- Chimera-users - RBVI Mailing Lists

Saving images of all scenes in session?
by Oliver Clarke 02 Oct '15

02 Oct '15

Hi all, Apologies for yet another post and thank you for your patience! :-) Feature suggestion (or maybe this exists already?): I would like a way to iterate over all scenes in a session and save an image at each scene, with the same display settings (e.g keep background or make transparent, image format, wall-eye/cross-eye stereo, etc). This would be really very helpful when making, remaking and updating figures. Most of the time, I will have a session, say “Fig1.py”, within which I will have a bunch of scenes corresponding to each panel. It would be really advantageous to be able to take images of each scene all at once, saving each as (for example) Fig1_scene_name.jpg, Fig1_scene_name2.jpg etc. This could work in the same way as saving series of maps or models does now - just have a checkbox in the Save Image dialog for “save images for all scenes in session”, or something similar. It can take quite a while to save each image when on a slow computer, or when using graphics intensive settings such as silhouettes and shadows, so being able to save matched sets of images (e.g. low and hi-res versions, stereo versions, etc) with a couple of clicks would save a lot of time, particularly for example if you realize that the versions you saved the first time were all too low res and you want to go back and save a higher res version of every panel. I realize you guys might not have time to implement this for Chimera 1, as development of Chimera 2 is top priority, so maybe I can write a script to do this in the meantime? Is there any way to return a list of scene names using one of the built in python functions? I guess something in Animate.Scenes ought to do this, but not being much of a python programmer I can’t quite figure it out - any tips much appreciated. Cheers, Oli.

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Problems detecting h-bonds
by Felipe Vasquez 02 Oct '15

02 Oct '15

Hi, I have recently obtained some docking results (I have a complex) and I am trying to detect any protein-ligand h-bonds. Soon, I faced a first problem when I obtain this error message: "More than 2 coplanar positions specified!", and I think I solved it once my ligand was selected and I enter into the command line: "setattr a idatmType sel". However, I obtained later an entire panel (with a big list in it) asking me to indicate the expetd geometries and number of substituents for a large list of atoms, from both ligand and protein. How could I overcome this issue knowing that there is several expected h-bonds to be detected in my complex? Thanks in advance for your help. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* Profesional - Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN Bogotá, D.C., Colombia

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Morphs
by Dr Kereiche 02 Oct '15

02 Oct '15

Dear Chimera team, lately I am facing some problems for creating a movie in which I would like to combine 2 morphs with each other. To make it clearer, I hope, I have 2 Em maps representing 2 states of my structure (vol #1 & vol #2) I did a morph maps (volume/ Morph map) after having recenter and align the 2 maps. it works perfectly. I did similar procedure with 2 pdb files (1.pdb & 2.pdb), corresponding to the fitted molecular structures of the 2 states (vol#1 & vol #2) , using the tool/Structures comparison/ morph conformation. The pbds are aligned with the EM map using VOP command. Now I would like to combine the 2 morphs together to have a final morph of the EM maps with the molecular structure, but I could not find a way to combine them. Thus I would like to know if it is possible to do it ? and if yes how to do it. Moreover is it possible to play the morph of the pdbs in way of the morph of the EM maps back and forth? Thank you in advance, Sincerely Sami

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Angle between pseudobond and principal axis
by Yasser Almeida Hernández 01 Oct '15

01 Oct '15

Hi all, I want to measure the angle between a pseudobond and the X, Y, Z axis. How can I do so? Best Yasser

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Re: [Chimera-users] metal coordination to display off
by Eric Pettersen 30 Sep '15

30 Sep '15

On 9/28/15 6:13 PM, "Luigi Di Costanzo" <dicostanzo(a)rcsb.rutgers.edu <mailto:dicostanzo@rcsb.rutgers.edu>> wrote: > > We have fetched 2MHR with Chimera and noticed that the middle nitrogen > of azide is bonded through a dashed line as following: > > FE2 FEO A 119 N2 AZI A 120 > > From the "structure analysis" tool and "metal geometry" window we are > unable to display off that dashed lines that is incorrect. > > The coordination table does not show that particular link and we can not > deselect it. > > Could you please look into it and provide some suggestions? > > Thanks. Hi Luigi, The spurious dashed line is due to a corresponding CONECT record in the PDB file. So one option is to locate that CONECT record and delete it. The other is to use the Metal Coordination tool to clean up the coordination of that iron. First, it is highly unlikely that the histidine nitrogens coordinating the iron are protonated, so you should select those hydrogens and “del sel” to get rid of them. Then if you bring up the metal coordination tool for the iron it will properly show the nitrogens as coordinating. If you already had the tool up when you deleted the hydrogens then you will have to force the tool to consider the newly deprotonated nitrogens by selecting them and clicking the “Add atoms selected in the graphics window" button. You can now remove the spurious coordination you noted above by first clicking the last atom in the coordination table (HIS 25.A NE2) and then clicking the “Create/Update metal-complex pseudobonds” button. I hope this helps. Let me know if you have any questions. —Eric Eric Pettersen UCSF Computer Graphics Lab

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Chimera
by Scapin, Giovanna 30 Sep '15

30 Sep '15

Good afternoon I am interested in downloading and installing CHIMERA. Could you let me know if there is any licensing cost involved and if so whom I should contact? Thank you very much Giovanna Scapin Giovanna Scapin Principal Scientist Structural Chemistry Merck & Co., Inc. 2000 Galloping Hill Rd K15-1800 Room B133C Kenilworth NJ 07033 Phone +1 908 740 3632 Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth, New Jersey, USA 07033), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.

