- Chimera-users - RBVI Mailing Lists

cannot save a Chimera session
by ouyang 06 Aug '14

06 Aug '14

Dear All, I use Chimera1.9 in WindowsXP. I failed to save Chimera session neither by using the 'save' command nor 'file/save session (or save session as)' menu. Somehow, the file menu choice 'save session' is always displayed in gray and not clickable. Could anyone know what problem it would be and how to fix it? Thanks a lot! Best. Ouyang

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Delphi electrostatic potential visualization
by Joshua Broyde 04 Aug '14

04 Aug '14

Hi, My name is Joshua Broyde, and I am a big fan of Chimera. I have recently been using Chimera to visualize Delphi outputs (i.e. .phi files).As per your advice here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2006-March/000710.html I have been using Delphi itself and visualizing the output in Chimera, rather than using the DelphiController within Chimera. Chimera seems to not consistently be able to visualize the output of Delphi on the surface of the proteins. After coloring 2 different protein models with the delphi electrostatic output, I tried to color the third protein surface I was examining with the Delphi output, and Chimera simply colored it gray. To double check that this was not a Delphi problem, I then took this protein structure and created a separate chimera session with it, and then Chimera was able to visualize the Delphi output on the protein surface. Is this a bug or something? Is there a way around this? I want to be able to visualize many Delphi outputs at once on Chimera. Thanks so much, you guys are great! Sincerely, Joshua Broyde

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Chimera script specify filetype
by Thomas Hrabe 02 Aug '14

02 Aug '14

Hi everyone, I have a donwload option on our page for chimera python scripts - one example is attached. When you open it, chimera asks for the filetype. How can I hardocde it’s a PDB file? Thanks, Thomas

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Setup for 3D workstations?
by Kenward Vaughan 30 Jul '14

30 Jul '14

Hello all, I apologize if this is skewed for the list; please correct me if so. I am putting together a proposal to set up a 3D/computational lab at our school for the STEM area, with Chimera at the top of the list of applications using it. The general idea is to have 10 workstations and one workstation-server (the server side being used for computational work), with students at each station doing their own things. Does anyone have an idea of the best setup for each station with respect to hardware for viewing in 3D?? I expect our Dell-camp school to go with something like an Inspiron T5610, using an nVidia K4000 card. I was thinking that the nVidia 3D vision system made sense, but honestly don't know if that would work with 10 different ones going at once. I am unfamiliar with other options. Would someone help me with this? There would be two or three students at each station, FWIW. Am I out in left field in my thinking? Cheers, Kenward -- In a completely rational society, the best of us would aspire to be *teachers* and the rest of us would have to settle for something less, because passing civilization along from one generation to the next ought to be the highest honor and the highest responsibility anyone could have. - Lee Iacocca

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About MD movie problem
by rama david 30 Jul '14

30 Jul '14

Dear Friends, I completed the simulation of peptide ligand and receptor in gromacs. I want to make the simulation movie. I am using latest version of chimera. I also converted the trajectory files into single pdb movie in gromacs. I did following process: 1. Through tool----> Md movie-- I choose the gromacs option and load the tpr and trr/xtc files. But the software shows that the memory is not enough. ( Frame 4000 and atoms 8000) 2. For second time I chose the PDB option for Mdvie. I load the PDB & now I am getting following message : Residue 4.C not in the first model on line 17718 of Md.pdb file. I am pasting the few lines of md.pdb starting from line 17718 ATOM 8852 N NH2 C 4 61.241 96.447 51.027 1.00 0.00 ATOM 8853 H1 NH2 C 4 61.539 97.208 50.457 1.00 0.00 ATOM 8854 H2 NH2 C 4 61.923 95.899 51.517 1.00 0.00 END Could you please help me in the above problem, I will be a very thankful to you for your help. This is very Important movie for my work. I am looking for reply, With best Wishes Rama David

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Changing Structure/Sequence Associations by a command
by Marek Basler 28 Jul '14

28 Jul '14

Hi, I'd like to be able to change an association between a sequence in a multiple sequence alignment and an opened structure model by a chimera command. I have a model that is a multimer and I'd like to color code one of its subunits according to its sequence conservation ... but I need to reassign the automatic association that Chimera does after opening of a fasta file. Any idea? Thank you!! Best regards, Marek

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[External] import error from module: Togl
by Mike Sivley 25 Jul '14

