- Chimera-users - RBVI Mailing Lists

MatchMaker algorithm
by 陈柳青 15 Oct '16

15 Oct '16

Respected Sir/Madam The ucsf matchmaker algorithm is "Needleman-Wunsch" and "Smith-Waterman", but other program use SSM algorithm, such as ccp4mg, cuemol et al., can chimera add SSM algorithm? and whether these algorithm will affect results differently? sincerely Liuqing chen -- Liuqing Chen School of Life Science & Biotechnology Minhang Campus Shanghai Jiao Tong University No. 800 Dongchuan Road Shanghai 200240 P.R. China Tel: +86 21 34207247

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MD trajectory analysis
by George Tzotzos 13 Oct '16

13 Oct '16

My task is to identify ligand interactions with protein residues throughout an MD trajectory. I thought of something along the lines sel ligand z<3.5 #for vdW interactions, etc. I don’t think this can be done using the MD movie interface but I may be wrong. I then tried the following: 1. sel protein/hold selection steady 2. sel ligand 3. calculate occupancy (MD Movie/Analysis) 4. Chimera/select/clear selection 5. turned the Volume Viewer to mesh/level2. What I obtained is a mesh grid enclosing solid surfaces (see attached snapshot). I’m not able to get rid of these surfaces? I think that the problem ma be in step 2 above (sel :ligand). My ligand is N,N-Diethyl-meta-toluamide. Should I select the aromatic ring part separately of the amide part, run the above process and then repeat selecting the amide part? I also tried MD movie/Analysis/Residue interaction network, first selecting the ligand. The results I obtained are not satisfactory. Is there a better way of dealing with my problem? Thanks in advance for your kind help George

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Re: [Chimera-users] question
by Jaynes, Jesse 12 Oct '16

12 Oct '16

Hi Folks: I am having difficulty in converting C-terminal carboxyl to C-terminal amide on a beta sheet of 16 amino acids in length. When I try to get the complete amino acids displayed, it doesn't work. It just displays the main peptide cylinder. Thanks for your help. Jesse Jaynes On Thu, Oct 6, 2016 at 6:11 PM, Jaynes, Jesse <jjaynes(a)mytu.tuskegee.edu> wrote: > Hi Folks: > > I am interested in generating a 23 amino acid peptide with several > ornithines present. Is it possible? If not can I construct it with > glutamine as a replacement for ornithine and then just take the carbonyl > group and replace the oxygen with 2 hydrogens. > > I just renewed my registration. > > Thank You, Jesse Jaynes > > On Thu, Oct 6, 2016 at 3:22 PM, Jaynes, Jesse <jjaynes(a)mytu.tuskegee.edu> > wrote: > >> Hi Folks: >> >> I am interested in generating a 23 amino acid peptide with several >> ornithines present. Is it possible? If not can I construct it with >> glutamine as a replacement for ornithine and then just take the carbonyl >> group and replace the oxygen with 2 hydrogens. >> >> Thank You, Jesse Jaynes >> > >

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Creating a dummy atom on a defined position
by Subha Kalyaanamoorthy 11 Oct '16

11 Oct '16

Hi There, Wondering if there is a way to create a dummy atom on a specified position(xyz coords) using a chimera command line? Thanks, Subha -- Dr. Subha Kalyaanamoorthy Post Doctoral Fellow Faculty of Pharmacy and Pharmaceutical Sciences University of Alberta Edmonton, Canada.

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Computing 'basic' structure characteristics
by Healey, Joe 11 Oct '16

11 Oct '16

Hi again Chimera Team, I have 2 questions, one specific and one quite general. If you see the emails below, I was speaking with Jaime about computing basic structure characteristics (pKa, net surface charge, proportions/predominance of 2ary structure etc). The general question I have is what suggestions might you have for functions within chimera capable of computing any or all of these features? (ideally commandline based so that I can run this over many PDB structures). The specific question that pertains to the below is that Jaime mentioned each residue has an int value that corresponds to a particular structure designation, ints from -1 to 6. Could you let me know what the correspondence is between these values and actual structure? Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> ________________________________ From: Jaime Rodríguez-Guerra <jaime.rodriguezguerra(a)uab.cat> Sent: 08 October 2016 09:55 To: Healey, Joe Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers Hi again Joe! No problem at all; I'll be pleased to help you. For charges, I think Chimera can calculate them as part of the Surface/Binding analysis> Dock Prep wizard. You also have some information about 2nd structure inside chimera.Residue objects, specifically ssId attribute. However, these are int values, and I don't really know which ss is each (ranging from -1 to 6, as I have observed). For pKa, you can use PropKa (https://github.com/jensengroup/propka-3.1) and then I guess you'll be able to get the pI somewhere around the code. I've been designing a GUI to use this in Chimera, but it's not yet ready... Sorry about that! I don't know if you need anything else... but I think the Python community will have you covered one way or another! BioPython.PDB might be useful too (http://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ) Cheers, Jaime. 2016-10-06 15:57 GMT+02:00 Healey, Joe <J.R.J.Healey(a)warwick.ac.uk<mailto:J.R.J.Healey@warwick.ac.uk>>: Hi again Jaime, Hope you don't mind but I had a couple of questions for you. You may have figured out from all the previous correspondance that I have a load of protein structure simulations. The RMSD script you helped me with was to sort of 'broadly' gauge whether the simulations looked realistic or not. For some of them, I'd like to build up a chart of their tertiary structure properties based on the simulations. Things like charge/hydrophobicity, isoelectric point, 2ndary structure dominance and so on. Could I ask you for any advice you might about what tools are available to analyse PDBs? I'm sure chimera is probably capable of it too. I've mostly found webservers at the moment for specific tasks, but I'd like to do most of the analysis locally. My group is full of bioinformaticians, but I'm the only one who really looks at proteins so I need the advice of a computational chemist I think! Cheers, Joe Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620<tel:%2B44%20%280%29%207536%20042620> | Email: J.R.J.Healey(a)warwick.ac.uk<mailto:J.R.J.Healey@warwick.ac.uk> Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> ________________________________ From: Healey, Joe Sent: 23 September 2016 11:51:40 To: Jaime Rodríguez-Guerra Cc: Eric Pettersen; chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers Not at all! Much appreciated, as I think I mentioned, this is my first go at writing anything remotely complex in python (and not a bad turn out for about a week I don't think...) A lot of the mess comes from copying functional bits from StackOverflow in the interests of just getting it working first, and making it pretty second as I'm sure you can appreciate (you'd hate to see my LaTeX preamble)! Not needed to close the file with 'with' is useful to know (takes some of the headache out of knowing where to place the close). I'll certainly make the tidy ups you've suggested, for my own learning. Thanks again, Joe :) Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620<tel:%2B44%20%280%29%207536%20042620> | Email: J.R.J.Healey(a)warwick.ac.uk<mailto:J.R.J.Healey@warwick.ac.uk> Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> ________________________________ From: Jaime Rodríguez-Guerra <jaime.rodriguezguerra(a)uab.cat<mailto:jaime.rodriguezguerra@uab.cat>> Sent: 23 September 2016 10:56:38 To: Healey, Joe Cc: Eric Pettersen; Jaime Rodríguez-Guerra; chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers Hi Joe! You're welcome! Glad to see you got it working. I've reviewed your code and would want to point out some details that might be helpful to you in the future, though. These are mostly style-related things, but those will contribute to a cleaner reading experience! 1. You don't need backslashes if you're inside parenthesis. So, in all those parse_argument lines, you can safely delete them. Related to this, you can wrap imports with parenthesis, so that backslashes are not needed. 2. Tuple unpacking does not need parenthesis in you're dealing with 1D-tuples. Only needed if you are dealing with more than one dimension (ie, (animal, fruit), sport = [['tiger', 'pear'], 'soccer'] 3. Since you are opening files with the "with" context manager, you don't need to manually close the file later. It's closed automatically as soon as you leave that with block. 4. Lines 166-170 could be replaced with a (cleaner, but not necessarily more performant) glob.glob() call. Check it out to see if it satisfies your requirements. 5. While you are at it, take a look at the PEP8 docs and the Google Python style guide. You don't need to follow all the rules, but they are really helpful in bringing consistency to your own style! That's it! Hope you don't mind these pieces of advice :) Cheers, Jaime. 2016-09-23 11:27 GMT+02:00 Healey, Joe <J.R.J.Healey(a)warwick.ac.uk<mailto:J.R.J.Healey@warwick.ac.uk>>: > That was exactly what I was after thanks! I figured the object orientation > should provide that somewhere but was barking up slightly the wrong tree! > > > Thank you all for all your help - definitely wouldn't have been able to do > it without you! > > > If it's of any interest, or it helps for any future questions where you > might want to refer back to code segments, I've put the > more-or-less-finished script in this paste: > > > http://pastebin.com/xJNSWJGq > > > Joe Healey > > > M.Sc. B.Sc. (Hons) > PhD Student > MOAC CDT, Senate House > University of Warwick > Coventry > CV47AL > Mob: +44 (0) 7536 042620<tel:%2B44%20%280%29%207536%20042620> | Email: J.R.J.Healey(a)warwick.ac.uk<mailto:J.R.J.Healey@warwick.ac.uk> > > Jointly working in: > Waterfield Lab (WMS Microbiology and Infection Unit) > and the Gibson Lab (Warwick Chemistry) > > Twitter: @JRJHealey | Website: MOAC Page > ________________________________ > From: Eric Pettersen <pett(a)cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>> > Sent: 22 September 2016 20:54:35 > To: Jaime Rodríguez-Guerra > Cc: chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>; Healey, Joe > Subject: Re: [Chimera-users] Recursive structure matching and acquisition of > descriptive numbers > > Thanks Jaime — exactly right. I realized that the “atoms1, atoms2” in my > original example didn’t really give any indication of which atoms were > which, which is why in my later examples I changed to "simAtoms, refAtoms”, > so it’s actually “atoms2” that are the reference atoms. > > —Eric > >> On Sep 22, 2016, at 11:45 AM, Jaime Rodríguez-Guerra >> <jaime.rodriguezguerra(a)uab.cat<mailto:jaime.rodriguezguerra@uab.cat>> wrote: >> >> Hi! >> >> Since you are getting lists of atoms back, you only need to do some >> attribute access (rather than method calling)! >> >> Every chimera.Atom object has an attribute called molecule: a >> reference to its parent chimera.Molecule. chimera.Molecule objects >> have an attribute called 'name', but sometimes this is not very >> informative (depends on your input), so you need to resort to the pdb >> filename, stored in the first element of the openedAs tuple. >> >> In code, this looks like this: >> >> for atoms1, atoms2, rmsd, fullRmsd in match(CP_BEST, [ref, sims], >> defaults[MATRIX], "nw", defaults[GAP_OPEN], defaults[GAP_EXTEND]): >> molecule1 = atoms1[0].molecule # any atom from the list will do >> molecule2 = atoms2[0].molecule >> print molecule1.name<http://molecule1.name>, "\t", molecule2.name<http://molecule2.name>, "\t", rmsd # >> molecule1.openedAs[0] will also work here >> >> I don't know if atoms1 comes consistently from the reference molecule, >> but I'd guess it does. >> >> Hope it helps! >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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Chimera using problem
by Chonghua Ren 11 Oct '16