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Proportional representation of missing segments?
by Oliver Clarke 28 Sep '15

28 Sep '15

Hi all, I think it would be handy, in a future version of chimera, to have an option to represent missing segments in a manner that is proportional to the volume of protein missing - this would be very useful for getting a sense of which chain breaks correspond to very large missing regions (e.g. whole domains), and which correspond to short linkers or loops that are missing. For example, in the structure of the ryanodine receptor, there are missing segments ranging in length from ~5-250 residues in length - it would be very handy to be able to get a quick sense, upon first opening a structure, about what fraction of the crystallized or reconstructed protein is actually present in the model. I can think of a couple of ways of doing this. One way would be to associate an attribute with each missing segment, corresponding to the number of missing residues, and allow the user to scale the radius, color or opacity of the missing segments in proportion to this value (maybe this attribute already exists somewhere internally?). Another way might be to create a completely different missing segment representation - perhaps an ellipsoid, with the ends of the ellipsoid at the N and C-terminal breakpoints, and the volume of the ellipsoid scaled to the volume of a random polymer of the known number of missing residues. I would try to do this myself by creating an extension, but I don’t really know where to start to get the information that would be required - I don’t know how to iterate over all missing segments, calculate the number of residues in each, and create a new representation. I guess there is probably a list somewhere in Chimera corresponding to the missing segments and their properties, but I have no idea how to find it. Cheers, Oliver.

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Forcefields and Molecular Radii
by Cale Martin 25 Sep '15

25 Sep '15

Dear Chimera users, Over the last few days I have been using Chimera 1.9 to model the Poisson-Boltzmann surface potential of a protein. I have been using the APBS software and the two main forcefields I have been using are the TYL06 and AMBER. When I model the chemokine using the AMBER forcefield the result seems to be normal and as expected, but when using the TYL06 forcefield, the final molecule surface seems to have larger molecule radii almost making it look a little more "bubbly" for lack of a better term. Is this a function of the forcefield in any way? Should this be expected from these two different forcefields? Another issue that I have had along the same line involves the APBS program. The settings allow for the selection of a "Smoothed Molecular Surface" and one that is just "Molecular Surface" but when I run the program with every thing the same except these settings, the results look exactly the same. Should this setting affect the visualization of my molecule surface in any way? Thank you, Cale Martin

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FW: How can I find H-bond between ligand and protein residues within selected angstrom?
by Williams, Joanne 25 Sep '15

25 Sep '15

On 9/19/15 1:29 AM, "高木友理子" <kagaribi-firefly(a)bs.s.u-tokyo.ac.jp> wrote: > Dear Chimera creator, > > I use Chimera to analyse protein-ligand interaction. > Especially, I would like to find H-bond between these. > I clicked HBonds and tried to search H-bond within selected distance. > However,I could not. > I guess the reason is that I was not able to understand "Relax > constraints" in H-Bond parameter window. > I ,of course, checked chimera's help. > What is relax constraints? > What does 0.4 angstroms indicate? Is this the Max distance between ligand > and protein residue? > I would like to find H-bond between them within selected angstrom. > What should I do to know that? > Please teach me how to do. > Thank you for being patient with my English. > > Best regards, > > Yuriko Takagi > Tokyo university student

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Way to extract path to file from model ID
by Oliver Clarke 24 Sep '15

24 Sep '15

Hi all, I’m wondering, is there any way (presumably via a python function) to get the path to the original file from the model ID? I’ve written a little python jiffy (below) so I can lowpass filter maps to a specified resolution on the fly inside chimera using EMAN, but is quite slow because I need to first write a copy of the map out (so I know where it is) and then modify it. If anyone knows of an easier way to do such things I would be most grateful. Cheers, Oli. Script: def cmd_lowpass(lowpass,args): from Midas.midas_text import doExtensionFunc def lowpass(model,resol): import os from chimera import runCommand import subprocess import sys #You may need to change the below to .bash_profile if on mac. #You must have EMAN2 in your bash path for this to work correctly. #If running multiple times, you need to close the first instance of lowpass.mrc before creating a second. bashrc_path=os.path.expanduser("~/.bashrc") freq=1.0/resol command="cd ~; system mkdir chimera_tmp; cd chimera_tmp; volume "+model+" save ./tmp1.mrc" runCommand(command) pathvar=os.path.expanduser("~/chimera_tmp") os.chdir(pathvar) e2string="--process=filter.lowpass.gauss:cutoff_freq="+str(freq) print(e2string) mrc_in=pathvar+"/tmp1.mrc" mrc_out=pathvar+"/lowpass.mrc" e2command="source "+bashrc_path+"; bash -c \"e2proc3d.py"+" "+mrc_in+" "+mrc_out+" "+e2string+"\"" print(e2command) proc=subprocess.Popen(e2command,stdout=subprocess.PIPE, stderr=subprocess.PIPE,shell=True) out, err = proc.communicate() print 'stdout:', out print 'stderr:', err runCommand("open lowpass.mrc") doExtensionFunc(lowpass,args) from Midas.midas_text import addCommand addCommand("lowpass", cmd_lowpass, help=False)

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Rendering protein molecule to a geometry format by Chimera
by Hsin-Yi Yeh 23 Sep '15

23 Sep '15

Hi, I try to render a protein molecule to a geometry format (from .pdb format to .obj format) by Chimera. I use 'Multiscale models' tool in 'Higher-Order Structure' choice and then make the model by resurfacing at some appropriate resolution. It turns out that the whole protein molecule can be modeled pretty nicely. However, I now have a similar problem; instead of rendering the whole protein molecule, I would like to render the whole structure separately. I want to render the exposed residues (those residues on the surface) and non-exposed/buried residues separately, so I will have two obj files (one for the exposed residues and the others for the non-exposed residues). I haven't been able to figure this problem out yet. Thus, I am wondering could you please give me some direction? Any advice will be greatly appreciated! Thank you, Hsin-Yi (Cindy) Yeh -- Hsin-Yi (Cindy) Yeh PhD Student Parasol Lab, Department of Computer Science and Engineering Texas A&M University Email: hyeh(a)cse.tamu.edu https://parasol.tamu.edu/people/hyeh/