25 Jul '14

I apologize in advance if this becomes too system-specific, as I believe an automatic update of our server's python libraries may be to blame for this error. However, my hope is that others may have run into the issue as well and have already found a solution. I have a python/chimera script that generates Chimera scenes with various annotations assigned to residues in a protein structure. This script worked without issue for several weeks. I returned from a week of vacation and now the script fails with the following error: ImportError: No module named Togl File "/ant2/Bush_eQTL/sivleyrm/bin/UCSF-Chimera64-2014-05-13/share/chimera/tkgui.py", line 73, in <module> import Togl Togl appears to be a deprecated library, so my best guess is that it was removed during some automatic update (possibly of PyOpenGL?) applied to our servers. However, Chimera is distributed with its own python executable and libraries, so I'm unsure how this type of change could have affected it. I am using the nightly headless linux build of Chimera from 05-13-2014. I have reinstalled chimera from the original .bin file, and I have also installed the most recent nightly headless build. Neither resolved the issue. I'm additionally confused because the exception is raised by tkgui.py, which by naming convention seems like it shouldn't even be called given that I am passing the "--nogui --silent --script" parameters to chimera. The specific call to chimera is this: chimera --nogui --silent --script 'lib/PDBMapVisualize.py 1hho 1 maf temp/61098856282.TEMP 1.000000 0.000000 data/rcsb/biounit/coordinates/all/1hho.pdb1.gz results/pdbmap_1kg_1hho_20140725-11 -' Where lib/PDBMapVisualize.py is my script and everything following are arguments to that script. Nothing about this call or the script it is calling have changed between when chimera ran successfully and now. Any help or advice in resolving this issue would be greatly appreciated. Thanks! Mike Sivley PhD Student in Biomedical Informatics Center for Human Genetics Research Vanderbilt University Medical Center

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distance between two residues in multiple pdb files
by Mahendra B Thapa 24 Jul '14

24 Jul '14

Dear Chimera users, One of the ways to find distance between two residues (say, residue no 10 and residue no 15 of a pdb file) is the use of command 'distance' in the command line of Chimera. How can I use the command 'distance' for a multiple pdb files (say, 20 pdb files which are generated by simulation of a protein)? I mean, may I need some scripts for looping? Any other alternatives will also help me a lot. Thank you, Mahendra Thapa University of Cincinnati,OH

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DNA nucleotide bases representation as long sticks
by roz orchidea 23 Jul '14

23 Jul '14

Dear all, I am trying to make nice DNA images with Chimera. I would like to have my nucleotide bases shown as long sticks like in this image: http://www.nature.com/cr/journal/v23/n2/images/cr2012170f1.jpg Does anybody know how to do that? Thanks in advance for you answer! Alexandra

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surface color by conservation among different sequences
by 李智海 21 Jul '14

21 Jul '14

Hi, I want to show a model in surface style which represents the conservation based on a series of sequences by its color. I have got a result of sequence alignment (.fas file). How can I apply this alignment result to the surface coloring in Chimera? Thanks! best wishes! Zhihai Li

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Re: [Chimera-users] Chimera-users Digest, Vol 135, Issue 20
by Boaz Shaanan 21 Jul '14

21 Jul '14

Hi, On top of what Elaine wrote there is also the interface between Consurf (http://consurf.tau.ac.il/) and Chimera, which is also a very nice option. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu [chimera-users-bounces(a)cgl.ucsf.edu] on behalf of chimera-users-request(a)cgl.ucsf.edu [chimera-users-request(a)cgl.ucsf.edu] Sent: Monday, July 21, 2014 10:00 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 135, Issue 20 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. surface color by conservation among different sequences (???) 2. Re: surface color by conservation among different sequences (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Mon, 21 Jul 2014 23:20:45 +0800 From: ??? <21620101152414(a)stu.xmu.edu.cn> To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] surface color by conservation among different sequences Message-ID: <211F19AF-2CA8-4E66-81D4-0F9BC20A868A(a)stu.xmu.edu.cn> Content-Type: text/plain; charset="us-ascii" Hi, I want to show a model in surface style which represents the conservation based on a series of sequences by its color. I have got a result of sequence alignment (.fas file). How can I apply this alignment result to the surface coloring in Chimera? Thanks! best wishes! Zhihai Li

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disulfide bonds ?
by Marek Maly 15 Jul '14