11 Oct '16

Dear there, I am learning how to use Chimera now, I like it so much and find it is so awesome. I have one question, if I want to input a DNA sequence like ID "1d86", how can I transfer the DNA sequence to PDB format? Another question, how can I know protein and DNA interaction using this software? Thank you so much! Best wishes, Chonghua Ren

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Assisstance to claculate RMSD value
by Shreyas Iyer 08 Oct '16

08 Oct '16

Respected Sir/Madam, I wanted to know how to calculate RMSD values between any 2 homology models of a protein with the help of USCF Chimera. Please guide me as soon as possible. Awaiting a positive reply. Yours Sincerely, Shreyas Iyer

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fit in map and multimodel pdbs
by Martin Lawrence 07 Oct '16

07 Oct '16

Dear Chimera Users, I have a pdb file for an entire virus (biological assembly) that I can read into Chimera just fine, as either a multimodel PDB with 60 different models, or as a PDB lacking model and endmdl cards, but with the atom number of the multi-model pdb preserved. The model is placed very close to the density for the virus in a tomogram. When I use the fit in map command, the single model pdb moves nicely by a couple of nm and a few degrees into the tomogram density. For the multimodel map I must first use the combine command in the model panel to combine the 60 differernt models, but that then also moves nicely into the density. However, in both cases, when I try to write out the slightly rotated/translated coordinates to a PDB file, I wind up with a semi-corrupted PDB file containing **** in many locations, especially for the last half of the file. Since the virus is pseudo T=31 with 18 chains in the viral asu, the pdb model has more than 2 million atoms and 1048 chains; the chains obviously cannot be uniquely identified with a single letter, the atom numbers exceed the the allowed format, and residues are renumbered and then also exceed the allowed format. I can fix this by hand to some extent, and could write a jiffy to put it back into the multiple model format, but feel like there is a more elegant solution to this problem already embedded in Chimera. Preferably one that will allow high throughput down the road. Any advice would be appreciated! Thanks, Martin Martin Lawrence Department of Chemistry and Biochemistry Montana State University Bozeman, MT 59717 USA

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question
by Jaynes, Jesse 06 Oct '16

06 Oct '16

Hi Folks: I am interested in generating a 23 amino acid peptide with several ornithines present. Is it possible? If not can I construct it with glutamine as a replacement for ornithine and then just take the carbonyl group and replace the oxygen with 2 hydrogens. Thank You, Jesse Jaynes

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Split view feature
by Markus Heller 04 Oct '16

04 Oct '16

Hi all, Not sure split view is the proper term for what I'm looking for but here goes: I want to compare to structures of two proteins bound to their respective ligands, and I do NOT want to do this as overlay. What I want is a split screen or split view in the Chimera main window, where one structure is displayed on the left, and the other on the right. Movements (rotation, translation etc.) would be synchronized between both windows, whereas other functionality such as Zone select, find Hbonds etc. would not. Is such a feature available for the current release, or is it planned for ChimeraX? Thanks and Cheers Markus

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Laptop to run Chimera
by Christianson, David T 04 Oct '16

04 Oct '16

Good afternoon, I would like to purchase a laptop for Chimera use, I am open to either an Apple or Windows based computer. Might any of you have a model that you would suggest? Thanks very much for your time, Dave

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comparing maps with different orientations
by Cathy Lawson 03 Oct '16

03 Oct '16

Dear USCF Chimera Team, I’m looking for suggestions on how to go about the following: For the EMDataBank map challenge we have sets of EM maps of the same molecule that have been submitted in different orientations. We’d like to automate production of images for each set of maps with a common orientation/scale so that they can be readily compared. Models fitted to each map are in principle available, so this could be part the process if needed (e.g., to define transformations between map positions/orientations). Many thanks, Cathy ****************** Catherine Lawson, Ph.D. EMDataBank, RCSB PDB Center for Integrative Proteomics Research Rutgers University cathy.lawson(a)rutgers.edu USA +1 (848) 445 5494 http://emdatabank.org

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build a homotetramer based on crystallographic symmetry
by Shuanghong Huo 30 Sep '16

30 Sep '16

Dear All, Can UCSF Chimera build a homotetramer from a dimer based on crystallographic symmetry? Thanks, Sharon Huo Clark University

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3D to 2D
by Sameer K Singh 30 Sep '16

30 Sep '16

Hi, I was wondering if it's possible to extract information from 3D plots in Chimera and render them as 2d plots.Specifically I'm trying to extract information from a .bild file displayed in chimera and display it as a 2D plot of some kind in an external program (eg: excel) Thank you very much. Best, Sameer ________________ Sameer Singh, PhD Albert Einstein College of Medicine 1300 Morris Park Avenue New York, NY - 10461 Phone: 718-430-2048 Cell: 917-848-9319

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differentiating lower and upper case chain ID's
by Melissa Jurica 29 Sep '16

29 Sep '16

Hi- Is it possible to differentiate between chain ID’s that are in upper vs. lower case (i.e. A vs. a) in the command line? Spliceosome complexes have too many chains (ex. 5GM6). Thanks, Melissa

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Surface area list
by esserlo＠helix.nih.gov 28 Sep '16

28 Sep '16

Hi, with the help of "split #0" I created 10 segments of my protein and calculated the surface of each fragment. I can go to tools and measure volume and area but I'd prefer to write out the results as a file. Can Chimera do this ? I am asking because I intend to do more complex things than just 10 surfaces and it would be rather tedious if not impossible to do all this by hand. Thanks for any advice. Lothar

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Problem with running Chimera
by Patty Tran 27 Sep '16

27 Sep '16

Hello! I installed two versions of Chimera (Microsoft Windows 64-bit chimera-1.11.2-win64.exe <https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=win64/c…> and Microsoft Windows 64-bit chimera-1.11-win64.exe) <https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=win64/c…> I have only been able to run the program once and that was when I clicked "start program" after installing the 1.11 version. I have been unable to find the Chimera desktop icons and the program itself in the list of programs. I thought I could find the programs under my C:/Program Files/Chimera but there are no folders. Could someone provide instruction on how to uninstall the programs and install them so I could find and use the program easily? Thank you. Patricia

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Measuring angles and distances between planes defined by two aromatic rings
by George Tzotzos 26 Sep '16

26 Sep '16

Having generated a 100ns trajectory, I’m interested in measuring the time evolution of the distance between to aromatic ring centroids as well as the angle between the planes of these two rings. The idea is to determine if I’m dealing with pi-pi stacking interactions. I’ve check past correspondence and tried various permutations of commands to no avail. Maybe my best option is to do this for selected snapshots and define for each snapshot two centroids (e.g. c1 and c2) and measure the distance c1 c2. I haven’t managed to find a solution for measuring the angles between the two planes defined by the ring atoms. I’d appreciate any suggestions on possible solutions to the problem described above. I’m attaching a snapshot of measuring distances between two atoms (not really a good solution). Thanks in advance George

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Interpolate colors in Morph after Color zone
by Haselbach, David 26 Sep '16

26 Sep '16

Hi everyone, Want to make a movie of a movement of a single domain in my complex through morphing through several cryo EM densities. However as it is very complex I wanted to color the domain of interest. I did so with color zone and got a nice result for all the intermediate states. However as soon as I start morphing the color is gone even though interpolate colors is on. Is there are trick to achieve that? I tried segmenting the map and then interpolating through the segmented maps which works in principle fine but I don't really like the edge that is created by the segmentation. Kind regards David Dr. David Haselbach Max-Planck-Institute for biophysical Chemistry Department for structural Dynamics Am Fassberg 11 37077 Germany Tel. +495512011302

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segmentation and resolution
by Kristin Parent 23 Sep '16

