- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] 3D printing a viral capsid
by Tom Goddard 22 Aug '14

22 Aug '14

Hi Jeremiah, The symmetry for your capsid is 222r, not 222. These both have 2-fold symmetry axes along x,y,z but they differ by a rotation by 90 degrees about z which puts the 5-fold symmetry axes in different locations. To figure out the right simmetry I used the Chimera Icosahedron Surface dialog (menu Tools / Higher-Order Structure) to show an icosahedral cage and then I try different standard orientations to find the one that matches. Tom On Aug 22, 2014, at 2:31 PM, Jeremiah Gassensmith wrote: > Many thanks. Using the OBJ did indeed work to get it into Blender (Freeware) to convert it to STL. > > Related to Tom’s suggestion I tried (before I emailed the listserv): > > >molmap #0 4 symmetry i,222 > > but I’m not sure why that didn’t work (that should be the right symmetry…?) > > molmap #0 4 sym biomt works, however. > > > > Again, Many thanks. > > Jeremiah > > > On Aug 22, 2014, at 4:27 PM, Tom Goddard <goddard(a)sonic.net> wrote: > >> Here’s the molmap capsid image. >> >> Tom >> >> <capsid.jpg> >> >> >> On Aug 22, 2014, at 2:25 PM, Tom Goddard <goddard(a)sonic.net> wrote: >> >>> Hi Jeremiah, >>> >>> The STL export of your virus capsid multiscale model is giving just one asymmetric unit and that is a Chimera bug. I’ll make a bug report and see if I can fix that. >>> >>> Here’s another suggestion about how to print it. Make a single density map for the entire capsid with the Chimera molmap command >>> >>> molmap #0 8 sym biomt >>> >>> This makes an 8 Angstrom resolution map using the asymmetric unit of the capsid PDB model #0 and uses the symmetry specified in the PDB file BIOMT remarks. I’ve attached an image of what it looks like. If you print on a single color printer this surface exported as STL is likely to work better than the Chimera Multiscale surfaces which may not be touching enough to hold together. Also it gives a better (and very different) appearance because it is single color. You can try different resolution values and see what works best. The resolution of 3d printers isn’t too good, so having too much detail doesn’t produce the best printed model. >>> >>> Tom >>> >>> >>> On Aug 22, 2014, at 10:33 AM, Hurt, Darrell (NIH/NIAID) [E] wrote: >>> >>>> Hi Jeremiah, >>>> >>>> I got a good import of your scene in Blender by exporting an OBJ from Chimera. Maybe give that a try. You can then convert to STL using Blender's tools. >>>> >>>> Hope it helps! >>>> Darrell >>>> >>>> >>>> From: Jeremiah Gassensmith >>>> Date: Friday, August 22, 2014 10:15 AM >>>> To: "chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>" <chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> >>>> Subject: [Chimera-users] 3D printing a viral capsid >>>> >>>> Hello >>>> >>>> I’m trying to produce an STL file from a model I have built in Chimera but it comes out incredibly deformed. I have created the model from a PDB file of a viral coat protein such that it is fully assembled into the proper capsid structure. You can see the model I’ve created here: >>>> >>>> https://dl.dropboxusercontent.com/u/9856122/CAPSID.py >>>> >>>> Problem is, when I export to STL and open in Blender I get a squished unrecognizable “clump” looking thing and not a beautiful sphere. Any help would be lovely! >>>> >>>> Thanks! >>>> Jeremiah >>>> >>>> _______________________________________________ >>>> Chimera-users mailing list >>>> Chimera-users(a)cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> >>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>> >>> >> >

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Generating surface for docking models
by fei.wu＠chem.utah.edu 22 Aug '14

22 Aug '14

Dear Chimera team, Is there a way of generating the surface for docking models from ClusPro so I can map electrostatic potential or coulombic potential on it? Since my docking models are composed of three enzymes (2 dimers and 1 monomer), I tried surfacing in "Multiscale Models"but it gave me a very low resolution surface. Thank you! Fei

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Intensity range shift
by Petr.Brazda＠seznam.cz 22 Aug '14

22 Aug '14

Hello, I would like to ask whether there is a possibility in Chimera to shift the intensity range. I have tomography data, which range from -32000 to 10000 in intensity. A would like to gradually erase parts of the tomogram with volume eraser but it is not possible because the intesity range does not start at zero. It is not possible to do the job with subregion selection. Is there a way to shift the intensity range? Petr

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Re: [Chimera-users] mmaker question
by Elaine Meng 21 Aug '14