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applying charges calculated by DFT to ligands in protein models
by Anne-Frances Miller 21 Sep '15

21 Sep '15

Dear Sir or Madam, Our protein has a bound FMN and the various tools accessible via Chimera are not able to apply charges to the atoms in FMN. However I have NBO charges for all the atoms from DFT calculations. Is there a way I can provide these to the FMN in my pdb file or in my Chimera session in order to then display a Coulomb electrostatic potential for the protein + FMN? My charges are not simply +1 or -1, but fractional charges for each atom. Can Chimera accommodate this ? If not, no problem, I will still benefit greatly even if all I can do is add -1 to the one atom at which most of the excess electron density is concentrated. Many Thanks, Anne-Frances Anne-Frances Miller Professor of Chemistry Director, Magnetic Resonance Centre University of Kentucky Dept. Chemistry, 505 Rose Street Lexington KY 40506-0055 “You never change things by fighting the existing reality. To change something, build a new model that makes the existing model obsolete.” Buckminster Fuller

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Fetch by ID EMDB + fit PDBs enhancement suggestion
by Ingvar Lagerstedt 21 Sep '15

21 Sep '15

Dear Chimera, Attempting to Fetch by ID an EMDB entry with a fitted model, where the model does exist in PDB format, causes an error: No such ID. The map is retrieved but not opened in Chimera. The two main reasons that the model is not available: A. The model is only available in mmCIF format. Since a wwPDB remediation at the end of last year, entries that are larger than what the PDB format can handle are no longer distributed as split entries. They are only distributed as mmCIF (and PDBx) files. This is common for say ribosomes. EMD-6315 with fitted model 3j9z is an example. Changing the command so that it attempts to retrieve mmCIF files rather than PDB files would fix this issue. B. The model has not been released, EMDB and PDB releases for maps and models are not always synchronised. An example would be EMD-6413, where the model 3jb9 is currently waiting for author approval. In this case it would be nice if the map was loaded. Many Thanks, Ingvar

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Re: [Chimera-users] large file size exporting scene with spheres
by Elaine Meng 17 Sep '15

17 Sep '15

On Sep 17, 2015, at 10:48 AM, Tom Goddard <goddard(a)sonic.net> wrote: Hi Elaine, Bill, Chimera export first writes x3d and then converts that to STL or VRML or whatever you requested. For atom spheres it writes the center and radius of the sphere in x3d. It does not write the number of triangles or the amount subdivision. The Chimera program x3d2stl controls how many triangles a sphere is turned into. It uses 100 triangles per square Angstrom. There is no option to change that. But it is possible to run x3d2stl by hand and specify the resolution option “-r 1” to request 1 triangle per square Angstrom, resulting in a file that is 100 times smaller and the spheres still look fine (using about 40 triangles per atom). ~/Desktop/Chimera\ 1.10.2.app/Contents/Resources/bin/.x3d2stl -o 1a0m_r1.stl -r 1 < 1a0m.x3d Note that .x3d2stl has a period as the first character. Eric Bell reported this problem about a year and a half ago but the ridiculous defaul STL sphere subdivision has unfortunately not been changed. http://plato.cgl.ucsf.edu/trac/chimera/ticket/13183 Tom > On Sep 17, 2015, at 9:51 AM, Eliason, William <william.eliason(a)yale.edu> wrote: > > Elaine, > > Thanks again for your suggestions. I had already seen that previous post you listed and found that the stl file size for spheres was unchanged with changes to the zoom. The subdivision box in the effects tool changes the spheres on on the chimera display but has no effect on the stl file size when exporting a scene. > > I will keep looking for a solution. If you have any other suggestions please email me. > > Thanks Again, > > Bill > ________________________________________ > From: Elaine Meng [meng(a)cgl.ucsf.edu] > Sent: Tuesday, September 15, 2015 3:42 PM > To: Eliason, William > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] large file size exporting scene with spheres > > Hi Bill, > You can decrease the “subdivision” setting in the Effects dialog (menu Tools… Viewing Controls… Effects) and also zoom out the view before exporting. > > These are discussed in more detail in this previous post: > <https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_pipe… > > > 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 Sep 15, 2015, at 11:52 AM, Eliason, William <william.eliason(a)yale.edu> wrote: >> >> Chimera-users, >> >> I am very new to chimera. I would like to export a scene with spheres for 3d printing but the ( .stl) file size is enormous. They contain way to many triangles. I tested a smallish molecule in MeshLab and I could decrease the number of faces from 699732 (34MB) to 34986 faces (1.7MB) with minor flattening of the sphere. Is there a way to have chimera generate spheres with fewer faces? >> >> Thank you, >> >> Bill Eliason > >

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Saving sessions including maps?
by Oliver Clarke 17 Sep '15

17 Sep '15

Hi all, Is there any possibility of altering the chimera session format (or adding a separate option) such that all maps (including those created during the session) are also saved? This would greatly facilitate sharing data with collaborators, and would also allow one to provide chimera sessions with saved scenes as supplementary data when publishing. It would also make saving sessions more practical when many different volumes are created during the session - for example, when using a molmap low resolution representation for each domain. This would not necessarily require creating a new format - just creating a tarball or folder with all the maps and relative paths specified in the python file would work fine I think? Cheers, Oli.

