ligand-bound (which is mostly the water exposed loops) region are quite similar. Now using some Chimera tool I need to estimate binding interfaces of two homologous proteins in terms of the conservation of the resides involved in binding of the_guy. Then I need to make more complex task- performing the same evolutional analysis but comparing 2 ensembles extracted from the MD trajectory represent simulation of binding of each of the protein with the_guy to track correlations of the statistics between the residues involved in the binding during MD as well as overall conservation for particular fold. Does the "Evolutionary tracing" might be useful here? Thanks for help! Gleb

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PDB post-processing
by James Starlight 25 May '16

25 May '16

Dear Chimera users! After some post-processing of MD simulation I have extracted from the trajectory several snapshots as individual pdbs which I need to 1- to re-assign information regarding chain letters (which was lost after some operations on pdbs) for all of those structures assuming that within each of these pdbs residues are ordered correctly e.g from (1-104 which should be chain A) than from 1-100 (it should be chain B), than 1-70 (in should be chain C) etc. 2- superimpose and combine all of the pdbs within one model in nmr-like format. Thanks for help!

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Long-ranged electrostatics analysis
by James Starlight 25 May '16

25 May '16

Dear Chimera users! I am analysing several snapshots etracted from the full atomistic md simulation of protein-protein assosiation. I wounder to ask what are the Chiemra plugins might be useful to study long-rang electrostatic effect mediated initial recognition of both proteins in this system besides APBS caclucation which is more focused on short-ranged electrostatics. Thanks for help! Gleb

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Script to open density from Coot in Chimera.
by Oliver Clarke 23 May '16

23 May '16

Hi all, Posting this in case it is useful to anyone else who uses both programs. This script will allow Coot to open the currently displayed molecules/maps in Chimera, and adjust display settings appropriately for taking a picture of electron density. Either put the appended code in your coot.py and use from the scripting interface, or place this longer script ( https://www.dropbox.com/s/0b4bebwxw0p9x0e/oli_custom.py?dl=0) in your ~/.coot-preferences directory, which will add a new "Custom" menu including this option under the "Display" submenu (as well as a bunch of other stuff, and some extra custom key bindings). The orientation of the molecules should be correct after loading in Chimera, but the zoom and clipping may require some adjustment (I am not sure exactly how to match these precisely between the two programs). The script will only load a fragment of the maps (the same region that is displayed in Coot), but this has the advantage that it takes advantage of Coot's ability to deal with crystal symmetry, so it can be used at crystal contacts with no problems. Let me know if you run into any bugs! Cheers, Oli. Code: #Open displayed models and maps in Chimera, set map levels and view def open_in_chimera(): if find_exe("chimera"): #If chimera exists do stuff, else raise an error import subprocess pwd=os.getcwd() #Dir from which coot was launched cofr=rotation_centre() #3-membered list [x,y,z] make_directory_maybe("coot-chimera") #Put coot droppings here coot_chimera_path=pwd+"/coot-chimera/" check_path=coot_chimera_path+"chimera_launcher.cmd" #Chimera run script that will be written later check_path2=coot_chimera_path+"matrix.txt" #Orientation matrix for chimera input view_number=add_view_here("tmp") # initial_zoom=zoom_factor() #Coot's zoom factor. 100 is the initial state, zooming out gets larger, in gets smaller. # reset_view() zoom=zoom_factor() # go_to_view_number(view_number,1) # scale_factor=initial_zoom/base_zoom # chimera_scale=base_zoom/initial_zoom chimera_scale=100.0/zoom #Approx - breaks down when initial views upon loading mol in Coot or Chimera are different map_radius=get_map_radius() #We'll use this to export a map_radius sized fragment if os.path.isfile(check_path): #if chimera script exists, delete it. os.remove(check_path) if os.path.isfile(check_path2): #same for matrix.txt os.remove(check_path2) map_list=map_molecule_list() mol_list=model_molecule_list() matrix_list=view_matrix() #9-membered list of rotation matrix elements. with open(check_path2,"a") as matrix_file: #Write orientation matrix (specify first pdb as model, then use matrixcopy to apply to all others). Translation vector in last column is 0,0,0 because we will take care of that separately. matrix_file.write("Model {model_id}.0\n".format(model_id=mol_list[0])) matrix_file.write("\t {a} {b} {c} 0.0\n".format(a=matrix_list[0],b=matrix_list[1],c=matrix_list[2])) matrix_file.write("\t {a} {b} {c} 0.0\n".format(a=matrix_list[3],b=matrix_list[4],c=matrix_list[5])) matrix_file.write("\t {a} {b} {c} 0.0\n".format(a=matrix_list[6],b=matrix_list[7],c=matrix_list[8])) with open(check_path,"a") as cmd_file: #Start writing stuff to chimera launch script. for mol_id in model_molecule_list(): if mol_is_displayed(mol_id): file_name=coot_chimera_path+"mol_{mol_id}.pdb".format(mol_id=mol_id) write_pdb_file(mol_id,file_name) path_to_file=file_name model_id=mol_id cmd_file.write("open #{model_id} {mol}\n".format(model_id=model_id,mol=path_to_file)) cmd_file.write("color gold #{model_id}; color byhet #{model_id}; ca_and_sidechains #{model_id}; disp ~protein\n".format(model_id=model_id)) cmd_file.write("matrixset matrix.txt\n") cmd_file.write("matrixcopy #{mol_id0} #{mol_id}\n".format(mol_id0=mol_list[0],mol_id=model_id)) map_id0=mol_id for map_id in map_molecule_list(): if map_is_displayed(map_id): map_level=get_contour_level_absolute(map_id) if map_is_difference_map(map_id): model_id=map_id0+map_id #make sure that the assigned model number of each map is unique and does not overlap with those of pdbs. if map_id==0: model_id=model_id+1 file_name=coot_chimera_path+"diff_map_{model_id}.mrc".format(model_id=model_id) path_to_file=file_name export_map_fragment(map_id,cofr[0],cofr[1],cofr[2],map_radius,file_name) cmd_file.write("open #{model_id} {diff_map} \n".format(model_id=model_id,diff_map=path_to_file)) cmd_file.write("volume #{model_id} capfaces false style mesh meshlighting false squaremesh false color \"#08882eefa222\" step 1 ; sop cap off ; set depthCue ; set dcStart 0.2 ; set dcEnd 1 ; background solid white ; set showcofr ; cofr view ; clip on; volume #{model_id} level -{map_level} color #da1200000000 level {map_level} color #0000bda00000 \n".format(model_id=model_id,map_level=map_level)) cmd_file.write("matrixset matrix.txt\n") cmd_file.write("matrixcopy #{mol_id0} #{model_id}\n".format(mol_id0=mol_list[0],model_id=model_id)) else: model_id=map_id0+map_id if map_id==0: model_id=model_id+1 file_name=coot_chimera_path+"map_{model_id}.mrc".format(model_id=model_id) export_map_fragment(map_id,cofr[0],cofr[1],cofr[2],map_radius,file_name) path_to_file=file_name cmd_file.write("open #{model_id} {map} \n".format(model_id=model_id,map=path_to_file)) cmd_file.write("volume #{model_id} capfaces false style mesh meshlighting false squaremesh false color \"#08882eefa222\" step 1 ; sop cap off ; set depthCue ; set dcStart 0.2 ; set dcEnd 1 ; background solid white ; set showcofr ; cofr view ; clip on; volume #{model_id} level {map_level} \n".format(model_id=model_id,map_level=map_level)) cmd_file.write("matrixset matrix.txt\n") cmd_file.write("matrixcopy #{mol_id0} #{model_id}\n".format(mol_id0=mol_list[0],model_id=model_id)) cmd_file.write("~sel; cofr {x},{y},{z} coordinatesystem #{mol_id0}; ac mc; center sel; cofr sel; clip hither 5 fromCenter true; clip yon -5 fromCenter true; cofr view; ~set showcofr; del sel; scale {chimera_scale}".format(x=cofr[0],y=cofr[1],z=cofr[2],mol_id0=mol_list[0],chimera_scale=chimera_scale)) chimera_exe=find_exe("chimera") info_dialog("Opening in Chimera...\nOrientation should be right but you will probably need to \nadjust the scale and clipping to get the same view as in Coot. \n If you can't see anything, try zooming out.") subprocess.Popen(["chimera",check_path]) else: info_dialog("Sorry, you need UCSF Chimera installed and accessible from the terminal for this to work!") #This works okay, though adjustment of zoom and clipping still not ideal. #would it be possible to add a subprocess.communicate() to use Coot as a controller for Chimera?