23 Sep '16

To whom it may concern, I am currently working on segmenting a high resolution cryo-EM map (~4Å by the ³gold standard FSC²) to phase crystallography data. After the segmentation, my colleague doing the phasing tells me that map appears more like 12Å resolution and I am worried I am doing something wrong during the process and somehow distorting my original data. I believe the 4Å of the original map based on structural features that I can clearly see. And the segmented density does not appear as defined. Therefore it appears that there has been some changes. In order to begin the process, I did some manipulations before I started. This is an icosahedral virus map created through Auto3dem. I am only using an small quadrant of the original map, and since it was in pif format originally, I used proc3d to convert to mrc and invert the contrast to be compatible with segger. Before segmentation the map visually looked the same as the original pif map when both were displayed in chimera. The procedure I followed after segmentation was: "Save selected regions to .mrc file... save density map masked by the selected <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html> segmentation regions to an MRC file (map dimensions set to the minimal box containing the regions)². I have made sure that the correct binning has been applied during segmentation. Any help would be much appreciated. Kristin -- Kristin N. Parent, Ph.D. Assistant Professor Dept. of Biochemistry and Molecular Biology Michigan State University 603 Wilson Road Room 519 Biochemistry Building East Lansing, MI 48824 Office phone: (517) 432-8434 https://kparentlab.natsci.msu.edu/

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Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers
by Jaime Rodríguez-Guerra 23 Sep '16

23 Sep '16

Hi! Since you are getting lists of atoms back, you only need to do some attribute access (rather than method calling)! Every chimera.Atom object has an attribute called molecule: a reference to its parent chimera.Molecule. chimera.Molecule objects have an attribute called 'name', but sometimes this is not very informative (depends on your input), so you need to resort to the pdb filename, stored in the first element of the openedAs tuple. In code, this looks like this: for atoms1, atoms2, rmsd, fullRmsd in match(CP_BEST, [ref, sims], defaults[MATRIX], "nw", defaults[GAP_OPEN], defaults[GAP_EXTEND]): molecule1 = atoms1[0].molecule # any atom from the list will do molecule2 = atoms2[0].molecule print molecule1.name, "\t", molecule2.name, "\t", rmsd # molecule1.openedAs[0] will also work here I don't know if atoms1 comes consistently from the reference molecule, but I'd guess it does. Hope it helps!

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Saving scenes
by Tom Goddard 22 Sep '16

22 Sep '16

Hi Josh, Chimera session files (menu File / Save Session) save the data, views, colors, display styles, what is hidden and shown. The savepos and reset commands save and restore the positions of models and clip planes and view direction and zoom, just in memory (e.g. “savepos view1”, “reset view1”). Positions saved this way are also saved in sessions so after reloading a session you can use the reset command to get those positions back. Savepos does not save the colors, display styles, or what is hidden and shown. “Scenes” are created by the “Animation” tool (menu Tools / Utilities / Animation) and the “scene” command and include positions, camera view, colors, display styles, what is hidden and shown. Scenes try to capture exactly how the scene looks so they are like sessions but no file is used (although the are preserved in session files). So to save the current scene use command “scene s1 save” and to restore it “scene s1 reset”. Like savepos/reset you can save as many scenes as you want with different names. Scenes are a more recent feature and are not completely reliable — they don’t record everything and sometimes the cause errors saving sessions. Tom > On Sep 22, 2016, at 5:38 AM, Broyde, Joshua E. wrote: > > Dear Tom, > I hope you are well. I was wondering how to save a particular view (i.e. with specified zoom, atoms displayed and angle of view) in Chimera? Currently, I simply save this as a different session, but I was wondering if there is a better or easier way? > > Josh >

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Re: [Chimera-users] Chimera-users Digest, Vol 161, Issue 19
by Healey, Joe 22 Sep '16

22 Sep '16

Ah yes now I see. mmaker is what I want. I've figured out the appropriate syntax for the command I'd want to execute in chimera syntax I think. In the code snippet below, it seems to me I have 2 options? I can synthesise a string and iterate the mmaker function in chimera syntax with something like: chimera.openModels.open(top_hit, type="PDB") # Open model structures for model_path in model_list: chimera.openModels.open(model_path,type="PDB") print("Opened: " + model_path) rmsd_file = '{0}.tsv'.format(rmsd) with open(rmsd_file, "a") as rmsd_output_file: for j in len(model_list): match_cmd = 'mmaker #0 #{0} alg nw iter false'.format(j) runCommand(match_cmd) # <somewhere in here retrieve the rmsd and append to a result file> or the other option would be to do the above but avoiding the string synthesis step with something like: chimera.module.mmaker() If the module can be accessed directly? If so which module is the mmaker function within? Though I still don't know how to access the RMSD value from the mmaker function in either of these manners. Would executing mmaker in either such way return a tuple or list where the RMSD is a particular index? Looking at your Match script the rmsd was the 3rd value of the tuple in the line: atoms1, atoms2, rmsd = match(CP_SPECIFIC_SPECIFIC, [(c1, c2)], defaults[MATRIX],"nw", defaults[GAP_OPEN], defaults[GAP_EXTEND],iterate=defaults[ITER_CUTOFF])[0] Would the same be true for mmaker? (Sorry to ask so many questions in one go. I don't know what your policy is on whether all related questions should be in the same issue, or whether I should be raising separate ones) Thanks again for all your help Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> ________________________________ 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: 20 September 2016 19:30 To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 161, Issue 19 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: Recursive structure matching and acquisition of descriptive numbers (Eric Pettersen) ---------------------------------------------------------------------- Message: 1 Date: Tue, 20 Sep 2016 11:30:38 -0700 From: Eric Pettersen <pett(a)cgl.ucsf.edu> To: "Healey, Joe" <J.R.J.Healey(a)warwick.ac.uk> Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers Message-ID: <30002D29-1B25-4596-8868-EB3370B72E42(a)cgl.ucsf.edu> Content-Type: text/plain; charset="windows-1252" Hi Joe, I guess the first thing is that the command equivalent for MatchMaker is ?matchmaker? or ?mmaker?, not ?match?. The ?match? command is for when you know a priori the exact set of atoms you want matched in the two structures. ?matchmaker? is for when you let Chimera figure out the set of atoms to use based on the sequences and secondary structure. The documentation for the matchmaker command is here: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html#opti… <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html#opti…> I looked at your script and didn?t see anything obviously wrong. What exactly isn?t working? And unfortunately the answer is no, you can?t run a GUI operation and easily find the command equivalent. ChimeraX will have that capability though. ?Eric > On Sep 20, 2016, at 5:07 AM, Healey, Joe <J.R.J.Healey(a)warwick.ac.uk> wrote: > > Hi again, > > I'm making decent headway with the problem I mentioned before with Jaime's help and the use of pychimera. I'm down to the nitty-gritty of doing the actual RMSD/Match function alignment though and could use a bit more information. > > Is there are resource with more information on the commandline implementation of match anywhere other than the link below? > > https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html#options <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html#options> > > I took a look at Eric's suggestion of the match.py script here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html> > > But I can't quite unwrap the options specified in the command for my uses. > > Perhaps another way to ask this is, can I run a command in GUI chimera, and find the EXACT command that was executed? > > I've put the semi-complete script in pastebin here http://pastebin.com/6k9cew55 <http://pastebin.com/6k9cew55> incase it gives you some indication of what I'm attempting to do. > > Many thanks > > > Joe Healey > > > M.Sc. B.Sc. (Hons) > PhD Student > MOAC CDT, Senate House > University of Warwick > Coventry > CV47AL > Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk <mailto:J.R.J.Healey@warwick.ac.uk> > > Jointly working in: > Waterfield Lab <http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) > and the Gibson Lab <http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) > > Twitter: @JRJHealey <https://twitter.com/JRJHealey> | Website: MOAC Page <http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> > From: Greg Couch <gregc(a)cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu>> > Sent: 08 September 2016 22:43:55 > To: Healey, Joe; chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB > Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers > > chimera --nogui can't access graphics. Headless chimera has software OpenGL rendering, so it can be used to create images. Make sure to use the windowsize command to set the size of the framebuffer. Don't know if pychimera cares. > > -- Greg > > On 09/08/2016 11:53 AM, Healey, Joe wrote: >> Brilliant, that sounds like the most likely option. I had stumbled across pychimera a couple of days ago while trying to find out if chimera could simply be imported as a module. I initially steered away from it as I don't have sudo rights for the server where I'm trying to set all this up (couldnt run pip), but I've since sorted it with our sysadmin. >> >> On a related point, is running chimera with --nogui equivalent to running headless chimera? I'm just wondering if pychimera is happy with either >> >> >> Joe Healey >> >> >> M.Sc. B.Sc. (Hons) >> PhD Student >> MOAC CDT, Senate House >> University of Warwick >> Coventry >> CV47AL >> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk <mailto:J.R.J.Healey@warwick.ac.uk> >> >> Jointly working in: >> Waterfield Lab <http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) >> and the Gibson Lab <http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) >> >> Twitter: @JRJHealey <https://twitter.com/JRJHealey> | Website: MOAC Page <http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> >> From: Greg Couch <gregc(a)cgl.ucsf.edu> <mailto:gregc@cgl.ucsf.edu> >> Sent: 07 September 2016 19:49:19 >> To: Healey, Joe; chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB >> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers >> >> Yes, Chimera's Python code is only "warrantied" to work with its own Python. See question 3b of the Chimera Programming FAQ,https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b <https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b>, for how to install other software into Chimera. Other parts of the FAQ may help you too. >> >> That said, Jaime Rodr?guez-Guerra took my previous comments on this subject, http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html <http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html>, and came up with pychimera, https://pypi.python.org/pypi/pychimera <https://pypi.python.org/pypi/pychimera>. I haven't checked to see how it handles all of my caveats, and it can't completely without using a modified Python, but I suspect that it would be good enough for you. >> >> HTH, >> >> Greg >> >> On 09/07/2016 07:36 AM, Healey, Joe wrote: >>> Hi Eric, >>> >>> That looks good thank you. I think I'm going about this slightly the wrong way after some investigation however. >>> >>> Am I right in thinking that chimera can't be imported in to python inside a normal bash shell, and rather it must be done the other way round? So file manipulation and such must be done by calls to the system from within the chimera python shell, rather than a python interpreter calling chimera modules in? >>> >>> It certainly makes the chimera steps I plan to do much easier, but I was going to include it in a pipeline with some other programs and it makes that a little more taxing (though not insurmountable!). >>> >>> Additionally, I plan to invoke this inside a script on a headless linux box (hence why running it through a python script was ideal), so whatever solution I use will need to be 'command line friendly'. >>> >>> In effect all I need is the actual algorithm for the matching process to be accessed somehow from a python script. >>> >>> Do you have any advice about how best to proceed? >>> >>> Many thanks, >>> >>> Joe Healey >>> >>> >>> M.Sc. B.Sc. (Hons) >>> PhD Student >>> MOAC CDT, Senate House >>> University of Warwick >>> Coventry >>> CV47AL >>> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk <mailto:J.R.J.Healey@warwick.ac.uk> >>> >>> Jointly working in: >>> Waterfield Lab <http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) >>> and the Gibson Lab <http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) >>> >>> Twitter: @JRJHealey <https://twitter.com/JRJHealey> | Website: MOAC Page <http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> >>> >>> From: Eric Pettersen <pett(a)cgl.ucsf.edu> <mailto:pett@cgl.ucsf.edu> >>> Sent: 31 August 2016 18:23 >>> To: Healey, Joe >>> Cc: chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> >>> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers >>> >>> Hi Joe, >>> This old chimera-users post has a Python script attachment that demonstrates how to call the underlying MatchMaker function to get the RMSD value programmatically. The mailing list gives the attachment a ?.bin? extension but it?s really a .py file. Just change the extension if you need to. Let me know if you have any questions about how to adapt the script to your needs? >>> >>> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html> >>> >>> ?Eric >>> >>> Eric Pettersen >>> UCSF Computer Graphics Lab >>> >>>> On Aug 31, 2016, at 3:02 AM, Healey, Joe <J.R.J.Healey(a)warwick.ac.uk <mailto:J.R.J.Healey@warwick.ac.uk>> wrote: >>>> >>>> Hi, >>>> >>>> I have several hundred structure simulations that were performed on our HPC resource. Each simulation has approximately 5 models associated with it. I also have HMM model homologies for each of these proteins. >>>> >>>> I would like to use chimera's matchmaker function to compare the simulated structured to their nearest 'real' counterpart with a resolved structure. In order to do this I plan to script chimera to pull in the simulated models as well as the near homolog and then run the matchmaker algorithm. >>>> >>>> My question is: can the RMSD value that is returned in the reply log be 'accessed directly' such that for each match that is performed, I can obtain the RMSD and thus a ranking for the best fitting structures - or will it require parsing the reply log? >>>> >>>> Thanks >>>> >>>> Joe Healey >>>> >>>> >>>> M.Sc. B.Sc. (Hons) >>>> PhD Student >>>> MOAC CDT, Senate House >>>> University of Warwick >>>> Coventry >>>> CV47AL >>>> Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk <mailto:J.R.J.Healey@warwick.ac.uk> >>>> >>>> Jointly working in: >>>> Waterfield Lab <http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) >>>> and the Gibson Lab <http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) >>>> >>>> Twitter: @JRJHealey <https://twitter.com/JRJHealey> | Website: MOAC Page <http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey>_______________________________________________ >>>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >> > >