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Re: [Chimera-users] FW: eps image in publication quality
by Mahendra B Thapa 16 Sep '15

16 Sep '15

Dear Eric & Greg Thank you for the suggestions. The only available option to save the *sequence alignment image* is EPS format, actually I am looking a way to save the image in tif or png format. In the pop-up window of sequence alignment image , there are following options available under 'File' heading: Save as, save EPS, save Association info, Hide & quit. As Greg pointed out, I didn't find "Save Image dialog". Eric, when I copied the so generated EPS image in MS-Powerpoint for further editing, the quality of the image was not good. I have attached one of the EPS image ( in which I have aligned two structures: pdb id 4ICB & 3BCI.) Thank you for help, Mahendra Thapa University of Cincinnati,OH On Tue, Sep 15, 2015 at 8:42 PM, Thapa, Mahendra (thapamb) < thapamb(a)mail.uc.edu> wrote: > > ------------------------------ > *From:* gregc(a)cgl.ucsf.edu > *Sent:* Tuesday, September 15, 2015 6:42:06 PM (UTC-06:00) Central America > *To:* Eric Pettersen; Thapa, Mahendra (thapamb) > *Cc:* chimera-users(a)cgl.ucsf.edu > *Subject:* Re: [Chimera-users] eps image in publication quality > > Actually, chimera's EPS files are at a fixed resolution. To get a higher > resolution, save the image with a higher resolution. An easy way to get a > reasonable resolution is to switch to print units in the Save Image dialog, > and choose a size in inches or cm. The default "Print resolution" of > 100dpi is generally more than adequate since printers need many dots to > represent a single pixel and most computer monitors are roughly 100dpi. > > Also, note that EPS files are huge compared to PNG or TIFF files. Most, > if not all, journals now accept TIFF or PNG images, so there is no need to > generate an EPS file. > > -- Greg > > September 15 2015 5:18 PM, "Eric Pettersen" <pett(a)cgl.ucsf.edu > <%22Eric%20Pettersen%22%20%3Cpett(a)cgl.ucsf.edu%3E>> wrote: > > EPS (Encapsulated PostScript) is resolution independent — it essentially > has infinite resolution. If it doesn’t look good in a viewer it’s because > the viewer is doing a poor job of rendering it. What are you using to look > at the EPS file? > —Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > > > On Sep 15, 2015, at 9:04 AM, Mahendra B Thapa <thapamb(a)mail.uc.edu> wrote: > > Dear Chimera Users, > Using the following procedures in chimera window, I saved a sequence > allignment image in eps format ( which looked like the first image of " > file:///opt/UCSF/Chimera64-1.6.1/share/chimera/helpdir/ContributedSoftware/multalignviewer/framemav.html"). > The image in the pop of window is nice but the saved image in the eps > format is not so clear. Let me suggest how to save the image in the > publication quality. > (i) structure ---> matchmaker > (ii) Tools ---> sequence ---> match ---> align > (iii) file ---> save as ---> eps > Thank you, > Mahendra Thapa > University of Cincinnati, OH > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

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large file size exporting scene with spheres
by Eliason, William 16 Sep '15

16 Sep '15

Chimera-users, I am very new to chimera. I would like to export a scene with spheres for 3d printing but the ( .stl) file size is enormous. They contain way to many triangles. I tested a smallish molecule in MeshLab and I could decrease the number of faces from 699732 (34MB) to 34986 faces (1.7MB) with minor flattening of the sphere. Is there a way to have chimera generate spheres with fewer faces? Thank you, Bill Eliason

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eps image in publication quality
by Mahendra B Thapa 15 Sep '15

15 Sep '15

Dear Chimera Users, Using the following procedures in chimera window, I saved a sequence allignment image in eps format ( which looked like the first image of "file:///opt/UCSF/Chimera64-1.6.1/share/chimera/helpdir/ContributedSoftware/multalignviewer/framemav.html"). The image in the pop of window is nice but the saved image in the eps format is not so clear. Let me suggest how to save the image in the publication quality. (i) structure ---> matchmaker (ii) Tools ---> sequence ---> match ---> align (iii) file ---> save as ---> eps Thank you, Mahendra Thapa University of Cincinnati, OH

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how to move subunits of a pentamer receptor in a controlled way
by Zhang, Yinghui 14 Sep '15

14 Sep '15

Dear Sir, This is Yinghui Zhang from Massachusetts General Hospital. I am a frequent user of Chimera to understand the structure of a neuronal pentamer receptor which is ion channel. Now we want to do some modification of the receptor by manipulating the coordinates of the atoms of the receptor pdb files. The aim is to move each subunit radially away from the receptor’s central symmetry axis(which should be the central channel axis ) or tilt each subunit outward. The symmetry of the receptor cannot be disrupted and we want to do it in a quantitative manner(move by a specific ‎Å or tilt by a specific degree value). Could you please give us some clues if we can realize these aims in Chimera? Many thanks and regards! Yinghui Zhang The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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setting solvent density threshold at 2.5 times of the bulk solvent density
by Mohan Pradhan 10 Sep '15

10 Sep '15

Dear Chimera users, I am using the Volume Viewer application in Chimera to visualize the solvent density around protein at a threshold value of 2.5 times of the bulk solvent density. My understanding is that the iso value corresponding to the bulk solvent density is marked by the peak in the plot of the volume viewer. I am then multiplying the iso value of the peak by 2.5Is this the right way of identifying regions in protein that have a solvent density of 2.5 times of the bulk solvent density? Kindly suggest. Thanks,Mohan

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Question regarding 3D surface coordinates
by Guirguis, Christopher Amin 10 Sep '15