1 0

Chimera does not start with mesa-11.2.2
by Jaime Rodríguez-Guerra Pedregal 23 May '16

23 May '16

Hi guys, just to let you know that mesa-11.2.2 is messing with Chimera startup sequence.: $ chimera --debug initializing general preferences loading Tix initializing graphics libGL error: unable to load driver: i965_dri.so libGL error: driver pointer missing libGL error: failed to load driver: i965 libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 154 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 1410 Current serial number in output stream: 1411 $ `chimera --root`/bin/linuxdist /etc/os-release: NAME="Antergos Linux" VERSION="2015.11-ISO-Rolling" ID="antergos" ID_LIKE="arch" PRETTY_NAME="Antergos Linux" CPE_NAME="cpe:/o:antergosproject:antergos:2015.11" ANSI_COLOR="1;34;40" HOME_URL="https://antergos.com/" SUPPORT_URL="https://forum.antergos.com/" BUG_REPORT_URL="https://github.com/antergos" /etc/arch-release: Antergos Linux release 2015.11 (ISO-Rolling) /proc/cpuinfo: cpu: 8 GenuineIntel Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz (x86_64) cpu MHz: 3884.625 cache: 8192 KB /proc/meminfo: MemTotal: 16296392 kB Graphics: 00:02.0 VGA compatible controller: Intel Corporation Xeon E3-1200 v3/4th Gen Core Processor Integrated Graphics Controller (rev 06) 01:00.0 VGA compatible controller: NVIDIA Corporation GM204 [GeForce GTX 970] (rev a1) I had to rollback to mesa-11.2.1 to make it work again. Cheers, 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.