2 6

Two open positions on molecule visualization and virtual reality in Paris
by baaden＠smplinux.de 21 Sep '16

21 Sep '16

Dear Colleague, It's already 2,5 years since Faraday discussion #169. I hope this message finds you well. Because of your interest for molecular visualization, I thought I share the following in the hope you can circulate it, or even direct candidates towards me :) Thanks in advance! We have two open positions in Paris, France, both relating to molecule and network visualization developments in Unity3D, and one specifically to VR. We are looking to hire ASAP and funds are available. The first position is for a postdoc on Development and Application of a Virtual Reality Immersive Modelling Platform for Enabling Drug Discovery. You can find an html version at [1] and PDF at [2]. The second position is for an engineer (or postdoc) on Computational Analysis, Visualization and Modeling of Redox Signaling Networks. You can find an html version at [3] and PDF at [4]. Thank you, Marc [1] http://www.baaden.ibpc.fr/ns16/pdoc1.html [2] http://www.baaden.ibpc.fr/ns16/pdoc1.pdf [3] http://www.baaden.ibpc.fr/ns16/inge1.html [4] http://www.baaden.ibpc.fr/ns16/inge1.pdf -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baaden@smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217

1 0

Recursive structure matching and acquisition of descriptive numbers
by Healey, Joe 20 Sep '16

20 Sep '16

Hi, I have several hundred structure simulations that were performed on our HPC resource. Each simulation has approximately 5 models associated with it. I also have HMM model homologies for each of these proteins. I would like to use chimera's matchmaker function to compare the simulated structured to their nearest 'real' counterpart with a resolved structure. In order to do this I plan to script chimera to pull in the simulated models as well as the near homolog and then run the matchmaker algorithm. My question is: can the RMSD value that is returned in the reply log be 'accessed directly' such that for each match that is performed, I can obtain the RMSD and thus a ranking for the best fitting structures - or will it require parsing the reply log? Thanks Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey>

3 8

Chimera input from command line
by José Almeida 15 Sep '16

15 Sep '16

Hello, I am a beggining Chimera user and was wondering if it was possible to run, all in the same command, something that enabled me to use a function (e.g. hbonds) without utilizing the console or the gui. I am trying to include this into a program so that I can calculate H-Bond data on several proteins in order to automatize the procedure, but I haven't been able to do so. Already thanking any attention given to this problem, Best regards, José Guilherme de Almeida

3 3

Problem in installing Chimera in Linux
by Chau Phi DINh 14 Sep '16

14 Sep '16

Dear my friends, I tried to install Chimera on Ubuntu. I followed the instruction in Release Note of UCSF. I typed in Terminal command the following: chmod +x chimera-installer.bin chimera-installer.bin but it shows me : chimera-installer.bin: command not found Can you tell me how I can do to install it ? Regards, Phi Sent with Mailtrack <https://mailtrack.io/install?source=signature&lang=en&referral=dinhchauphi@…>

3 3

RMF Viewer and Resolution Selection
by Chemmama, Ilan 14 Sep '16

14 Sep '16

Dear developers, I am trying to select hierarchical features based on resolutions (for example to show or hide). Using the resolution sliders does not seems to work however. I could not find anything in the documentation page though. Is there an easy way (command line would be the best) to select a given resolution? Thanks, Ilan

2 1

Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers
by Jaime Rodríguez-Guerra 09 Sep '16

09 Sep '16

Joe, If admin permissions are an issue, you can always install the Miniconda 2.7 distribution, which will install all packages in your user folder, virtualenvs included. I cannot recommend it enough! Greg, I have not come across any problems without that windowsize command, so I guess it just works? I posted a gist which shows how to render images programatically for a bunch of pdb files. Let me know if it works! https://gist.github.com/jaimergp/09104ca2bbccb81ff430374f9c2522a7 Cheers!

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Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers
by Jaime Rodríguez-Guerra 08 Sep '16

08 Sep '16

Hi! Such an honor to see my name listed here! Yes, with pychimera you should be able to do it! All you need to do is to patch the environment so that Chimera can find its libraries and dependencies, and then initialize it. In practice, this means importing pychimera and calling pychimera.patch_environ() and pychimera.load_chimera() at module level. Then you can proceed as you'd do with a standard Python distribution. If you don't want (or are not able) to modify the script, pychimera also installs a binary that will patch and load Chimera for you, so you can just do "pychimera myscript.py" However, it's a bit buggy when it comes to parsing additional arguments for your script. That said, the binary is very useful to fiddle with Chimera internals from the command line, since it provides a patched python in which you can import chimera, and also hooks for ipython and jupyter notebook (with magic calls to render inline!). pychimera will do its best to locate your Chimera installation, but if it doesn't succeed, you can always provide it manually with the envvar CHIMERADIR, which is what you would probably need to load the headless edition of Chimera. Additionally, it will load your current Python distribution sys.path, which means it will be able to import already installed packages in such distribution. As a result, you don't need to install the packages again for Chimera. This is particularly useful if you are using virtual envs or conda envs! I think that's all. If further questions arise or something is not working as you'd expect, please report that in the issues page of GH ( https://github.com/insilichem/pychimera) or write to me directly. Cheers, Jaime.