10 Sep '15

Hello, A quick question: is there any output file type where coordinates of the surfaces are typed rather than just the center of the individual atoms? I want to insert my molecules into a modeling software like Maya to create an .obj file for viewing on mobile devices. Thank you for your time. Best, Chris Guirguis

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question
by A G Szabo 09 Sep '15

09 Sep '15

I go to tools and open the sequence of the protein that I am interested in. The minimum number of amino acids in a row that I can select is 2. I am interested in visualizing a selected number of amino acids that are not in linked to one another. Eg. A specific Lys residue in a helical sequence. I have found a work around. I highlight two adjacent residues, and visualize the two of them as sticks. I then select the amino acid I do not wish to highlight together with the amino acid on the other side of the one that I am interested in. I can that way eventually deselect and not highlight the amino acid I am not interested in. There has to be a simpler way. Thanks for your assistance. Arthur G. Szabo Professor Emeritus Chemistry Wilfrid Laurier University.

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on mrc map
by Smith Liu 09 Sep '15

09 Sep '15

Dear All, Suppose I have a mcr map for a protein of 4 subunits. Will you please introduce to me how to split the whole map to 4 different maps, with each map corresponding to the part of each subunit in the whole map, without loosing any data in the spitted map in comparison to that specific subunit part of the whole map? Best regards. Smith

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Help needed urgently
by Clare Nattress 08 Sep '15

08 Sep '15

Hello there, I have just sent this file to a 3D printers and sadly it has disintegrated when post printed and the model has been bathed and washed. Attached is the link to the STL. file https://www.dropbox.com/sh/2nytyw6989h0v2l/AADiXrhb8mUfi53J95co-Bvja?dl=0 I was wondering how I could perhaps make the structure 3D print safe. Would you be able to help me join the bonds and also make them a lot thicker? Any help would be most appreciated as this is meant to be in an exhibition come Friday. Best Wishes, Clare Nattress Artist/Writer www.clare-nattress.com LinkedIn - Clare Nattress @ClareNattress

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Align and average intensity images in Chimera
by 許紹君 07 Sep '15

07 Sep '15

To whom it may concern, I am willing to use Chimera for aligning several images from the structure illumination microscope (SIM). Here is the surface maps generated by Chimera from two images. cid:image005.jpg@01D0E986.2CF5F370 After alignment by the tool “Fit in Map”, they are aligned very well. cid:image006.jpg@01D0E986.2CF5F370 My next step is to average the intensity from two aligned images and generate a new map which will be used to fit other images. Can anyone tell me how to do it in Chimera? By the way, please also tell me what the values mean in the reply log. cid:image007.jpg@01D0E986.2CF5F370 It helps me to use another software to complete the mission, if I can get the rotation, voxel shift, or even scaling values from the alignment. Thank you! All Best, Peggy Hsu, PhD Institute of Cellular and Organismic Biology, Academia Sinica 128 Academia Rd Sec 2, Nankang, Taipei 11529, Taiwan Tel: 886-2-2787-1531 (O) email: peggyschsu(a)gate.sinica.edu.tw

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Distance in pi-interactions
by George Tzotzos 03 Sep '15

03 Sep '15

I’m trying to work out the distance between two arene rings involved in pi-interactions. Is there a way of measuring the distance centre-to-centre of each arene ring? Or any other sensible way? I’m attaching a snapshot for easy reference. Thanks in advance for any suggestions. Regards George

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make a movie showing the process from an ASU model to the complete model of virus
by 李智海 02 Sep '15

02 Sep '15

Hi, I just obtained an atomic model of the asymmetric unit of an icosahedral T=7 virus capsid , and I want to make a movie to play the whole process from the ASU model to the full capsid model by imposing its icosahedral symmetry. Please show me some examples of the command lines to generate such kind of movies. Thanks! Best regards! Zhihai Li

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chimera visualization
by Valerio Chiarini 02 Sep '15

02 Sep '15

Dear Elaine, I would like to produce images from chimera showing an NMR bundle structure (backbone only) with stick-represented residues each one belonging to different single structures. I know it´s possible to do it with pymol but unfortunately the structures superimposition is not as good as in chimera. Would it be possible? Thank you in advance, Valerio

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Rapid residue identification near ligands
by Korbin West 01 Sep '15

01 Sep '15

Greetings all, We need to be able to easily assign ligands to a chain (or chains) and to rapidly ID the residues in contact with it. I believe Chimera processes the structures and immediately displays ligands and maybe contacts, so it "knows" this information somehow. Does anyone know of a way to identify these easily and quickly so we can analyze large numbers of files? Also, if the output could be in the form of a text file or such that would be beneficial as well. Thank you all for your help. Best, Korbin West Wabash College

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make a movie showing the process from an ASU model to the complete model of virus
by 李智海 01 Sep '15

01 Sep '15

Hi, I just obtained an atomic model of the asymmetric unit of an icosahedral T=7 virus capsid , and I want to make a movie to play the whole process from the ASU model to the full capsid model by imposing its icosahedral symmetry. Please show me some examples of the command lines to generate such kind of movies. Thanks! Best regards! Zhihai

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Hydrogen bonding calculation issues with PDB2PQR/AMBER/CHIMERA
by Fenton Heirtzler 31 Aug '15