1 0

How to convert Coot rotation matrix to something Chimera can read?
by Oliver Clarke 19 May '16

19 May '16

Hi all, I'd like to write a little python function in coot to open the current view with Chimera, because manually replicating in Chimera views that were identified in Coot is a little painful. The file handling aspects of this seem straightforward - the one aspect I haven't quite got yet is how to set the view in Chimera to match that seen in Coot. I would like to load up all molecules/maps that are displayed in coot, in their default orientations, and then apply the view matrix from coot using matrixset to get the equivalent view. Coot outputs a 3X3 rotation matrix which seems to be the same as that generated for an equivalent view by matrixget in Chimera, except that in Chimera the matrix is 3X4, with the last column representing the translation vector. This I cannot access directly within coot, but I can probably calculate it if I know what it represents. This is probably a stupid question, but is this simply the vector from the origin to the current center of rotation? Or is it something else? Cheers, Oliver.

1 1

Re: [Chimera-users] Analysis of the contact maps from the MARTINI MD trajectory
by James Starlight 16 May '16

16 May '16

update: with the up-to-date chimera Trajectory is loaded fine now the question is related to the analysis of the binding interface. is it possible to make contact maps plots based on the 2 selections from the input trajectory assuming that I am using martini CG model? Gleb 2016-05-16 10:39 GMT+02:00 James Starlight <jmsstarlight(a)gmail.com>: > OK will try to update Chimera today ! > > What chimera's tools could be useful for the contact map based > analysis of md trajectories related to my case ? E.g to determine > binding interface between 2 proteins from long md simulation. > > Gleb > > 2016-05-13 19:52 GMT+02:00 Eric Pettersen <pett(a)cgl.ucsf.edu>: >> Hi Gleb, >> If you are using Gromacs 5 trajectories, you have to be using at least >> version 1.10.2 of Chimera. If you are using that version (or later), please >> use “Report a Bug” in Chimera’s Help menu to file a bug report and attach >> your topology file to the bug report. Thanks! >> >> —Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> >> >> On May 13, 2016, at 1:46 AM, James Starlight <jmsstarlight(a)gmail.com> wrote: >> >> Dear Chimera users! >> >> >> I am in charge with the analysis of protein-protein association during >> long molecular dynamic simulation where my system was parametrized >> using MARTINI CG force field. In particularly I am interesting to >> find residues on one of the protein which are crustal for the binding >> interface established during this MD. >> For that purpose I am trying to use Chimera to load trajectory and >> corresponded tpr file using MD movie plugin and than to >> map contact maps produced by Gromacs onto the 3D structure using Chimera. >> The problem that Chimera does not recognize properly the trajectory >> and topology. Briefly I have removed all solvent from both files >> before loading them to the Chimera using editconf and gmx convert-tpr >> obtaining eventually trajectory and topology with the same number of >> atoms. >> >> >> Than when I load it to Chimera that is the error which MD movie sent me: >> >> VERSION 5.0.2 >> using floats >> version 100, generation 26 >> 8 atoms >> Traceback (most recent call last): >> File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", >> line 1747, in __call__ >> File "CHIMERA/share/chimera/baseDialog.py", line 328, in command >> File "CHIMERA/share/chimera/baseDialog.py", line 543, in OK >> File "CHIMERA/share/Trajectory/EnsembleLoader.py", line 92, in Apply >> File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line >> 56, in loadEnsemble >> File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line >> 67, in loadEnsemble >> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 25, >> in __init__ >> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 86, >> in __init__ >> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line >> 345, in _readTopology >> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line >> 338, in _readString >> File "CHIMERA/lib/python2.5/xdrlib.py", line 197, in unpack_fstring >> raise EOFError >> EOFError >> EOFError >> >> File "CHIMERA/lib/python2.5/xdrlib.py", line 197, in unpack_fstring >> raise EOFError >> >> See reply log for Python traceback. >> >> Will be thankful for any suggestions! >> >> Gleb >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >>

2 5

question
by zona cat 14 May '16

14 May '16

Good afternoon, My name is Daniel Heller, and I am working with Helen Berman at Rutgers University on a PDB project. We are trying to analyze multiple DNA binding proteins simultaneously (via matchmaker) and looking to visualize the surface electrostatic potential of each structure as a tiled picture. We are deleting the nucleotide chains for all proteins when complexed with DNA. However, I am only able to get the surface electrostatic coloring for one structure (the reference structure), subsequent structures will not apply the columbic coloring after i hit apply, they just maintain the monotone default surface structure . Could you please help me with this issue. Thank you very much,Dan

2 5

Analysis of the contact maps from the MARTINI MD trajectory
by James Starlight 13 May '16

13 May '16

Dear Chimera users! I am in charge with the analysis of protein-protein association during long molecular dynamic simulation where my system was parametrized using MARTINI CG force field. In particularly I am interesting to find residues on one of the protein which are crustal for the binding interface established during this MD. For that purpose I am trying to use Chimera to load trajectory and corresponded tpr file using MD movie plugin and than to map contact maps produced by Gromacs onto the 3D structure using Chimera. The problem that Chimera does not recognize properly the trajectory and topology. Briefly I have removed all solvent from both files before loading them to the Chimera using editconf and gmx convert-tpr obtaining eventually trajectory and topology with the same number of atoms. Than when I load it to Chimera that is the error which MD movie sent me: VERSION 5.0.2 using floats version 100, generation 26 8 atoms Traceback (most recent call last): File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ File "CHIMERA/share/chimera/baseDialog.py", line 328, in command File "CHIMERA/share/chimera/baseDialog.py", line 543, in OK File "CHIMERA/share/Trajectory/EnsembleLoader.py", line 92, in Apply File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line 56, in loadEnsemble File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line 67, in loadEnsemble File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 25, in __init__ File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 86, in __init__ File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 345, in _readTopology File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 338, in _readString File "CHIMERA/lib/python2.5/xdrlib.py", line 197, in unpack_fstring raise EOFError EOFError EOFError File "CHIMERA/lib/python2.5/xdrlib.py", line 197, in unpack_fstring raise EOFError See reply log for Python traceback. Will be thankful for any suggestions! Gleb