21 Aug '14

Hi Joshua, If you are fine with CA atoms only, approach (B) may be easier than using the "rmsd" command, especially if the structures have different numbering and/or contain different numbers of residues. The problem with selecting and using "sel" in the command is that unless you picked atoms one by one, it isn't an ordered selection and you wouldn't necessarily get the desired pairing. If you get some ridiculous RMSD, that is definitely the problem. Instead you would need to use specification by residue numbers and atom names in the command line. Whereas mmaker figures out pairing for you, the "rmsd" (and "match") commands do not, and you have to specify the atoms in corresponding orders. For CA-only calculations, approaches (B) and (C ) both done correctly will give the same result. Command-line atom specification: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#basic> Elaine On Aug 21, 2014, at 11:22 AM, Joshua Broyde <jb3401(a)c2b2.columbia.edu> wrote: > Elaine, > Thanks for the help. I was looking for something like C, so I guess I will just select the C alpha atoms and get the RMSD. > > Sincerely, > Joshua Broyde > > ----- Original Message ----- > From: "Elaine Meng" <meng(a)cgl.ucsf.edu> > To: "Joshua Broyde" <jb3401(a)c2b2.columbia.edu> > Cc: chimera-users(a)cgl.ucsf.edu > Sent: Thursday, August 21, 2014 2:00:44 PM > Subject: Re: [Chimera-users] mmaker question > > Hi Joshua, > Not sure I understand the question. I'll try to answer some possible interpretations, but if I didn't answer your question, feel free to write back! > > (A) To use your own sequence alignment to define the residue pairing for superposition and RMSD calculation, just open your alignment, make sure both structures are associated, and then from the Multalign Viewer menu (the menu of the window showing the sequence alignment) choose Structure…Match. There are some additional options in the resulting GUI. You could use the pairwise alignment from a previous mmaker command with "show true", if that helps. > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> > > (B) To just calculate the RMSD of structures in their current positions WITHOUT moving them, again starting with an alignment in Multalign Viewer with both structures associated, use the mouse to draw a region (which could be a single box in the alignment, or multiple disjoint boxes if you use Shift-drag) then from the Multalign Viewer menu choose Info…Region Browser. The resulting dialog will show the RMSD for the region you defined with the mouse. > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/f…> > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> > > (C ) The above use the Multalign Viewer graphical interface, not commands, and use only CA atoms. There is also a "rmsd" command to calculate RMSD between 2 sets of atoms in their current positions without moving (it does NOT calculate the best-fit RMSD, just uses the current positions). It would be harder to use because now you have to specify all the atoms in the command, e.g. if the residue numbering is different in the two structures, you would have to list the residue ranges. You could specify any atoms common to both structures, not just CA atoms. > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html> > > 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 Aug 21, 2014, at 8:49 AM, Joshua Broyde <jb3401(a)c2b2.columbia.edu> wrote: > >> Hi again, >> I was wondering if the mmaker command had an option (or if there is some other way within chimera) of reporting the RMSD (as calculated by mmaker) of an alignment without actually superimposing one structure on the other. The reason that I am doing this that for a group of structures I can see with mmaker that they superimpose very well, but I want to show that when you compute the RMSD of those same structures when each is bound to a partner they are not quite as well aligned. >> In essence, what I want mmaker to do is not really realign the structures for me, but to calculated the RMSD of an alignment that I provide it. >> I looked at the mmaker command page but I couldn't seem to find an option for this. >> https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html >> >> Thanks again, and Chimera is a wonderful piece of software! >> >> Sincerely, >> Joshua Broyde >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

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mmaker question
by Joshua Broyde 21 Aug '14

21 Aug '14

Hi again, I was wondering if the mmaker command had an option (or if there is some other way within chimera) of reporting the RMSD (as calculated by mmaker) of an alignment without actually superimposing one structure on the other. The reason that I am doing this that for a group of structures I can see with mmaker that they superimpose very well, but I want to show that when you compute the RMSD of those same structures when each is bound to a partner they are not quite as well aligned. In essence, what I want mmaker to do is not really realign the structures for me, but to calculated the RMSD of an alignment that I provide it. I looked at the mmaker command page but I couldn't seem to find an option for this. https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html Thanks again, and Chimera is a wonderful piece of software! Sincerely, Joshua Broyde

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Match two small molecules with command line : "match"
by Jo Sourbron 19 Aug '14