31 Aug '15

Hello- I’m trying to use CHIMERA to model the hexameric hydrogen bonding of isophthalic acid. I’m just an organic chemist, not a computational chemist. The PDB2PQR subroutine is returning the reply “Error encountered: No heavy atoms found!”. Here is sequentially what I have done: 1. A pdb file of isophthalic acid hexamer was imported. 2. The covalent bond lengths and angles were set to realistic ones. 3. The names of the concerned atoms were defined in the Build Structure/Modify Structure/Change Modified Residue’s name box, as described in the User Guide (i.e., Cac, O2, O3 and H) 4. The default limits of 3.4 Å and 30° were used 5. The AMBER force field was chosen. Thanks very much Fenton (PS – I’m a private person, not associated with either academia nor industry) -- Dr. Fenton Heirtzler Phone: +1-301-312-5145 On LinkedIn <http://www.linkedin.com/in/fentonhorgchem/> Skype: fentonheirtzler Supporter of the International Day of Climate Action <http://www.350.org/> *********

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Query related to chimera
by Akhilesh Verma 31 Aug '15

31 Aug '15

Dear Manager, Is it possible to do Protein protein docking using chimera program? Your response will be highly appreciated. Thanking you. -- Sincerely yours, *Akalesh Kumar Verma* *Morehouse School of Medicine* *Microbiology, Biochemistry & Immunology* Atlanta, Georgia, USA Pin / Zip: 30329 *Mobile: +1 (678) 497-6404* *http://www.msm.edu/ <http://www.msm.edu/>* _______________________ ______________ *Personal Disclaimer:--* *Any information contained in this e-mail and/or any attachments is confidential and only intended for reception and use by the specified person. If you are not the intended recipient, please return the email to the sender and delete it afterwards. In this case any copying, forwarding, printing, disclosure and use are strictly prohibited.* *_________________* *__________*

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How can I can calculate or know Gibbs free energy from UCSF Chimera
by Awah.Chidiebere.U＠mh-hannover.de 28 Aug '15

28 Aug '15

Dear Colleagues, Thanks for developing such wonderful tools as Chimera for molecular dynamics analysis of structure. Please I have two questions: 1. Is it possible to calculate Gibbs free energy from complexes on UCSF Chimera, for examples when complexes are solvated? 2. On building structures , is it possible to simulate how a given complex could bind DNA oligos , for example when one makes changes in single nucleotides and ask a given DNA binding TF structure to bind it on Chimera? I would look forward to your response to these questions. I would also be very happy if I could speak by phone with the administrators. Thanks. Best wishes, Chidiebere U Awah MD Msc PhD student , Molecular Medicine Hannover Medical School , Germany.

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Re: [Chimera-users] a question relate to Chimera
by Elaine Meng 27 Aug '15

27 Aug '15

On Aug 26, 2015, at 6:27 PM, Smith Liu <smith_liu123(a)163.com> wrote: > Dear Elaine, > Thanks for the reply. > > Here let us consider the first question on "a particle has a diameter of 100 pixels ", which I think may be done by Chimera with your help. From http://www.imagescience.de/fsc/index.htm, we can download a software which can be used to calculate the resolution of the map by FSC. When we use that software for calculation, we need to input "Filling degree" D/L, where the value of object size D in voxels, and the L, the linear ssize of the 3D volume (x, y,z). A typical value of "Filling degree" D/L would be 0.66, indicating that 2/3 of the linear width of the 3D volume is filled by the object. > > Thus will you please show me by Chimera how can we know "the value of object size D in voxels"? > > I am looking forward to getting your reply. > > Best regards. > Smith Dear Smith, Please send Chimera questions to chimera-users(a)cgl.ucsf.edu (instead of to me directly). Others may be able to answer your questions better than I can, for example in this case where I don’t know the answer. For linear size of the whole volume (the map), we already discussed that you can see the number of grid units (voxels) in X,Y,Z to the right of the dataset name in the Volume Viewer dialog, and see angstroms per grid unit in the Features: Coordinates section of Volume Viewer. You could multiply the values to get the size of the map in angstroms. <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-August/011437.html> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-August/011433.html> However, I don’t know how you could measure the voxel size of the object in Chimera. As far as I know you could only estimate it by eye, or by measuring angstrom dimensions, converting to grid units, and then multiplying them to roughly estimate the area of the object in voxels. It would only be an estimate, assuming your object is not a perfect circle or square. See previous posts on measuring angstrom dimensions in a map: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010609.html> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-January/009503.html> My guess is that people would normally get this information from the software used in the original data collection, not by doing measurements in Chimera. 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

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Re: [Chimera-users] Icosahedral net from PDB
by Tom Goddard 27 Aug '15

27 Aug '15

Hi James, There are a few Chimera commands that let you show a icosahedral cage around a virus PDB model. Basically you use the sym command to make the virus capsid from the PDB asymmetric unit, then use the shape command to make the cage, then optionally use the meshmol command to show the cage with cylinders instead of lines. For example, open 2bbv sym #0 surf true shape icos radius 200 lattice 1,1 meshmol #2 3 color gold #3 There’s also a video showing how to make the cage for an electron microscopy map http://www.cgl.ucsf.edu/chimera/videodoc/cage/index.html <http://www.cgl.ucsf.edu/chimera/videodoc/cage/index.html> Here is the command documentation for more info about sym, shape, meshmol commands: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/framecommand.html <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/framecommand.html> Tom > On Aug 27, 2015, at 5:11 AM, Geraets, James A > Hi Tom, > > A colleague of mine has told me that you have previously made available a script for displaying icosahedrally-symmetric pdb files on an icosahedron net. Would you happen to still have it? I can’t find any sign of it online… > > Cheers (and thanks for your continued work on Chimera) > > James > > ---------- > > James Geraets > EU Marie Curie Actions Fellow > AIROPico Project > > Institute of Biotechnology > PL 56 > FI-00014 University of Helsinki > Finland

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addgrp command
by UCSF-xiaobowan 26 Aug '15