2 1

Suggestion for ChimeraX - interruptible Matchmaker?
by Oliver Clarke 12 May '16

12 May '16

Hi, Matchmaker takes a *really* long time when dealing with long chains, particularly if it has been (unwisely/accidentally) directed to find the best matching pair of chains. This is as expected, but as Chimera is unresponsive while this happens, if the wrong matchmaker parameters are accidentally selected, there is no way to recover the session except by waiting for the operation to complete or force-quitting the app. If feasible, maybe in ChimeraX it would be useful to execute this operation in a manner that allows for cancelling a structural alignment in progress? And perhaps displaying an estimate of time to completion in the taskbar? Cheers, Oli.

2 1

Averaging multiple structures
by Yehuda Halfon 11 May '16

11 May '16

Hi there, I'm using Rosetta using comparative modeling of protein, and I get 1000 new PDBs. I wanted to upload all of them together and average them into one structure and to see if the average one is the better then the last one the software creates, which needs to be the best. Thanks, Yehuda

2 4

building and positioning disordered sequence
by thereal sisterdot 11 May '16

11 May '16

Dear Chimera Users, i would like to do something in chimera, that is not exactly science but more graphics :-) i have a known structure with 5 positions that i know are crosslinking to a 100aa intrinsically disordered partner sequence. now just in order to better imagine how the disordered binding partner wraps around the structure, i would like to put 5 lysines in the open space near the known crosslinking positions in the pdb structure, and than somehow build the rest of the disordered partner sequence connecting those lysines. its not about getting a estimate of the structural arrangement of the partner. its just so i can better imagine how the partner sequence extends around the interacting residues (as the residues are not in a patch but really all over the 100 aa) or if the arrangement would be sterically possible. any ideas if and how i could achieve that in chimera ? i know that is sound more like a task for illustrator, but :-) THANKS A LOT!!! sisterdot

2 3

Join models
by shazia sabir 10 May '16

10 May '16

Hi dear all, I have to join two models in one single model. For this I have to select N and C terminal of each of the model. But I couldn't find a way how to select/pick atom from N terminal of one model and C terminal of the other model. Please can anyone help me on that? kind Regards, Shazia.

2 3

surfaces
by A G Szabo 10 May '16

10 May '16

I am trying to represent a large homodimer with 840 residues per subunit, as a surface. On a smaller protein, 350 residues I was able to get a surface representation and color different domains. When I try to produce the surface representation of the larger molecule, I receive an error message saying that I have to split it because it is too large a molecule. So how do I do that? Thanks AGS

2 1

repeat question
by A G Szabo 10 May '16

10 May '16

I am trying to make the sphere of an ion in an active site larger than what appears in the structure. I asked a similar question back in December, and on checking my notes I tried to use the command setattr ballScale 0.5 I first selected the ion using control<click). The ion was selected. I then tried the command line as I show it above. Nothing appeared to happen. Indeed I tried to do the same for an atom of a residue that I had selected using control <click> again nothing. I must have forgotten something. A message from Elaine suggested that I use setattr m ballScale 0.5 Am I supposed to select the residue and leave out the m? Thanks for your patience. Arthur Szabo

2 2

opengl error with quadro k620
by Krishnan, Raman 10 May '16

10 May '16

[cid:image001.jpg@01D1A9F2.DB70AF30] Get this error on running chimera -debug-opengl option. Using quadrok620 nvidia card on windows 7.0 thanks Director Structural Biology, Biocryst Pharmaceuticals.

1 0

rainbow color scheme
by Shreeramesh 09 May '16

09 May '16

Dear Sir, I guess blue represents N-terminal of protein in rainbow coloring and would like know the indication of other colors in rainbow scheme of chimera for protein structure. Thanks & regards *Ramesh M* Email: shreeramesh(a)gmail.com Mobile: (91) + 9646469938 (27) + (0) 844556164

2 1

I get this when i tried to start chimera 1.11rc on windows 7. any suggestions?
by Krishnan, Raman 09 May '16

09 May '16

[cid:image001.jpg@01D1A55D.8C415B10] krish Biocryst Pharmaceuticals.