1 0

Re: [Chimera-users] Mesh points from volume data
by Elaine Meng 07 Sep '16

07 Sep '16

Hello, Sorry, I can’t help on this one, so I’m forwarding to the list! Best, Elaine On Sep 7, 2016, at 6:24 AM, Michał Kadlof <m.kadlof(a)cent.uw.edu.pl> wrote: > Hello, > > I'm almost home. There are several issues: > 1. I need not only points but also planes -> point triples from surface triangulation. > 2. I have quite a lot of points (more than 30 000). PDB file format fails in the CONNECT records: > > In the end of file they looks like this: > CONECT3051230171301923050530506 > CONECT3051230511 > CONECT3051330165301663018830508 > CONECT3051330514 > CONECT3051430188302133050830509 > CONECT305143051330515 > CONECT3051530213302163050930510 > CONECT305153051430516 > CONECT3051630193302163021830510 > CONECT305163051130515 > END > > Is there any walkaround? Preferably it would be best solution for me if I could access both points and planes (faces) programatically with python. Is it possible? > > -- > pozdrawiam serdecznie > Michał Kadlof <m.kadlof(a)cent.uw.edu.pl> > > > On Sep 6, 2016, at 12:36 PM, Michał Kadlof <m.kadlof(a)cent.uw.edu.pl> wrote: > > > > Works like a charm! :) > > > > -- > > pozdrawiam serdecznie > > Michał Kadlof <m.kadlof(a)cent.uw.edu.pl> > > > > 2016-09-06 19:28 GMT+02:00 Elaine Meng <meng(a)cgl.ucsf.edu>: > > Hi Michal, > > You can use the “meshmol” command to make the isosurface mesh into a fake molecule, where the the points are “atoms” and the mesh lines are “bonds” shown as sticks. > > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html> > > > > Although the new “molecule model” is suppressed from appearing in the File… Save PDB dialog, you can still save it to PDB from the command line with “write” … or save it as a marker set using the File menu of the Volume Tracer tool. > > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html> > > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/…> > > > > Either of those formats will contain the coordinates. The marker format will do a better job of preserving the stick bonds and their radii, if that matters to you. > > 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 6, 2016, at 6:48 AM, Michał Kadlof <m.kadlof(a)cent.uw.edu.pl> wrote: > > > > > > Hello, > > > > > > I have density data in .cmap file format. I want to save a coordinates for points that are on the surface for given cutoff. I need exactly that points which are visible in mesh representation. > > > > > > How can I do that? > > > -- > > > pozdrawiam serdecznie > > > Michał Kadlof <m.kadlof(a)cent.uw.edu.pl> > > > >

2 1

Mesh points from volume data
by Michał Kadlof 06 Sep '16

06 Sep '16

Hello, I have density data in .cmap file format. I want to save a coordinates for points that are on the surface for given cutoff. I need exactly that points which are visible in mesh representation. How can I do that? -- pozdrawiam serdecznie Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

2 2

extracting chaing colors from session file?
by Melissa Jurica 06 Sep '16

06 Sep '16

I am analyzing a structure containing many individual chains that I have colored. I would like to transfer these colors to another structure of the same complex in a different conformation. Is there a way to extract the colors into a text file so that I can write a command file with the same color designations? For example: color #6168c8fb41bc #0.17 Also- How do I get that color to apply to the little square that shows up on the model panel? Melissa ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Melissa S. Jurica, Ph.D. Professor, Molecular, Cell & Developmental Biology Center for Molecular Biology of RNA University of California, Santa Cruz 1156 High Street Santa Cruz, CA 95064 Office: 450 Sinsheimer Labs Lab: 434 Sinsheimer Labs Office phone (831) 459-4427 Lab phone (831) 459-2463 Fax (831) 459-3139 http://www.mcd.ucsc.edu/faculty/jurica.html ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

3 4

Bonds
by Igor Peixoto Rodrigues 06 Sep '16

06 Sep '16

Hi my name is Igor Peixoto, and I have a question. There is some way to count the number of bonds in molecule? Like how much bonds of kind B-C, C-C, B-N.... for example?

2 1

secondary structure incomplete
by Ming 06 Sep '16

06 Sep '16

Dear Chimera team, I was using chimera to do some pdb editing and exporting the file for pymol printing. However after the editing with chimera the pdb file won't show secondary cartoon in pymol (It still shows perfect secondary structure in chimera). I used the file--export function in chimera and I have checked the pdb file and the secondary structure description in the pdb file is intact. Do you think if I export the file in a wrong way that caused the incomplete cartoon? If not what do you think could be the reason causing the issue? Thank you, Ming

2 1

Command line doesn't work properly on Mac
by Li, Leon 04 Sep '16

04 Sep '16

Hello All, The command line in Chimera seems not working properly on my Mac. Any input in the command line will not show unless you select them. Does anybody experience this problem? Or any idea about this? Both versions of 1.11 and 1.11.1 have been tried. My mac is iMac (Retina 5K, 27-inch) OS X EI Capitan. Thanks, Leon

2 2

disabling previous state
by david gae 02 Sep '16

02 Sep '16

Dear Chimera Users, I am wondering if anyone can help me with this question: Whenever I start up CHIMERA. My previous settings and panels show up. Is there a way to prevent my previous preferences being saved? Thanks, David

2 2

Deleting invisible structures?
by max taylordavies 31 Aug '16

31 Aug '16

Hello all, Is there any way to selectively delete the 'invisible' (undisplayed) parts of a structure and keep the visible parts without having to use the usual atom-spec approach? For example, if I run per-model clipping on a protein, is there any way to delete the part that has been rendered invisible by the clipping? If this isn't possible, is there a way to export only the visible/displayed components of a scene? Many thanks in advance, Max Taylor-Davies

2 4

ETA ChimeraX
by Chris Sander 30 Aug '16

30 Aug '16

Just curious when ChimeraX will appear and what it will be able to do! Keep up the good work. Chris Sander www.evfold.org

2 1

Integrating chimera into a database
by McCafferty, Caitlyn (NIH/NEI) [F] 29 Aug '16

29 Aug '16

Hi, I have a number of colored protein structures from chimera that are saved as python files. I would like to put these structures on a database so other users may access them. Is there a way (preferably using html) that a user could click on the python file and it would open up in chimera through the database-- even if the user does not have chimera installed? Thank you, Caitlyn McCafferty Postbaccalaureate Fellow Ophthalmic Genetics and Visual Function Branch National Eye Institute Bldg. 10 Rm. 6-3350 Tel: (301) 402-7058 Email: caitlyn.mccafferty(a)nih.gov

5 6

bond formation
by A G Szabo 26 Aug '16

26 Aug '16

I am working with a PDB file that has two proteins docked together. As this is a model the two proteins do not have a bond between them. The model number is the same for the two chains designated A and B. I have looked through the various tutorials, functions and tools to figure out how to actually place a bond between two residues that link the two chains. It is well established as to how the two proteins would be linked if the bond had been formed. The linkage is between the S of a Cysteine and carbonyl carbon at the C-terminal of the other protein. I think I have managed to select both atoms, but cannot determine how to include a bond. Your assistance is appreciated. Arthur Szabo

2 3

Creating and saving Multiscale Models using Python functions
by Jon David 24 Aug '16

24 Aug '16

Hi Friends, I would like to use Python to perform operations equivalent to the following GUI operations; I'd like to be able to do this as a batch script (e.g., I don't want the Chimera GUI to appear because I don't want to have to close it.): 1) Open a PDB file (I know how to do this part). 2) Tools > Higher-Order Structure > Multiscale Models (this opens the MultiScale Models popup window). 3) Click on the "Make models" button. 4) File > Export Scene... (this opens the Export Scene popup window) 5) In the Export Scene popup window, select File type to be "OBJ [.obj]", enter file name "test.obj" 6) Click on the "Save" button. I have used Python to open a PDB file, and translate, and rotate it around before. But I don't know where to begin with selecting Multiscale Models' parameters. Any tips? Any help would be much appreciated. Thanks, --Jon

2 1

volume viewer - planes
by Michael Elbaum 24 Aug '16

24 Aug '16

Hi. I'm using the volume viewer and the Planes function is extremely useful in order to see a subsection of the volume. Often I want to compare different processing or filtering of the same dataset. When I load several datasets, all the visualization parameters are set individually. Normally this is good, for example in setting different colors, but for Planes it's problematic. In order to switch among the various representations and see the same section of the volume I have to scan them individually, and when two are visible I can move only one. Is there a way to link the Planes among the maps? Perhaps there's a command line trick? thanks, Michael

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question
by A G Szabo 23 Aug '16

23 Aug '16

I recently downloaded the new version of Chimera. No issues with that so far. However, when I save a session it is still saved as a Chimera file, or a PYC file on my desktop. So when I went to my desktop file list, and tried to open one of the files I would click on "open with ." Two programs would be listed, Adobe, and Chimera. So I would select Chimera and the file would open satisfactorily. However, with the new version of Chimera, if I repeat the above, the only program that is listed is adobe. If the file type is listed as Chimera, then adobe would be listed, and there would be other programs listed but not Chimera. I can open the file in a round about way, but the former way was more efficient and user friendly. If I go to my programs list, there doesn't seem to be a way that I can conveniently open the file without first opening up Chimera. Your comments will be appreciated. Arthur G. Szabo

2 1

Select Non-conserved residue
by Markus Heller 23 Aug '16

23 Aug '16

Hi all, I used matchmaker to align two homologues proteins, and to calculate the sequence alignment. How can I select all non-conserved residues, in one fell swoop? Thanks and Cheers Markus -- Markus Heller, Ph.D. Senior Scientist, NMR 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 | www.cdrd.ca Follow us: 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.