15 Jul '14

Hellow, I just visualized my Amber MD trajectory with protein containing several disulfide bonds. These bonds as well as all the other bonds are written in the given Amber topology (*.prmtop) file, which is read in by Chimera. Moreover the distance of sulfur atoms connected by disulfide bond is in all cases quite reasonable ( 2-2.1 A). In spite these facts Chimera draws some of those bonds in "stick" and some of them in "dashed line" style, even if one sets globally "stick" or "ball & stick" representation. Please see the attached illustrations. Why Chimera is doing such unwanted differences in graphical representations here ? It is possible, to force Chimera to draw all of those bonds unanimously in "stick" representation ? Thank you in advance for your help, Best wishes, Marek Maly -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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Calculate RMSD over SSE of NMR ensemble
by Markus Heller 14 Jul '14

14 Jul '14

Hello, The subject says it all. How do I calculate the RMSD of secondary structure elements of an NMR ensemble? I did RTFM, but I'm hoping that I can avoid spelling out the residues comprising the SSEs ... Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F: (604) 827-1299 | E: mheller(a)cdrd.ca<mailto:mheller@cdrd.ca> | www.cdrd.ca [cid:image002.png@01CF9C4B.5C0363C0] Follow us: [Description: cid:image003.jpg@01CD86A6.39B41A10] <https://twitter.com/C_D_R_D> [Description: cid:image005.jpg@01CD86AE.B197F5D0] <http://www.linkedin.com/groups/CDRD-3186016/about?report%2Esuccess=3NcE4iZo…> [Description: cid:image009.png@01CD86AE.B197F5D0] <https://www.facebook.com/pages/The-Centre-for-Drug-Research-and-Development…> [Description: cid:image010.png@01CD86AE.B197F5D0] <http://www.youtube.com/user/CDRDCVI?view_as=public> This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email.

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Can't open the file generated by NORMAD-REF
by Mahendra B Thapa 14 Jul '14

14 Jul '14

Dear Chimera users, I can't open the pdb file (one of them is attached) generated by NORMAD-REF( http://lorentz.immstr.pasteur.fr/decoys/submission.php) in chimera (version 64-1.9). The format of the pdb file looks like ok while trying to follow the former posts like " http://www.cgl.ucsf.edu/pipermail/chimera-users/2012-June/007704.html". Please help me to find the errors which might have remained unnoticed to me. Thank you, Mahendra Thapa Doctoral Student,Physics University of Cincinnati,OH

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local cross-correlation coefficient
by 李智海 08 Jul '14

08 Jul '14

Hi, I performed tool "Fit in map” to calculate the correlation value, i was wondering whether the value is the same as local cross-correlation coefficient (local CCC). Thanks in advance for your help! Best wishes for you! Zhihai Li

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Chimera Using Problem
by christophe 08 Jul '14

08 Jul '14

Hi,I'm trying to import chimera in python but when i try to make it i've bug, it said to me the following thing just after have execute:>>>from chimera import *Traceback (most recent call last): File "C:\Python27\Lib\site-packages\Chimera 1.9\share\testMM.py", line 1, in <module> from chimera import * File "C:\Python27\Lib\site-packages\Chimera 1.9\share\chimera\__init__.py", line 16, in <module> from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, XformImportError: No module named _chimeraI'm on windows 8 64 bits and i have chimera 1.9 and python 2.7.7 i've this following structure of directories:C:\Python27\Lib\Site-packages\chimera 1.9And i've run my script under the python.exe of chimera.So can you said to me what is wrong to fix it cause of i need chimera to made a script using superposition ( so with MatchMaker)? Cordially,Christophe Linhard.

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Suggestion - secondary structural element as an additional level in the selection hierarchy?
by Oliver Clarke 07 Jul '14

07 Jul '14

Greetings, Currently, the selection hierarchy in Chimera is as follows - atom<residue<chain<model<all. I don’t know how complicated it would be to implement, but perhaps it might be desirable in a future version of Chimera to include “secondary structural element” (being coil, helix or strand) as an additional level, between residue and chain? This would enable easy/quick selection/coloring of specific loops, helices or strands in a structure. E.g, say I am working on a helical repeat protein like an importin, and I want to color all the helices on the concave, inside surface one color, and all the helices on the outside surface another color - to do that at present is possible, but somewhat laborious, as it is necessary to explicitly specify the boundaries of each helix, and if there are many helices in the desired selection that are not sequence-adjacent then this becomes complicated. If SSE was a level of the selection hierarchy, I could select one residue in each helix on the desired surface, press the up arrow once to broaden the selection and all the helices on the inner surface would then be selected, without needing to know the location in the sequence of each helix. It seems like there would be quite a lot of use cases where this might save time - selecting individual surface exposed loops, or a specific set of helices or strands that form a binding surface for a ligand or partner protein, for example. Best regards, Oliver.