2 1

Re: [Chimera-users] [chimera-dev] suggestions for better STL export - remove internal, reduce atom vertices
by Tom Goddard 09 May '16

09 May '16

Hi Jakob, We discussed the excessive STL vertices in atoms and bonds last week and I put a fix into the daily build and release candidate. http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-April/012134.html Apparently you are not using those versions since your images show the high vertex density. I’ve attached an image using the current Chimera release candidate that shows reasonable vertex density. Unfortunately eliminating internal structures and stitching together meshes for atoms, bonds and ribbons at the seams is very difficult. Yes $10000 CAD software packages can do it but we don’t have the resources to solve that problem. Since every 3d printer has to deal with this problem I expect the printer software to be able to handle it, but perhaps it is too hard a problem for the 3d printer companies as well. Perhaps there is free software that can eliminate internal structures and stitch mesh intersecting edges together, I have not researched it — I’d start looking at MeshLab. Tom > On Apr 15, 2016, at 4:33 AM, Jakob Suckale wrote: > > Dear Chimera developers, > > Chimera has the great feature of STL export, very useful for 3D printing models for research and teaching. May I make two suggestion to improve this feature even further. > > > 1 - Remove invisible internal and therefore unnecessary structures. > > Chimera generates a lot of internal structures that complicate printing and are pointless for STLs. This includes inside surfaces at the end of ribbon cartoons (red below). > <Screen Shot 2016-04-15 at 13.24.44.png> > as well as copious amounts of invisible internal surfaces for wire and ball and stick models. > <Screen Shot 2016-04-15 at 13.27.36.png> > If these were automatically removed, STLs would not only be much smaller but also much easier to print without remashing. > > > 2 - Reduce the number of vertices for atom models. > > Ribbon conversion to vertices is already good, but as can bee seen above atom models are converted using far too many vertices inflating the resulting STL files. I'm aware that this has been discussed and listed previously as a bug but the problem remains and makes for difficult to use STLs and bad 3D prints. > > Best regards, > > > Jakob Suckale, PhD > Lecturer in Biochemistry > University of Tübingen > +49-7071-29-73363 > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev

3 3

Alter both clipping planes at same time?
by Oliver Clarke 05 May '16

05 May '16

Hi, is there any way to alter both global clipping planes at the same time? This is handy to move the current viewable section, without altering its thickness. At the moment I use an alias for this: # move both clip planes hither or yon. # Usage: zslab x # Move hither and yon clip planes towards (positive) or away (negative) alias ^zslab clip hither $1; clip yon $1 This works fine, except when the clip planes are close together - in that case, I get an error stating that I'm trying to move the near clip plane behind the far clip plane. It would be nice to have an option to move both planes at once - e.g. maybe changing the syntax of clip so either hither, yon, or both can be specified in the same command would be possible? Cheers, Oliver.

2 1

ImportError: No module named Chimera
by Eiros Zamora, Juan 04 May '16

04 May '16

Hi, I’m running a per-frame script to display the time in a MD movie. I used to run it without problems until I downloaded the new Mac OS X 64-bit 1.11 version. (I erased the old app, also tried to re-download the old version with no success). More specifically, I load the MD movie, and in the command line I write: 2dlabels create timer text "0 ns" color white ypos .9 xpos .9 size 50 then I open a per-frame script with the following commands: from Chimera import runCommand runCommand("2dlabels change timer text '%.1f ns'" % (mdInfo['frame']*0.02)) and get the error: Problem in per-frame script: ImportError: No module named Chimera I’ve googled it and found this reply: [Chimera-users] How to install chimera as a python module http://www.cgl.ucsf.edu/pipermail/chimera-users/2014-July/010120.html I’ve tried setting the $CHIMERA_PATH environment variable to /Applications/Chimera.app/Contents/Resources/share but I still run into the same problem. Now, I don’t want to run the script directly from the command line, as it’s a per-frame script I have to run after I load the MD movie and create the 2dlabel object. Anything obvious I’m missing here? Cheers Juan

3 2

how to move the model and save as mrc
by rongjian li 04 May '16

04 May '16

Hi, I am trying to move the model/protein in some MRC file and save it as a new MRC file. I know how to do it in Windows by clicking the mouse, but I have lots of such operations expected. So I am wondering how could I realize this in Linux such that it can be done automatically. Thank you very much. Best, Rongjian

2 1

Multiple Docking Using Chimera
by SOBAHY, TURKI MOHAMMED 02 May '16

02 May '16

Hello, I have a protein of interest that I need to perform molecular docking on by multiple ligands (~1000,000). The protein is in PDB file format, while ligands are in a SDF file format. Initially, the ligands were divided into multiple SDF files (mini) for hardware sake. Then, a python script was developed to handle the docking of each mini SDF file against the protein of interest. This works nicely, however docking scores (tables) have no ligands IDs associated to distinguish each score. So, basically I have scoring tables without any key IDs!! Kindly, I want to know if you have encountered the same problem and what approach you took to solve this. Thanks,? ______________________________ Turki Sobahy Research Associate Research Center (J-04) King Faisal Specialist Hospital & Research Center (Gen.Org.)-Jeddah Branch PO Box 40047, Jeddah 21499, Saudi Arabia Tel# +966 667 7777 ext. 66736| MCD# 40716 Mobile# +966 505837027 email tsobahy(a)kfshrc.edu.sa<mailto:ESan-Diego@kfshrc.edu.sa>

2 1

Solicitud Información
by luz Martinez 02 May '16

02 May '16

Cordial Saludo Soy estudiante de licenciatura en Química de la UNIVERSIDAD PEDAGOGICA NACIONAL. Colombia, Cordialmente solicito información acerca del modelo matemático general que el programa UCSF Chimera utiliza, lo anterior con el fin llevar a cabo una investigación en el espacio académico de Química Computacional que curso. Agradezco la atención y pronta respuesta Luz Angela Martinez M. Estudiante Decimo semestre