2 1

Re: [Chimera-users] What is the default of ribbon?
by Elaine Meng 20 Aug '16

20 Aug '16

Hi Root, You cannot change this preset, but you can control what is shown “manually," for example hiding all atoms and then displaying residues within 5 angstroms of ligand and 3.2 angstroms of ions with commands: ~disp disp ligand z<5 disp ions z<3.2 To make a more simple one-step action, you can make an “alias” combining several commands, and that could be listed in an Aliases menu. This is sort of like “make your own preset”. For examples, see this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-February/007230.html> I hope this helps, Elaine On Aug 19, 2016, at 1:03 AM, 郭尚哲 <b02b02049(a)ntu.edu.tw> wrote: > Dear Elaine, > I have another question. How can I change this 3.6 Å criteria, if it is possible? > Root > ________________________________________ > 從: Elaine Meng [meng(a)cgl.ucsf.edu] > 寄件日期: 2016年8月19日上午 12:54 > 至: 郭尚哲 > 副本: chimera-users(a)cgl.ucsf.edu > 主旨: Re: [Chimera-users] What is the default of ribbon? > > Hi Root, > It is described in the “preset” documentation: > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/menu.html#menupresets> > > … specifically, > "Interactive 1 (ribbons) - shows most peptide and nucleic acid chains as ribbons, plus atomic detail (excluding hydrogens on carbon atoms) for residues within 3.6 Å of a ligand residue or metal ion. Atomic detail is also used for chains that are very short.” > > In other words, if the amino acid residue has any atom within 3.6 Å of what Chimera thinks is “ligand” or “ion” the whole sidechain will be shown, except any H atoms attached to C atoms. > > You do not need to search on the net, you can just look at the manual included with your download, using menu: Help… Search Documentation. For example, you could search for “presets” or “ribbon interactive preset”. The information you found is explaining something different: why the backbone atoms are not shown. > > 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 17, 2016, at 11:13 PM, 郭尚哲 <b02b02049(a)ntu.edu.tw> wrote: >> >> Hi all, >> I have some pdb files of ligand binding protein structures, and when I check these structures with the ribbon diagram (Presets -> Interactive 1 (ribbons)) with chimera, it not only show the "ribbon" but also the sidechain of some residues. I would like to know why, so I search on the Net. And I just find the site below: >> https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbo… >> It says "By default, when ribbon is shown for a residue, the mainchain atoms of that residue are hidden, except where bonded to other displayed atoms (such as the sidechain)." >> I can't get more imformation, and still don't understand. >> What is the rule chimera follow to show the sidechain of certain residues? >> Thanks, >> Root > >

2 1

segmenting cryoEM maps
by giulia palermo 19 Aug '16

19 Aug '16

Dear all, I am new to chimera and I am working with density maps. I have segmented my cryoEM map successfully. I want now to group some of the segmented regions in a single region and subequently save the obtained map. Is there a way of doing it? Thank you very much Best wishes Giulia Palermo

2 2

Re: [Chimera-users] Add Hydrogens - non standard residue - protonation state
by Elaine Meng 19 Aug '16

19 Aug '16

Hi Subha, This is out of my area, since I don’t know python. (We always recommend sending questions to the chimera-users list, CC’d here, since you are more likely to get a good answer by asking multiple people!) I can only say that as far as I know if it works in the command line, then you should be able to use python to run the same command, as described in this page in the Chimera programmer’s guide: <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> Best, Elaine On Aug 19, 2016, at 1:57 PM, Subha Kalyaanamoorthy <kalyaana(a)ualberta.ca> wrote: > Hi Elaine, > > Just another question, > > Is there anything I need to import for using setattr in a python script. I get an error when I use it as a part of script. But, it works fine when I type it on the command-line of Chimera gui. Not sure what I am missing. > > Thanks and Best Regards, > Subha >

2 1

Default contour level in Volume Viewer
by MICHAEL POTEAT 19 Aug '16

19 Aug '16

Hello all, How is the default contour level in the Volume Viewer calculated when you first open up a .mrc file? I've tried the average density, and the root-mean-square of all voxels, but both do not match Volume Viewer's default level. I've tried looking here [ http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/frame…] for documentation on this, but it does not mention it. Thanks, Mike

2 1

Add Hydrogens - non standard residue - protonation state
by Subha Kalyaanamoorthy 18 Aug '16

18 Aug '16

Hi There, Can anybody please suggest me how to use 'setattr' (or any other function) to assign a protonation state for an atom in a non-standard residue. I have a ligand and I am using a python script to add hydrogens and charge to the ligand molecule using chimera no-gui. I see that chimera adds an extra hydrogen to a nitrogen atom in the ligand and assigns a charge of +1 to the molecule. Removing this hydrogen using GUI is simple but not practical for large set of molecules. So, it would be helpful if somebody suggest me a command-line to set specific protonation states for atoms (in non-standard residue). Thanks and Best Regards, Subha

2 2

splitting and surfaces
by A G Szabo 18 Aug '16

18 Aug '16

I am working on a large multi subunit structure (4CR2). Originally I selected one of the subunits, and received the error message that suggested I should use the split command. Which I did and obviously I must have been successful in splitting the subunits. Each of the subunits is now labelled as being split, i.e. (#0.14) etc. I was successful in showing the surfaces of 4 subunits, and colored them differently. However, when I tried to show the surface of one of the subunits with 437 residues, (several residues cannot be resolved) I received this error message One subunit which I successfully was able to show the surface in the image had 467 residues and also had a large number of residues that were not resolvable. So I am stuck! Your help would be appreciated. AGSzabo

2 5

further
by A G Szabo 18 Aug '16

18 Aug '16

Further to my last message regarding surfaces it would be highly convenient to have the url listed at the bottom of the error message open as a link. Secondly it is not even possible to copy it and paste it into my browser. ags

1 0

What is the default of ribbon?
by 郭尚哲 18 Aug '16

18 Aug '16

Hi all, I have some pdb files of ligand binding protein structures, and when I check these structures with the ribbon diagram (Presets -> Interactive 1 (ribbons)) with chimera, it not only show the "ribbon" but also the sidechain of some residues. I would like to know why, so I search on the Net. And I just find the site below: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbo… It says "By default, when ribbon is shown for a residue, the mainchain atoms<https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbo…> of that residue are hidden, except where bonded to other displayed atoms (such as the sidechain)." I can't get more imformation, and still don't understand. What is the rule chimera follow to show the sidechain of certain residues? Thanks, Root

2 1

Joining models
by Jie, Jing 16 Aug '16

16 Aug '16

Hi all, Is there a way in chimera to fix the position of one model when creating a peptide bond between two models? I selected 'move atoms on C side' but the N side chain still moves. Thanks in advance! Jing

3 4

Problem
by Kari Boyett 15 Aug '16

15 Aug '16

I have alot of these Chimera Modules on my phone that I didn't authorize and I need to know how to remove them please.

2 1

measure rotation command questions
by Joseph Atherton 15 Aug '16

15 Aug '16

Hi, When I use the command 'measure rotation' I get a matrix in the reply log. 1) The fourth column is 'translation'. At most the translation I see is 5 Angstrom, so how do I get these numbers (see below)? I also have a shift along axis reported, which seems a more reasonable number, but what if the shift is in a a different vector to the axis? 2) I can get depiction of the rotation axis, but can I also get a depiction of the translation vector? Cheers, Joe Position of model2 (#20) relative to model1.pdb (#1) coordinates: Matrix rotation and translation 0.98820614 -0.14982292 -0.03165001 43.44553134 0.14930460 0.98862441 -0.01816347 -23.90940685 0.03401127 0.01322376 0.99933396 -9.65968865 Axis 0.10195507 -0.21328736 0.97165512 Axis point 180.93496764 275.63881775 0.00000000 Rotation angle (degrees) 8.85455905 Shift along axis 0.14318049

2 2

chimera crashing upon opening of trajectory
by Natesh Singh 12 Aug '16

12 Aug '16

Dear Sir/Madam, I am unable to open a trajectory (50 ns and about 25 gb size) in a chimera GUI. I am getting a python crash error after some time of initial message of 'reading PDB...' and then chimera shuts down. Is it the large file size that is causing the python to crash? Looking forward for the guidance. Best regards, Natesh

2 1

Re: [Chimera-users] Selecting specific atoms in MD Movie
by Thomas Faour (x2013gua) 12 Aug '16

12 Aug '16

Hi Elaine, I thought about sending the data but was hoping there was an easy solution to something I was doing wrong... Which there was! Using :52.water worked perfectly. Thanks a ton! Thomas On Aug 12, 2016 14:49, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: Hi Thomas, It's difficult to answer questions like this without the data... I only have one low-confidence guess, which is to try :52.water instead of :52 ...as mentioned in the "subcategories" section of <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> If that doesn't work, you would have to send us the data (or a smaller sample, if possible). You could send it to just me if you don't want to send to the whole list. 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 11, 2016, at 4:46 PM, Thomas Faour (x2013gua) <x2013gua(a)stfx.ca> wrote: > Hello there, > > I study water/ice systems and I have an algorithm which reads my trajectories and tell me if a certain water molecule can be considered "liquid", "hexagonal ice" or "cubic ice". So I can label each molecule at each frame as such. I am hoping to be able to use this data to create a movie where each group is coloured differently, and should a molecule change groups be re-coloured accordingly. > > I attempted this by running a PER-FRAME script which reads my labels from a data file, and colours the molecules. However I ran into a problem, running either of the following commands: > > colour blue,a :52 > select :52 > > in the PER-FRAME script, or even just on the command line during an MD Movie does NOT work for me. This works for a single configuration file, but not during a movie. The command: > > color blue,a @OW > > however does work. I am currently using XTC trajectories, in case that is relevant. > > What might fix my problem? Or is there a better way I could be doing this? > Cheers, > Thomas