26 Aug '15

Hi all, I am Xiaobo Wan, a postdoc at UCSF. I would like to learn how to add chemical groups (such as methyl) or change chemical atoms (Fluorine to Nitrogen) using the command in Chimera because I have thousands of compounds to do the same modification. I know the Build Structure in the Graphic interface can do this. I am not sure whether the addgrp command was supported by chimera now. Best, Xiaobo

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color suggestion
by Dougherty, Matthew T 26 Aug '15

26 Aug '15

1) button on the model panel to bring up the color editor that will edit the model selected. 2) very short pulldown menu on the color editor of the primary & secondary colors, along with black, white and gray50. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Re: [Chimera-users] a question relate to Chimera
by Elaine Meng 26 Aug '15

26 Aug '15

On Aug 25, 2015, at 6:16 PM, Smith Liu <smith_liu123(a)163.com> wrote: > Dear Elaine, > Here there is a sentence "a particle has a diameter of 100 pixels and the width of the reconstruction box is 256 pixels". Will you please tell me by Chimera how can I know the diameter of the particle and the width of the reconstruction box, as described in the cited sentence? > > I am looking forward to getting a reply from you. > Best regards. > Smith Dear Smith, It is recommended to send Chimera questions to chimera-users(a)cgl.ucsf.edu (CC’d here) instead of to me directly. I don’t know where that sentence came from, so I’m not even sure it is a Chimera question. By “pixels” maybe the authors mean grid units. They probably just knew this about their own data without trying to get it from Chimera, but at least for the width of the box, you can see the grid dimensions just to the right of the dataset name in the Volume Viewer dialog. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/fram…> 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

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on point-group symmetry used for the 3-D calculation
by Smith Liu 25 Aug '15

25 Aug '15

Dear All, By chimera, can we know the point-group symmetry used for the 3-D calculation? Best regards. Smith

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on voxel size measured in angstroms
by Smith Liu 25 Aug '15

25 Aug '15

Dear All, Will you please tell me by Chimera how can we know the voxel size measured in angstroms? Smith

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is the connection present?
by Dmitry 25 Aug '15

25 Aug '15

Dear Colleagues, I have 3d tetramer volume density where I fitted known x-ray structure of monomer (to each unit of tetramer). I want to check the inter-monomeric space, whether there is connections between 2 monomers. Is there a command or script that checks the presence of contacts between bounds of 2 structures? Thank you Sincerely, Dmitry

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Electrostatic Potential Visualization
by Chun, Minju 25 Aug '15

25 Aug '15

Hello, I am an intern working with Chimera, and I was wondering if I was missing a plug-in that calculated electrostatic potential. I attempted to load a dx and cube file to emulate electrostatic potential, but there seemed to be a problem finding/reading the files(perhaps I'm doing this wrong too). I thought that if I calculated electrostatic potential directly with Chimera, I could see electrostatic potential. It says on your website that Chimera can calculate the electrostatic potential with APBS: "electrostatic potential calculated with Adaptive Poisson-Boltzmann Solver<http://www.poissonboltzmann.org/apbs/> (APBS); the APBS<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html> tool in Chimera runs this program via web service provided by the NBCR<http://nbcr.ucsd.edu/>" Do you have a tutorial that goes in more detail in how to calculate potential with APBS? Thank you, Minju Chun

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Flattening of coloured icosahedron
by R.I.Koning＠lumc.nl 24 Aug '15

24 Aug '15

Is it possible to flatten a coloured icosahedron surface? I have an electron density of a virus, and using shape icosahedron and colour icosahedron surface and surface colour I can colour it according to this density. I would really like to generate a flattened icosahedron (compared to the flatten icosahedron command) from the coloured icosahedron surface. In order to get a 2D map of the colours. Is this possible somehow in Chimera? Is it otherwise possible to export the icosahedron with the coloured surfaces and try in another program (like Maya of Cinema4D?). Best regards, Roman Koning

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layering problem
by Joseph Atherton 20 Aug '15

20 Aug '15

Hi! I'm trying to make videos at the moment but I have a problem with layering, as in the model seems to be 'hiding' behind the density even when the density is transparent. This occurs when I set transparency also in the model, even at low transparency (e.g command #19:transparency 5,a,r #0:259-271). See the example attached- the left hand most part of the model, and the ADP is hidden when their transparency is non-zero. Can I prevent this? Cheers, Joe

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Re: [Chimera-users] [chimera-dev] distance measurements
by Elaine Meng 19 Aug '15