2 1

Thank you and a suggestion
by Mohamed Elrobh 01 May '16

01 May '16

Dear UCSF Chimera, Just wish to say big thank you for your program. If you kindly allowed me to ask if there is a possibility to make a live webinar tutorial on Mohamed Elrobh, Ph.D., Assistant Professor, Room 2A 66 B5, Department of Biochemistry, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia Phone +966 114675944, Fax +966 114675791, Mobile +966 502072937 Email melrobh(a)ksu.edu.sa<mailto:melrobh@ksu.edu.sa> Site http://fac.ksu.edu.sa/melrobh<http://faculty.ksu.edu.sa/elrobh> ________________________________ Disclaimer: This communication is intended for the above named person and is confidential and / or legally privileged. Any opinion(s) expressed in this communication are not necessarily those of KSU (King Saud University). If it has come to you in error you must take no action based upon it, nor must you print it, copy it, forward it, or show it to anyone. Please delete and destroy the e-mail and any attachments and inform the sender immediately. Thank you. KSU is not responsible for the political, religious, racial or partisan opinion in any correspondence conducted by its domain users. Therefore, any such opinion expressed, whether explicitly or implicitly, in any said correspondence is not to be interpreted as that of KSU. KSU may monitor all incoming and outgoing e-mails in line with KSU business practice. Although KSU has taken steps to ensure that e-mails and attachments are free from any virus, we advise that, in keeping with best business practice, the recipient must ensure they are actually virus free.

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Manually adjusting alignment
by Visvaldas K. 30 Apr '16

30 Apr '16

Dear All, I wasn't able to adjust alignment in the Alignment window, and search did not find an answer (because I get great number of false negatives)...I tried shift-arrow, ctrl-shif-arrow and many times but only once the region moved "by accident", and I wasn't able to repeat this feat. To simplify the task, let's say I have in the alignment window: seqA NQDF.RFRDseqB MKTFIEHKD I want to move "RF" by one residue to the left so that the top part becomes NQDFRF.RD What would be the sequence of keys, clicks/drags and so on to do that (also, how is the active region which is ready to move signified: green, green in a dashed frame, or perhaps white dashed frame)? Sincerely yours, Vis Kairys

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need help joining existing pdb files with new sequence
by John Hess 28 Apr '16

28 Apr '16

HI folks, I have asked Elaine a couple questions about this project of mine. She’s been very helpful, but I’m such a beginner, I feel guilty wasting her time and the rest of the folks reading the entire chimera list as I ask how to connect this and move that. I would like to take at least 2 existing pdb files and link them to some additional peptides sequence that would be between them. The resulting pdb would describe a structure that looks like this: > protein 1 -> peptide linker -> protein 2 I’m dealing mainly with alpha helices (in coiled-coils), and I know how I want them positioned. I joined a helical peptide sequence (made using Build Structure) to one pdb file but the orientation was way off and I’m wondering how to “grab” the entire helical peptide region and move it where I want it (sorry, in the past, I have tried to modify structures with Foldit and have had a collaborator who used Rosetta to try and model my data.). Is anyone else on this list from UC Davis and willing to get together for some tutoring? Does anyone not at Davis have time to answer my questions and help? If we work well by email and I make progress, I think that this could be a $ for time or co-authorship situation. thanks, John Hess jfhess(a)ucdavis.edu

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Labeling and coloring chains
by Elaine Meng 28 Apr '16

28 Apr '16

> On Apr 28, 2016, at 8:15 AM, Deniz Simsek Buck <simsekd(a)stanford.edu> wrote: > > Hi Elaine, > Thank you for your reply. > > I already changed the chain IDs to different names. I am working with ribosome structure: 44 chains are large subunit and then I want to color them the same color. > If I already changed chain A to L23, lets say, how do I choose them? > > Also, is there a way to choose different colors than the available ones and also how do I make the label the same color as the chain? > > Thank you very much, > Deniz > Hi Deniz, I do not know how you changed the chain names, so it is hard to say. In PDB format there is only one column allotted to chain ID in the ATOM lines, <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#co…> ...so it can only be one letter or number, as far as I know. So it would depend on what Chimera thinks are the chain IDs…. for example, it may have only read the single character in column 22 as the chain ID. You could probably tell by putting the mouse over some atom in the chain and see what information is in the pop-up balloon. But maybe you used some other format that allows more characters of chain ID. Nevertheless, it might not be possible to use the range syntax I showed in my previous message (first example included below). You could try it, but if ranges didn’t work, you’d have to specify all the IDs (again, all of what Chimera thinks are the IDs) in one long command, or in multiple separate coloring commands. > color red,r :.A-D > (meaning: color red ribbons-only in chains A-D in all models) > > color green,a #0:.B,.D > (meaning: color green atoms-only in chains B and D of model #0) Instead of changing chain IDs I would recommend using “alias” to give new names to the set of atoms and then use these new names in the coloring commands, e.g. alias L23 :.X (meaning assign the name L23 to chain X) color hot pink,r L23 … of course you could assign the name to a collection of multiple chains if you wanted, e.g. alias L23 :.X,.Y,.H You could also use alias with your existing changed chain IDs providing you can figure out what Chimera thinks they are. As for colors, you can specify an infinite number of colors as RGBs or hexadecimal or first define new color names and use those names, if the built-in set of named colors doesn’t have what you need. Color specification is described in the same “color” manpage I mentioned before. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/color.html> Also described in that page are how to specify coloring labels, e.g. color orange,r,l (meaning coloring ribbons and labels only) Again I’ve CC’d the recommended address for chimera questions, chimera-users(a)cgl.ucsf.edu 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