19 Aug '14

Dear, I really appreciate the features that Chimera has (as I read them in yhe user's guide). Though there seem to be a problem: I want to match two small molecules (and in the future maybe more), but If I open the pdb files in Chimera and use the command line match, it says that there is missing an atom spec. Then I looked again in the user's guide and I noticed the "#" that they use. I don't know how what this "#" means. I just want to overlap the two structures and get a percentage of homology or something like that. That would be great. You can always contact me, kind regards, Jo Sourbron PhD Student Laboratory for Molecular Biodiscovery Department of Pharmaceutical and Pharmacological Sciences Katholieke Universiteit Leuven O&N2, Campus Gasthuisberg Herestraat 49, box 824 B-3000 Leuven, Belgium j.sourbron(a)gmail.com GSM. +32 474 94 84 17 TEL. +32 16 37 78 07 http://be.linkedin.com/pub/jo-sourbron/33/496/77a/

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Ligand Problem
by Marcus Fabiano A. Mendes 15 Aug '14

15 Aug '14

Hi, My Name is Marcus, and I am a huge fan of Chimera. Currently, I'm using Chimera to visualize p:MHC complex and it's electrostatic potential map. p:MHC occurs as an α chain composed of three domains - α1, α2, α3, β2 microglobulin and a ligand present in the groove. Chimera automatically recognizes the epitope as a ligand, since they have on average less than 10 amino acids. There's someway to make the Chimera don't recognizes this epitope as a ligand? A option to set the parameters that Chimera uses (ligand = <10 amino acids)? Thanks for All SincerelyMarcus Mendes

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Re: [Chimera-users] Volume viewer chimera
by Elaine Meng 15 Aug '14

15 Aug '14

On Aug 15, 2014, at 2:08 AM, Matteo Allegretti <maallegr(a)biophys.mpg.de> wrote: > Dear prof. Meng, > it would be possible in the future to have more than three panels on the > volume viewer of Chimera? > Thank you so much, > Matteo > -- > Matteo Allegretti > PhD candidate > Max Planck Institut für Biophysik > Max-von-Laue-Straße 3 > D-60438 Frankfurt am Main > Office: +49-69-6303-3015 Dear Matteo, If you mean showing the histograms of more than 3 datasets at the same time, you can already do that. In Volume Viewer menu, choose "Features… Data display options", and then in the resulting options you can increase the “Maximum number of histograms shown” from 3 to some bigger number. It’s better if you send Chimera questions and suggestions/discussion to the chimera-users(a)cgl.ucsf.edu address (CC’d here) instead of directly to me. There are other people who also answer the questions, and I might be gone or not know the answer. Thanks! 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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does chimara allow changing of the primary sequence of the protein?
by Marta Mikolajczak (BIO) 14 Aug '14

14 Aug '14

Dear Sir/Madam, I am a PhD student working for the University of East Anglia. I have just downloaded the Chimera software and I really like the look of it. So far I have found it very user friendly. I was wondering if the software allows incorporating changes into the protein structure? I am working on the mutant of my protein of interest. I have found, through experimental procedures, that when I mutate one residue it changes the properties of the protein. I was wondering if the effects I am seeing are due to changes in the protein structure. I would like to visualise it. I am not interested in generating crystal structure of the mutated protein or anything like that. I really would like to insert a different amino acid into the structure that already exist. I understand it might be incorrect but all I want to achieve is a "prediction". Would chimera software do that for me? Kind regards, Marta Mikolajczak

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Error with partial charge calculation during minimisation
by Ahir Pushpanath 13 Aug '14

13 Aug '14

Hey there, whenever I try to do a minimisation of a ligand in presence of protein, with a few residues selected as flexible , rest held as rigid, I get past the adding hydrogen box, but it always has a error saying it cant calculate partial charge for the first N-terminal residue, N atom , for example. If I try and delete that residue, it just moves up and says it cant do it for the second one. The PDB file seems fine, and I have opened in Discovery studio and seen it has partial charges assigned fine. Can you enlighten me on what maybe going wrong? I am using the latest build of Chimera. PDB is 1BW9 chain A (only one conformation chosen in multiple conformation residue positions). The ligand is the PPY inside. the flexible residues are all those 5A away apart from NAD. -- Dr. Ahir Pushpanath* PhD.* Senior Biologist, Johnson Matthey.