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Change default display settings?
by rswett＠chem.wayne.edu 07 Jul '14

07 Jul '14

Hi, I was wondering if there was a way to change my startup preferences so that the default is to show only ribbons? No atoms?

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How to install chimera as a python module
by Ivan Castro 07 Jul '14

07 Jul '14

Hi everyone, Looks like Chimera can be installed as a python module, but I can't find the first steps to do that. Anyone can suggest me a tutorial or webpage for this purpose. Thanks. -- Iván Castro, B. Sc (Hons). M. Sc Student - Biology at Universidad del Valle, Colombia. Member of Grupo de Estudios en Genética, Ecología Molecular y Fisiología Animal. Member of Fundación Colombiana para la Investigación y Conservación de Tiburones y Rayas.

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how to connect broken ribbon
by Pu Qian 07 Jul '14

07 Jul '14

Hi there, Sometime, when I use chimera to make a ribbon presentation of protein, the helix region will either broken or does not present properly. Similar thing can be happened in Pymol. But, Pymol provides a command called "alter". When I rebuilt it after altering, broken helix can be repaired. I'm wondering is there similar function in Chimera, or is there a suitable method which can be used to deal with it. Thanks Best regards Pu Qian

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Measure correlation for rotated map positions
by Tom Goddard 03 Jul '14

03 Jul '14

Hi Rakesh, The “measure correlation” rotationAxis option only accepts a specification of two atoms to define the rotation axis. This is explained in the Chimera documentation. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#correlat… Specifying 3 numbers is not enough since you need both a direction and a point on the axis. If you have a center x,y,z position and axis vector ax,ay,az then you could use the “turn” command to do the rotations and the “measure correlation” command without the rotationAxis option as follows. perframe "turn 0,0,1 10 center 0,0,0 coord #1 model #1 ; measure corr #0 #1" frames 36 This does a rotation by 10 degrees about center 0,0,0 and axis 0,0,1 using map #1 coordinates then measures the correlation between map #1 and #0, repeating this 36 times (covering 360 degrees). Results are reported in the reply log. Tom On Jul 3, 2014, at 2:56 PM, Rakesh Ramachandran wrote: > Hi, > > I wanted to know how can I measure correlation starting from a fit and rotating the model around an axis with respect to the map. I tried calculating the centroid of the model and then rotate it using measure correlation but it did not work, the rotationAxis field was not taking the x,y,z position of the centroid of the model. > > Regards > Rakesh

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Structure editing
by George Tzotzos 02 Jul '14

02 Jul '14

I’m dealing with a X-ray model in which some of the residues are shown in two conformations. Is it possible to edit the structure keeping the higher occupancy conformation ONLY? Another question is whether it is possible to delete all waters but the selected ones (e.g. HOH molecules in the binding pocket that are conserved). I’ve been doing this manually using an editor and I wonder if there is better way of doing this. Thanks in advance for your advice Regards George

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suggested improvements
by Dougherty, Matthew T 02 Jul '14

02 Jul '14

1) first suggestion on the sym command the following is defined icosahedral symmetry I[,orientation] around center Example: i,n25 where orientation can be: 222 (default) - with two-fold symmetry axes along the X, Y, and Z axes 2n5 - with two-fold symmetry along X and 5-fold along Z n25 - with two-fold symmetry along Y and 5-fold along Z 2n3 - with two-fold symmetry along X and 3-fold along Z 222r - same as 222 except rotated 90° about Z 2n5r - same as 2n5 except rotated 180° about Y n25r - same as n25 except rotated 180° about X 2n3r - same as 2n3 except rotated 180° about Y In the chimera tool->higher order structure -> the icosahedral structure it defines similar orientations, assume in the same order. It would be helpful on the selections to include the sym syntax as part of the icosahedral structure text ie {222} xyz 2 fold {2n5} x 2 fold z 5 fold 2) second suggestion When reading an MRC file I occasionally see situations that make me question whether the file is EMDB complaint. It would be good to have the means to dump the MRC header, even if chimera refuses to read the file in its entirety. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Re: [Chimera-users] Attaching a Probe to Modify an Existing Amino Acid
by Eric Pettersen 02 Jul '14