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Three-dimensional structural model of the VP7 trimer
by Dr Omer Naseer 28 Apr '16

28 Apr '16

Hi I am s student of PhD and working on the Rota virus A, I want to created "three-dimensional structural model of the VP7 trimer". by using "UCSF Chimera", can you please tell me How to do this? because I tried a lot but unable to produce a structure like yours. Regards Dr, Omer Naseer Ph.D Scholar University of Veterinary & Animal Sciences, Lahore, Pakistan. +92 321 640 89 56

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The question about fitting
by Zhongjun Hu 28 Apr '16

28 Apr '16

Hi, everyone: Once I fit one map to the reference map, there will be some fitting result. I want to use this fitting result to align the map to the reference map using another software, for example, EMAN. How do I this? It seems that I am not clear about the fitting result, could anyone give some idea? or, is there other protocol/software to do this? Thank you! Best, Zhongjun

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electron density map
by 陈柳青 28 Apr '16

28 Apr '16

Hi! I display the 2Fo-Fc map in chimera, but i wonder what the meaning of step 1, step2,etc in volume viewer. The other question is what the relationship between the level in chimera volume viewer and Coot map level ? Best regards -- Liuqing Chen School of Life Science & Biotechnology Minhang Campus Shanghai Jiao Tong University No. 800 Dongchuan Road Shanghai 200240 P.R. China Tel: +86 21 34207247

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Re: [Chimera-users] electron density map
by Oliver Clarke 28 Apr '16

28 Apr '16

Dear Liuqing, Step size refers to whether every point in the map is displayed (step 1), or every second point (step 2), or every fourth point (step 4) and so on - basically, the coarseness of the grid. Loading a map at a larger step size will have less detail, but will be faster to load and manipulate. See here (https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#sampling) for details. The level in Chimera is the same as in coot in absolute terms (e-/Å^3) - it is just that in Coot, by default, maps are adjusted in steps of r.m.s. (often called “sigma”), whereas the default behaviour in Chimera is to deal directly with absolute electron density levels. You can mimic the Coot behaviour, however, by adjusting the volume level on the command line with the option sdlevel, for example “volume #1 sdlevel 1” will set the volume with id #1 to 2xr.m.s. See here (https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#level) for details. For convenience (really due to my forgetfulness), I use an alias to do this, as follows: "alias ^map_sig volume $1 sdlevel $2" so then one can use the command “map_sig #1 5” to adjust map #1 to 5xr.m.s., which should match the corresponding level in coot. If you want to mimic how maps look in coot, adjusting some of the mesh options is handy, as follows: "alias ^cootmode volume $1 capfaces false style mesh meshlighting false squaremesh false color "#08882eefa222" step 1; sop cap off; set depthCue; set dcStart 0.2; set dcEnd 1; background solid white; cofron” Where “cofron" is an alias that mimics the centering and navigation behaviour of coot: "alias ^cofron set showcofr; cofr view; clip on” Cheers, Oli.

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Re: [Chimera-users] Viewing one biological unit of a model
by Derrick Lau 28 Apr '16

28 Apr '16

Hi Elaine, Very clear instructions. Thank you very much. Best regards, Derrick Lau PhD student University of New South Wales - Molecular Machines Group - (02) 9385 8639 *Cellular and Molecular Biology* 2016-04-26 8:09 GMT+10:00 Elaine Meng <meng(a)cgl.ucsf.edu>: > Hi Derrick, > That PDB entry is an “NMR ensemble” including 100 different conformations > of the same thing. You can hide or delete any of those 100. To first see > what you have, show Model Panel from the Favorites menu. Initially all the > conformations are collapsed into a single line with ID “0.1 … 0.100” or > something like that. If you scroll down to click the “group/ungroup” > function in the right side of the Model Panel, that entry will expand out > (ungroup) to 100 entries. > > You could show any one by clicking to highlight only that line on the > left-hand side of the Model Panel, then clicking the “show only” button on > the right-hand side, for example. You can also toggle the Shown checkboxes > individually, or highlight multiple lines and “show only” those or “close” > (delete) them leaving only the others. > > Or you don’t have to use the Model Panel at all. For example, if the > structure was opened as model #0 and you wanted to hide all except the > first conformation, command: > > ~modeldisplay #0.2-100 > - OR - > ~modeldisplay #0.2-end > > …or even delete them > > close #0.2-end > > It might take a few seconds to execute the command. > > Note that a single NMR conformation is not necessarily a biological unit. > It is just one copy of the coordinate set. > 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 Apr 24, 2016, at 8:00 AM, Derrick Lau < > derrick.lau(a)student.unsw.edu.au> wrote: > > > > Dear Chimera, > > > > Hi. My name is Derrick. I have recently started learning to use Chimera > to look at the capsid structure of HIV. I would like some help in the > interface. One particular crystal model, the HIV-dimer model PDB 2M8L, > strangely loads a bunch of ribbon structures. Would you know the way of > switching off other biological unit so I can see one pair of dimer? > > > > I didn't have this problem with other capsid structures (like 3P05). > Your help is appreciated. Thank you in advance. > > > > Best regards, > > > > Derrick Lau > >

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Re: [Chimera-users] [chimera-dev] Labeling and coloring chains
by Elaine Meng 27 Apr '16