19 Aug '15

Hi Feixia! Yes, you could use Chimera to measure all lysine CA-CA distances in many structures, but it would require some scripting to loop through the structures, find the lysines, and do the measurements. There is some information on looping through structures and running Chimera commands here: <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> Now, for each structure, you might imagine the script should first find all the lysines and then use the “distance" command on each pairwise combination, substituting in the proper residue numbers. However, there is an easier way with the “findclash” command. You can use it for multiple distance measurement in a single command. For example: open 2gbp findclash :lys@ca test self overlap -1000 log true … will measure all distances among lysine CA atoms in structure 2gbp and list results in the Reply Log (open from Favorites menu). The -1000 in the command says to measure the distance even if the atoms are “overlapping” by -1000 (more than 1000 angstroms apart). The last column in the results is the atom-atom distance, and they are given in order of increasing distance, in this case: 464 contacts atom1 atom2 overlap distance LYS 191.A CA LYS 189.A CA -1.802 5.562 LYS 227.A CA LYS 223.A CA -2.137 5.897 LYS 300.A CA LYS 246.A CA -2.800 6.560 LYS 169.A CA LYS 164.A CA -4.676 8.436 LYS 270.A CA LYS 276.A CA -4.677 8.437 [… several lines removed …] LYS 276.A CA LYS 203.A CA -53.705 57.465 LYS 276.A CA LYS 137.A CA -56.756 60.516 LYS 61.A CA LYS 137.A CA -56.829 60.589 LYS 58.A CA LYS 137.A CA -59.598 63.358 464 contacts The log contents can be saved to a text file, for example see <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003184.html> However, your log would have a huge amount of results for all structures and it might be hard to tell which results go with which structures, so another possibility would be to save a separate file of results for each structure, and in that case your script would need to substitute in an output filename, e.g. findclash :lys@ca test self overlap -1000 saveFile ~/Desktop/2gbp.log See findclash documentation for all the options. Then you can embed the command in the python looping script as described in the first link above. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.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 On Aug 18, 2015, at 8:36 AM, Feixia <feixia.chu(a)unh.edu> wrote: > Hi there, > I am interested in retrieving distance information from large dataset in an automatic fashion. For instance, can we use Chimera to get the distances between lysine alpha-carbons of current PDB entries. Presumably, we can download all PDB structures on our local desktop, and just call functions one structure at a time. I wonder if we can do that with Chimera. Your advice will be highly appreciated. > Best, > Feixia

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measure the vertical distance between aromatic planes
by Wang, Bing 19 Aug '15

19 Aug '15

Hi Chimera, Is there a way to measure the vertical distance of two planes in the structure? I do know how to measure the angle between two planes or one line and one plane by the Axes/Planes/Centroids in Chimera. I don't need the distance of two centroid of two planes. I do need the vertical distance of two planes. Could you please show me in detail? Thanks a lot! Bing Wang

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How to select a plane from the command line
by JUAN PABLO REYES VALVERDE 17 Aug '15

17 Aug '15

Dear UCSF Chimera Team: Please, I would much appreciate your advice on the following: First issue: Given a number of planes - calculated/created through the 'define' command - I would like to select one of them, with some command entered at the command line .... How can I do it? The reason why I want to select it through the command line, and not by directly by clicking at it at the axes/planes/centroids table, is because later I would like to use the command inside a runCommand statement, in a Python/IDLE script (with *.py extension) ... Second issue: By the way, do you think this piece of code could work? Assume that the desired plane is already selected .... I want to internally handle the plane as 'p1' in my Python code: p1= chimera.Plane() from chimera import selection p1= selection or perhaps this single instruction ..... p1= chimera.selection Let me try to explain: Within my Python code, I want to have a way to make reference to a plane created by the 'define' command ( should I call it a ' handle'? ... not sure whether it is the correct term ...). Well, I hope that I managed to make it sufficiently clear ... Thanks in advance for your kind attention. Cheers, Juan Dr. Juan Pablo Reyes Valverde Laboratorio de Neurobiología Molecular y Celular (D15) Instituto de Neurobiología UNAM Campus UNAM Juriquilla Boulevard Juriquilla 3001 Querétaro, QRO CP 76230 MÉXICO Tel +52 (442) 2381064

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Charges for PTR+DT
by Amali Guruge 17 Aug '15

17 Aug '15

Dear all, I have to prepare the pdb structure 1K4T to my study. When I do the dock prep process, it gives net charges as, PTR+DT -2 TGP +0 I added charges for standard resides by AMBER ff12SB. For other residues, I added charges by Gasteiger method. My problem is why PTR+DT gives -2 charge? I am not familiar with this one. <http://www.google.lk/intl/en/options/> Can anyone help me? Thank you.

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Modification of ribbon scaling to intersect guide atoms at termini and chain breaks?
by Oliver Clarke 14 Aug '15

14 Aug '15

Suggestion - would it be possible at some point in the future to add a new ribbon scaling option (I guess in Chimera 2.0 or later) so that all internal residues behave like the current “Bspline” scaling, but residues at termini or chain breaks behave like “cardinal” - where the ribbon path exactly intersects the guide atoms? The attached image illustrates the kind of situation this would address - where one wants to show secondary structure in cartoon, but pick out a loop or structural feature of interest in backbone or CA+sidechains, with no ugly discontinuities between the all-atom and ribbon representations. This would allow seamless mixing of nice looking cartoon representation and nice looking backbone or C-alpha+sidechains representation, which I don’t believe is possible at the moment. Cheers, Oliver. Also, in case anyone finds it useful, the following alias applied to a selection or model will generate the CA+sidechains representation depicted below: #Show CA trace with sidechains #Usage: ca_and_sidechains #model_id (or selection/atom-spec) alias ^ca_and_sidechains sel $1; namesel tmp; ~ribbon tmp; ~disp tmp; sel tmp&@CA&protein; repr stick sel; disp sel; setattr m stickScale 1.00 tmp; sel side chain/base.without CA/C1'&tmp; repr stick sel; disp sel; setattr b radius 0.1 sel; color orange tmp; color byhet tmp; sel @CAA |@CB; namesel tmp2; sel tmp&tmp2; repr stick sel; setattr b radius 0.1 sel; sel @CD,N&:pro&tmp; disp sel; repr stick sel; setattr b radius 0.. 1 sel; ~sel

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~select doesn't work on axes?
by Oliver Clarke 14 Aug '15

14 Aug '15

The command "~sel” does not unselect selected axes/planes/centroids - is this intended, and/or is there another way to unselect these objects from the command line? Also, is there a command to undisplay selected axes/planes/centroids? I can only figure out how to do so from the GUI but I would like to do this from the command line, as when you have many axes defined and only want to hide a few it would be easier to have an equivalent of “~disp sel” rather than hunting for the specific axes in the Axes/Planes/Centroids list. Cheers, Oliver.

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