02 Jul '14

Hi Shana, Well, you might be able to get away with just setting that atom's "name" attribute to "SD", but since you are writing Python code anyway and residues hold their atoms in a name-indexed structure, it would be better to do it the right way by removing the atom from the residue, renaming it, and putting it back. Assuming you have the CYS residue in a variable named 'cys': s = cys.findAtom("SG") cys.removeAtom(s) s.name = "SD" cys.addAtom(s) --Eric On Jun 19, 2014, at 11:25 AM, Shana Burstein <sburstei(a)haverford.edu> wrote: > Hi Eric, > I was able to move the CN atoms from the CN residue to the CYS residue and call it MSCN. I actually need it to be called MSCN in order for the modified residue to be recognized by a force field in an MD simulation. My only problem now is that the S atom of cysteine is labeled as "SG" and I need it to be called "SD." I know how to do this by going through the Tool menu, but is there a way to automate that? > > Thanks, > Shana > > > On Wed, Jun 18, 2014 at 2:35 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > Hi Shana, > If you were starting from scratch, the procedure to add the CN would probably be simpler by using chimera.molEdit.addDihedralAtom() to add the C and then the N at the appropriate bond length, angle and dihedral and then rename the residue with: r.type = "MSCN". Nonetheless, you have come a long way down the road with your script and probably would not prefer to start over from scratch! So let's suppose you have your two relevant Residue instances in variables named 'cys' and 'cn'. The code to do what you want would be: > > for a in cn.atoms: > cn.removeAtom(a) > cys.addAtom(a) > cys.type = "MSCN" > # empty residues are problematic in various parts of Chimera, so... > cn.molecule.deleteResidue(cn) > > If you don't know how to get the 'cys' and 'cn' variables but you know an atom specifier that selects each, you can use this code to set the variables: > > runCommand("sel atom-spec-for-cys") > cys = chimera.selection.currentResidues()[0] > runCommand("sel atom-spec-for-cn") > cn = chimera.selection.currentResidues()[0] > > There's a couple of further relevant things here. Strictly speaking, 4-letter residue names are not legal in PDB format (while there is a column where a 4th character could go, according to the format definition that column is supposed to be blank). Therefore if you export your modified structure to other software programs, they may or may not be able to handle the 4-character residue name without problems. Therefore I recommend you use the same residue name that the PDB uses for this moiety, 4CY (which can be found in the 3or0 entry). > Along the same lines, 4CY can actually be found in the SwissSidechain rotamer library plugin for Chimera (SwissSidechain - A database of non-natural side chains) and therefore if you install that plugin then the entire substitution process becomes a single command: swapnaa 4CY cysteine-atom-spec. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > On Jun 18, 2014, at 6:50 AM, Shana Burstein <sburstei(a)haverford.edu> wrote: > >> Hello, >> I am an undergraduate student at Haverford College and I am attempting to attach thiocyanate probes onto different sites along a protein by first replacing the existing amino acid with a cysteine and then by adding a C and N onto the S- of the Cys residue. I know it is possible to carry this out manually using Tools>Structure Editing>Modify Structure, but I am hoping to automate this process by calling an external .py script that will primarily contain a list of preexisting Chimera commands. >> >> I have been successful at converting the targeted amino acid to Cys using "swapaa," building a CN residue called MSCN (using the createMolecule.py as a guide), combining the two models into one ("combine selected close True") and forming a bond between the Cys S and CN C atoms ("bond"). >> >> At this point, I am seeking help in automating the renaming of the modified residue to MSCN. Currently, Chimera sees this residue as two different separate residues called CYS and MSCN. Is there a way to combine these two structures so that the label corresponds to MSCN and the residue number corresponds to CYS? >> >> Sincerely, >> >> Shana Burstein >> Haverford College '15 >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > >

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Making a hole in a volume
by Dieter Blaas 01 Jul '14

01 Jul '14

Hi, I am trying to make a small hole in a volume with 'erase octant' but either it cuts away some of the volume at the wrong place or the hole created is much bigger than the green box. Sometimes it does not do anything until I make the box bigger. What might I am doing wrong ? (chimera 1.6.2) Thanks, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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