1 0

Selecting specific atoms in MD Movie
by Thomas Faour (x2013gua) 12 Aug '16

12 Aug '16

Hello there, I study water/ice systems and I have an algorithm which reads my trajectories and tell me if a certain water molecule can be considered "liquid", "hexagonal ice" or "cubic ice". So I can label each molecule at each frame as such. I am hoping to be able to use this data to create a movie where each group is coloured differently, and should a molecule change groups be re-coloured accordingly. I attempted this by running a PER-FRAME script which reads my labels from a data file, and colours the molecules. However I ran into a problem, running either of the following commands: colour blue,a :52 select :52 in the PER-FRAME script, or even just on the command line during an MD Movie does NOT work for me. This works for a single configuration file, but not during a movie. The command: color blue,a @OW however does work. I am currently using XTC trajectories, in case that is relevant. What might fix my problem? Or is there a better way I could be doing this? Cheers, Thomas

2 1

APBS mobile ion option
by Eita Sasaki 12 Aug '16

12 Aug '16

Hi, I'd like to run APBS command with mobile ions (150 mM NaCl). I tried the following command, but it did not work. apbs molecule #1 ion true _posion 1,0.15,1.16 _negion -1,0.15,1.67 If I typed just "apbs molecule #1" it works (without mobile ions). I am wondering my command was perhaps wrong but don't know the right one. I hope you could help me to solve the problem Thank you in advance. Eita

2 4

(no subject)
by Karel W. F. de Pourcq 09 Aug '16

09 Aug '16

Dear Chimera team: I am a student of a Msc. in Bioinformatics at the Autonomous University of Barcelona. I am using Chimera to prepare visual representations of molecular events, and I write in order to ask if there is a straightforward way in which to: a) Create a sphere of a certain diameter: Yes, I found how to do it already: with the "shape" command. This is solved. b) In an orderly and distributed way, cover that sphere with a number of copies of a molecule chain, anchored over the sphere's surface by one of their ends (and the other end of the molecule protruding towards the outside). I believe I could do it manually for a small system. Is there some kind or automated and more convenient way to do this for a large sphere, linking its surface with hundreds of molecules of -for instance- dodecane? I could not find explicitly a way to do something similar to what I am trying to do. I attach an image of a 2-d representation of something similar to what I would like to represent. The difference is that I would like to cover the surface. [image: Imágenes integradas 1] I thank you a lot in advance for your time. Kind greetings from Barcelona, Spain, Karel De Pourcq

4 4

chimera minimize script
by Bylund, Tatsiana (NIH/NIAID) [F] 09 Aug '16

09 Aug '16

Dear all, I need to minimize a lot of protein complexes and am trying to do it with a script. I have a protein complex structure without Hydrogens, but when they are added in Chimera, it outputs error Non-standard atom names: ASN HA2 (:33.K@HA2) ASN HA3 (:33.K@HA3) Total charge for #0: 32.039 Total charge for #0: 32.039 The following residues had non-integral charges: :33.K 0.039 Correct charges are unknown for 2 non-standard atom names in otherwise standard residues Charges of 0.0 were assigned to the unknown atoms 1 model(s) had non-integral total charge Details in reply log Dock prep finished Error while processing chimera_mini.py: No MMTK name for atom "HA3" in standard residue "ASN" When I delete residue K 33 (which DOES NOT have H in pub file) chimera runs minimization. Would you have any suggestions? Thank you! Kind regards, Tatsiana

3 3

UCSF
by Amali Guruge 05 Aug '16

05 Aug '16

Dear All, What is UCSF referring to? Is it University of California San Francisco ? Thank you.

2 1

Volume and mesh data simultaneously? Coordinate space is different
by Marvin Albert 03 Aug '16

03 Aug '16

Hi all, I process 3d objects and want to visualise them as meshes and volumes simultaneously. However, when I load them into chimera the coordinates of the two are different (meaning they don’t overlap). Is there an obvious reason for this? Would the volume viewer show a .tif file with different coordinates than chimera shows the .wrl mesh? (this tiny cube exemplifies my problem: http://www.filedropper.com/cube_3 <http://www.filedropper.com/cube_3>) Thanks a lot in advance, Marvin

3 5

precalculated void representation as surface
by Michalska, Karolina M. 03 Aug '16

03 Aug '16

Hi, I have a precalculated cavity represented as a grid in the pdb format, where “atoms” are spaced by 0.3 A. What would be the option to visualize this as a surface? I can easily show it as point or spheres, but I cannot display it as surface. I appreciate your help, Karolina

2 6

APBS webservers not working
by Ursula Schulze-Gahmen 02 Aug '16

02 Aug '16

I used to run APBS from within Chimera. But recently, the webservers that are called for the APBS calculations are not working. Do I need to go to the APBS website directly or what is the solution? Ursula -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491

2 1

chimera 1.11 question
by Dixon, John 01 Aug '16

01 Aug '16

Hi I was wondering if you could help When I install chimera on my main physical PC I can use function left CTRL and mouse to highlight atoms in green in the graphics interface as below. [cid:image003.jpg@01D1E728.1FE9F730] However when I install chimera on a virtual PC, this function does not work. Any ideas on how to get around this issue? thanks John Dixon Application Integration Team Client Platform Services Information Services Division, UCL Tel: 02076799163 Ext: 09163

3 2

help for make figures
by 陈柳青 30 Jul '16

30 Jul '16

HI How to make the figures in attachment, which highlight part of a structure. Thanks very much for advise. -- Liuqing Chen School of Life Science & Biotechnology Minhang Campus Shanghai Jiao Tong University No. 800 Dongchuan Road Shanghai 200240 P.R. China Tel: +86 21 34207247

2 2

help for make figures
by 陈柳青 30 Jul '16

30 Jul '16

HI How to make the figures in attachment, which highlight part of a structure. Thanks very much for advise. -- Liuqing Chen School of Life Science & Biotechnology Minhang Campus Shanghai Jiao Tong University No. 800 Dongchuan Road Shanghai 200240 P.R. China Tel: +86 21 34207247

1 0

UI suggestions - Save map
by Oliver Clarke 29 Jul '16

29 Jul '16

Hi, minor suggestion for Chimera, related to dealing with large numbers of maps: It would be really helpful if there was a 'Save map' dialog in the 'File...' menu, with similar dropdown menus to select the map one wants to save as for the 'Save PDB' dialog. Doing so via the volume viewer is a bit clunky when there are lots (e.g. 10+) of maps loaded. Even better would be if it included a 'Save relative to map' dropdown, analogous to the 'Save relative to model' drop down in the 'Save PDB' dialog, which would resample the map to be saved on the grid of the selected target map (perhaps warning of the potential for a modest loss of quality). This would be really helpful when one aligns many different conformations of a molecule (e.g. from 3D classification) to a reference subvolume and wants to save the resulting transformed maps. Cheers, Oli.

1 0

Re: [Chimera-users] [chimera-dev] B factor
by Elaine Meng 27 Jul '16

27 Jul '16

On Jul 26, 2016, at 5:12 PM, Bashayer Althufairi <althufairib(a)mymail.vcu.edu> wrote: > Hello > As you know many crystallographers need to determine the ave. B factor of selected amino acids or sometimes they wanna know B factor of N-termius Vs. C-terminus of a protein. I'm working on a protein where I need to predict B factor of certain amino acids sequence as well as difference between the values for analysis. Is this possible by Chimera? If yes, I'd like to know Please the way step be step, If no, I wish you could recommend a simple way to do it by educational simple software like PyMol. > Thank You in Advance > -- > Bashayer Althufairi > Medicinal Chemistry department > Virginia Commonwealth University Hello Bashayer Althufairi, This is really a Chimera user question so I’m CCing the chimera-users mailing list. The chimera-dev list is for Chimera programming questions. Chimera doesn’t predict any B-factors, but you can see the B-factors from the PDB file for a structure, e.g. in a histogram in the Render by Attribute (in menu under Tools… Structure Analysis). This tool can color the structure to show the B-factor values. It also automatically calculates the average B-factor per residue (over the atoms in each individual residue so that each residue can have one number). It can also save the values to a file (see File menu of that tool) although of course the PDB file already contains the per-atom B-factor values. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.htm…> See also the tutorial for coloring by B-factor: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html> But maybe you mean that you want to select several residues and then calculate a single average B-factor for them. You can do that with Attribute Calculator (in menu under Tools… Structure Analysis) <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calcul…> For example, you could select several residues and open Attribute Calculator, turn on the options to “Restrict formula domain to current selection” and “Show calculation results in Reply Log”, calculate a new attribute named whatever you want for “molecules” with formula: average(atom.bfactor). Click Apply to calculate a single average over all selected atoms, value reported in Reply Log. If you have predicted B-factor values you can also read them into Chimera as a custom attribute (see file format for doing that <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defi…> … it is the same format as used for the saving mentioned above). When you read in those values they are also available for use in Render by Attribute and in Attribute Calculator, and with the latter you could calculate the differences between the bfactor attribute from the PDB file and your custom attribute (the predicted values). The differences would then be another attribute also available for coloring using Render by Attribute. See also the attributes tutorial for examples of using Attribute Calculator and Render by Attribute: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html> I don’t use other programs so I don’t have any advice about using them for this purpose. 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

1 0

Help with Autodock Vina
by Jonathan Y Wang 27 Jul '16

27 Jul '16

To whom it may concern, Hi, I was trying to dock a ligand into my receptor and all of the other ligands so far have worked and outputted a value, but this one compound never outputs a .pdbqt file. The other files such as the .conf and .pdb files have been created, the bottom of the screen no longer says "execution in progress", and the green box remains. I've looked at the tutorial for AutodockVina online and tried fidgeting around with it, but I seem to be extremely lost. I was wondering if you had any pointers, tips, or anything at all that could help me. All the best, Jonathan Wang