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Surface color by electrostatic potential
by roz orchidea 13 Aug '14

13 Aug '14

Dear all, I am trying to get some images of the electrostatic potential surface of my complex. But I have noticed that by using the same .dx file in chimera and vmd, I am getting different coloring results. Chimera gives more negatively charged areas. I used the -5 0 5 coloring for both. Is it a difference in reading the .dx files between the 2 software? I also think that Chimera colors each side chain by the avg charge. Is it possible to have a more detailed coloring of the surface according the charges? Thanks in advance, Alexandra

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Re: [Chimera-users] [chimera-dev] Feature request
by Elaine Meng 11 Aug '14

11 Aug '14

Dear Xavier, I personally don’t recommend the Chimera/Povray approach… my neon/conic suggestion is better-looking, but not as easy as the feature you request. There is limited programmer time, so I can’t say it will happen, but we can put it on the list of requests. You can enable showing backbone atoms at the same time as ribbon with command “ribbackbone” — then try displaying the carbonyls. You may also need to unchain (avoid drawing long bonds between different carbonyls, e.g. command: setattr m autochain 0). However, the default ribbon path is smoothed, so in some places the backbone atoms will appear to be floating away from the ribbon. You can try reducing that problem by using a different method to calculate the ribbon path, for example, with command: ribspline cardinal smooth strand …but see the manual for other command options and parameters. The cardinal spline tries to follow CA positions, so it is still possible you won’t be able to totally eliminate spaces between ribbon and C atoms. It may be necessary to show the C atoms as balls (slightly larger than stick-ends) to obscure the gapping. The ribbackbone and ribbon path issues are discussed in more detail here: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbo…> I hope this helps, Elaine On Aug 11, 2014, at 1:48 AM, F.Xavier Gomis-Rüth <xgrcri(a)ibmb.csic.es> wrote: > Dear Elaine & Eric, > thanks again for your and Eric's suggestions. The issue is that the POV-Ray rendering is not as attractive as the CHIMERA rendering. > Would it be possible to kindly and humbly request that this minor feature be implemented at a certain time point in a new version > of the program :-) ? > Another issue I have currently problems with: > it would be very helpful to be able to display the main-chain carbonyls sticking out from the ribbon at the right place. I tried with the > licorize option of the ribbon trace but it was not solving the problem. This is particularly helpful when representing e.g. metal-binding sites. > Thanks again for your help and dedication to constantly improve this fantastic program. > Best wishes, > Xavier > > On 1/8/14 9:11 PM, Elaine Meng wrote: >> A few caveats of the Povray approach: >> In my tests (current daily build), it always makes cylinders with the same aspect ratio regardless of whether I am showing the lines as dotted or dashed in Chimera. Also, it is hard to tell they are cylinders unless you make the linewidth fairly large. >> >> Elaine >> >> On Aug 1, 2014, at 11:28 AM, Eric Pettersen >> <pett(a)cgl.ucsf.edu> >> wrote: >> >> >>> Hi Xavier, >>> In addition to Elaine's neon suggestion, if when you save an image you change the rendering from "Chimera" to "POV-Ray" then any dashed or dotted lines will be converted into equivalent cylinders and spheres in the POV-Ray image. I've attached an image that shows how a distance looks. >>> >>> --Eric >>> >>> > > -- > <fxgr_signanew.jpg>

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huge electrostatic range for APBS
by Dennis N Bromley 07 Aug '14

07 Aug '14

Hi all, I have two proteins models from different points in an MD simulation. I colored the surface by Coulombic Surface Coloring, which ran AnteChamber and such. Then I ran APBS. When I color by the APBS data, they look more or less similar. But when I click the "Set full range" button, the kBTe unit range on one is about +-3 and the unit range on the other is about +-300. Any ideas why one would be so much larger? Or am I misinterpreting something? Both were run with exactly the same parameters, all default except for temperature = 310. thanks- -denny-

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"match" command with serialNumber specifier
by Hiroyuki ISOBE 06 Aug '14

06 Aug '14

Dear Sir: I would like to run “match” with two models by using serialNumber specifiers but fail to specify multiple atoms. I would like to match the following sets of atoms: SerialNumber=14,31,91,74 for model #0 and SerialNumber=74,91,31,14 for model #1 How should I include multiple atoms in the command line? The command for one atom, match #1/serialNumber=14 #0/serialNumber=74 works nicely, but I cannot include, for instance, two atoms with match #1/serialNumber=14,31 #0/serialNumber=74,91 or match #1/serialNumber=14 31 #0/serialNumber=74 91 Could you please let me know the correct commands for this purpose? Thank you for your kind help in advance. Sincerely, Hiroyuki -- Hiroyuki ISOBE Advanced Institute for Materials Research (WPI-AIMR) Department of Chemistry Tohoku University Sendai, 980-8578, Japan Tel: +81-(0)22-795-6585 Fax: +81-(0)22-795-6589 Email: isobe(a)m.tohoku.ac.jp Homepage: http://www.orgchem2.chem.tohoku.ac.jp

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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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