27 Apr '16

Hi Deniz, (1) It is easy to specify multiple chains in the command line. Show the command line from the Favorites menu. Example commands: color red,r :.A-D (meaning: color red ribbons-only in chains A-D in all models) color green,a #0:.B,.D (meaning: color green atoms-only in chains B and D of model #0) See manpages for color command and for command-line atom-residue-chain specification: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/color.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> … and you may want to try a “getting started” tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html> <https://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html> (2) For labeling the chains there are 2 general choices. A. For 3D labels that move along with the structure, there aren’t exactly chain labels, but you can choose to label one residue in each chain and then only show the chain ID and not the other residue information. For example, command “select :10” will select residue 10 in every chain that has a residue 10. Then you could use menu: Actions… Label… residue… custom, and in that dialog specify you want labels of the form: %(chain)s , Apply. Disadvantage is that they may be on top of things and hard to see. Advantage is they move around with the structure and will stay near that residue when you rotate and translate. B. you can arbitrarily add 2D labels that are just in the XY plane and do not move with the structure, containing whatever text and symbols you want. In menu, Tools… Depiction… 2D Labels. Click the Help button on that dialog to see its help. You can type in each label manually and move it around in the XY plane. You would want to get the final view for a figure or something close to it, before bothering to add 2D labels. There are examples of 2D labels in these tutorials: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/density.html> C. Actually there is a 3rd related choice, just putting the mouse over an atom or residue will pop up temporary information that includes its chain ID, and sometimes that will suffice. As you can see, there are lots of tutorials and manual pages to explore. For future reference, chimera-users(a)cgl.ucsf.edu (CC’d here) is the address for Chimera usage questions. The chimera-dev list is more for programming-related questions. 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 Apr 27, 2016, at 12:48 PM, Deniz Simsek Buck <simsekd(a)stanford.edu> wrote: > Hi, > I am very new to Chimera. If you have time, I would really appreciate your answers. > I am working with a structure that contains 80 chains. > 1. I would like to color 40 chains at once the same color, rather than manually doing it one by one. > How do I do this? > 2. Also, I would like to add labels to the individual chains I choose on the structure. > How do I do this? > Thank you, > Deniz

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Define plane or planes matched to hither or yon clip planes
by Oliver Clarke 27 Apr '16

27 Apr '16

Hi, I often encounter cases where I am showing a slab of density or model (or both), clipped using the global clip planes, and would like to show the viewer a thumbnail illustrating the position of these clip planes from an orientation orthogonal to the viewing direction (similar to what is shown in side view), to give context. Is there any way to define either two planes, one matched to the current yon and one matched to the global hither, or one thick plane with the thickness defined such that one side matches hither and the other yon? Alternatively I guess I can do this using the model-specific clip planes, but that's a little cumbersome to do when many models/maps are involved. Cheers, Oli

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how to change map origin in the map file
by 许靖蔚 27 Apr '16

27 Apr '16

Dear all: I recently have to match two maps and calculate the CC value between them. The origin of these two maps are different and the pixel value are also not the same. I could open these two maps in chimera and align them by map fitting. However, after I matched one of them to the other and saved the map, the re-opened map was still at the same position as the previous! So do you know how to same the map after fitting? Best wishes.

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HBond on every frames of a large trajectory
by Jérémie KNOOPS [531802] 26 Apr '16

26 Apr '16

Hi, What is the easiest and fastest way to get the number of H bonds on every frame of a large trajectory (>10 000 frames) and print it to a file? The hbonds command does not seem to work with the perframe command and displaying the whole trajectory to run a per-frame script is quite slow. Jérémie Knoops PhD Student Laboratory for Chemistry of Novel Materials<http://morris.umh.ac.be/default.aspx> University of Mons<http://portail.umons.ac.be/en2/> 20, Place du Parc B-7000 Mons (Belgium) Tel : +32(0)65 37 38 65<tel:%2B32%280%2965%2037%2038%2065>

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Save as GIF (animated or otherwise)
by Oliver Clarke 26 Apr '16

26 Apr '16

Hi, It would be very useful if Chimera (prob ChimeraX) was able to save either single frames, or, preferably, record movies in GIF format. This is not so much out of a desire to make animated gifs (although these can be handy for presentations and use on the web), but more because it makes it very easy to create labeled movies in vector graphics programs (one can edit a single frame in a vector graphics program and then insert it and alter the duration in for example GIMP or similar), which can then be easily converted back to mp4. Otherwise adding labels and custom annotations to movies is a pain for a novice like me, though if any one has any suggestions for recommended software I'd love to hear them! I've tried using iMovie and found it incredibly frustrating for the kinds of simple things like to do - adding labels, boxes, arrows etc to highlight specific domains during a morph, for example. At the moment I make a movie in chimera and convert it to a GIF using videoblend, edit in affinity designer and GIMP and then convert back to mp4 using online tools, but a more direct route would definitely be useful. Cheers, Oliver.

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need help to plot electrostatic surface charge distribution
by ashok rout 26 Apr '16

26 Apr '16

Hi, I have NMR structure of a protein. I want to plot electrostatic surface charge distribution. Can you please write me step by step commands how I can do it. I want to remove hydrogens first and then want to plot electrostatic surface charge distribution. Ashok -- thanks & regards, Ashok

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