2 1

Auto start and nogui option causing segmentation fault?
by Daniel P Farrell 26 Jul '16

26 Jul '16

Hello, I don't know if maybe i'm doing something wrong, or if there's a problem, but I'm on a mac el capitan 10.11.6 and I'm getting these weird errors when I try to start chimera in nogui mode. I usually set various tools to auto-start once I start chimera, but recently I was messing around and added a few, and now I'm getting these errors when i start chimera via --nogui. Problem is, I don't know which one is causing the seg fault, but I feel like it shouldn't be calling these gui options with the nogui options on anyway. Once I started getting these errors I went to Favorites->add to favorites/toolbar->reset & save, and now I don't get the segfault. I do get a few other errors if I adda few back to the auto start / on toolbar options. chimera production version 1.11 (build 41179) 2016-07-15 05:43:21 UTC with many auto-start options on """ >chimera --nogui Exception in Tkinter callback Traceback (most recent call last): File "/Users/danpf/Desktop/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 1538, in __call__ return self.func(*args) File "/Users/danpf/Desktop/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 589, in callit func(*args) File "/Users/danpf/Desktop/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 280, in _initialPositionCheck if not preferences.get(GENERAL, DIALOG_PLACEMENT): File "/Users/danpf/Desktop/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", line 607, in get return self._category[category].get(name, KeyError: 'General' [1] 1045 segmentation fault ~/Desktop/Chimera.app/Contents/MacOS/chimera --nogui """ after removing most auto-start options """ >chimera --nogui Exception in Tkinter callback Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 1538, in __call__ return self.func(*args) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 589, in callit func(*args) File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 280, in _initialPositionCheck if not preferences.get(GENERAL, DIALOG_PLACEMENT): File "/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", line 607, in get return self._category[category].get(name, KeyError: 'General' Starting extension 'Model Panel' failed Starting extension 'Keyboard Shortcuts' failed Starting extension 'IDLE' failed > """ should I be adding a different flag or something when I start chimera via nogui? Thanks, Dan

3 2

Saving Attribute settings and Worm Radius Consistency
by Nicole Persky 26 Jul '16

26 Jul '16

Hi All, I've started using Chimera to map two different datasets onto structures. For one, we use color, and for the other we use worm radius. I've encountered two problems while trying to make figures for publications: 1- when I save my session the image is saved but when I go to "render by attribute" to tweak the settings a little, the threshholds under colors and worm radius have been reset. How to I get them not to reset, but to keep the thresholds? 2- I am trying to compare three different images with the same worm radius thresholds. For one of the images the lowest number of my attribute is LARGER than the lowest number I want to define on my threshhold (I would like to set the lower worm radius to 1 for a value of 1 however for this dataset my lowest value is 2. I cannot just set the value starting at 2 because there is a gradient to the largest value that gets thrown off). Yet, I cannot set the threshold lower than the lowest value of my attribute. Does anyone know a way around this? thanks so much, Sincerely, Nicky

2 1

saving multiple models in Chimera
by Kamil Kuder 26 Jul '16

26 Jul '16

Dear Sirs/Madamme I have multiple PDB'a (ca.40) in the model panel. While trying to save each model in single file using option "Save multiple models in multiple files" I got this message: You must provide a file name that contains either $name or $number. I set the name to eg. A1_01 and/or A1_$01 but none of this works. How shall I manage that? Many thanks Kind regards Kamil J. Kuder, PhD Jagiellonian University Medical College Faculty of Pharmacy Department of Technology and Biotechnology of Drugs Medyczna 9 30-600 Krakow POLAND tel.: +48 12 602 55 86

2 2

Solvate Tool Trouble
by Mike Bergman 25 Jul '16

25 Jul '16

Hey there. I am having trouble with the solvate tool. I am using a dimeric model (PDB ID: 2Q1E) that isn't attached. Every time I try to solvate (model TIP3PBOX), it squishes the dimer together. I tried different angstrom box sizes - 3, 5, 10, 20. Running the simulation with them overlaid wouldn't give me any useful data as I'm looking for the changes in the dimer interface. Is there a way I can stop it from doing this? Should I use a different solvate method like Shell? Thanks. Sincerely, Mikey Bergman

2 4

Threshold change
by Anindito Sen 25 Jul '16

25 Jul '16

Dear All, What will be the command (to be put in a script) for the change in the threshold of one of the displayed volumes without disturbing the others. Thanks Andy Dr. Anindito Sen (Ph.D)

2 1

Linking four proteins
by Aditya Padhi 22 Jul '16

22 Jul '16

Dear Chimera users, I have predicted a protein structure having 4 different domains (for e.g. 1-94, 95-247, 248-444 and 445-509 residues) and all are part of a single protein from 1-509 residues. They have been predicted from different web-servers. Now, I want to join them together to form a single PDB file i.e. make a single PDB file containing the entire protein from 1-509 residues from the above 4 PDB files. Afterwards, I want to run a simulation of the built structure. I searched in google for possible solution but not sure which method would be better. Is there any solution to build this one structure in Chimera? Please let me know. Thank you so much. Aditya

2 1

Color by hydrophobicity - select default scale?
by Oliver Clarke 21 Jul '16

21 Jul '16

Hi, As explained here ( https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html) Chimera currentlyuses the Kyte-Doolittle scale by default for coloring proteins by hydrophobicity. I wonder whether it might be worth updating this to use e.g. the scale described by Karen Fleming and co here ( http://www.pnas.org/content/108/25/10174.full)? This scale (and indeed most more recent scales in the literature, see review here: http://www.sciencedirect.com/science/article/pii/S0968000411001320) differ quite dramatically from the Kyte-Doolittle scale, which places trp and tyr as comparable to serine, which does not seem reasonable based on analysis of membrane protein structure. The Moon et al scale has the advantage that it is derived from studies of the energetics of protein folding and membrane insertion, as opposed to the energetics of isolated amino acid partitioning between ethanol and water, which as I understand it is what the K-D scale is mostly based on. Alternatively, would it be possible to allow users to select the default scale which it used for this purpose (I know it is possible to define a custom attribute for this, but this is a little cumbersome for something which sees frequent use). Cheers, Oli

2 3

Positioning changing over time
by Marvin Albert 21 Jul '16

21 Jul '16

Dear chimera users, I was wondering whether any of you could help me with this simple problem: The aim is to make a movie displaying the evolution of predefined meshes over time (see attached python script). Overall the script works and produces a movie. However the mesh gets displaced slightly between the different time points. This results in an annoying random wiggling. I checked the original .wrl files and the indicated coordinates do have consistent positions (meaning the displacements are produced by chimera). How can I get a smooth movie? Might there be something unexpected happening when I repeatedly call runCommand(“open <file1.wrl>”) and runCommand(“close all”)? Thank you so much in advance! With kind regards, Marvin

2 2

Docking Crystal Structure in to Cryo EM Structure
by Senavirathne, Gayan 20 Jul '16

20 Jul '16

Hello, I am trying to dock some crystal structures (PDB: 1KX5 and 3OS1) in to a cryo EM structure EMDB:2992. How can I do this task using the UCSF chimera software and how can I know the alignment is accurate? Thank you very much Regards, Gayan Senavirathne, PhD Postdoctoral Researcher The Ohio State University Wexner Medical Center Cancer Biology and Genetics 460 West 12th Avenue, Room 1040 Columbus, OH 43210 Phone (313) 316-6658 senavirathne.1(a)osu.edu<mailto:senavirathne.1@osu.edu>

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new release of UCSF Chimera
by Elaine Meng 18 Jul '16

18 Jul '16

Hello everybody, A new production release of UCSF Chimera (version 1.11) is available: http://www.rbvi.ucsf.edu/chimera/download.html Download is free for noncommercial use. Platforms: Windows, Mac OS X, Linux. 64-bit builds are recommended for all capable platforms; this will be the last release to support 32-bit builds. New since version 1.10: Molecular Dynamics Simulation tool, more Add Ions types, residue interaction networks (RINs) from trajectories shown in Cytoscape, protein contact/distance map data export, Segment Map updated to new version of Segger, volume contour levels can be specified in RMSDs from zero or SDs from mean, "flat ribbon" publication preset, Ribbon Styles tutorial, "set showCofR" to show crosshairs at center of rotation. More details are given below; see release notes for the full list: http://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.11.html General I/O, Display: * standard shortcuts for File menu (Ctrl/Cmd-q for Quit, etc.) * "wall-eye stereo pair" option in Save Image dialog * PubChem fetch uses PubChem3D instead of Pub3D * "set showCofR" command to show "+" at center of rotation * "pipes" command-line implementation of PipesAndPlanks * reduced triangles in STL output for atoms/bonds Structure Analysis and Modeling: * Molecular Dynamics Simulation tool (thanks to V Munoz Robles and JD Marechal, Universitat Autonoma de Barcelona) * many more ion types in Add Ions tool * axes can be defined normal to previously defined planes * RR Distance Maps can show distance differences for a pair of structures (means, std devs already available), export data * MD Movie calculation of trajectory RINs, display in Cytoscape * PDB2PQR updated to use new web service URL Volume Data (density maps, electrostatic potential): * new input map format: IMAGIC density * Segment Map updated to new version of Segger * "volume" command options "rmsLevel" and "sdLevel" to specify thresholds in units of RMSD from zero and SD from the mean * "vop" options to sharpen map, create new zero-valued map Enjoy! On behalf of the Chimera team, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

using scipy with Chimera
by Xiao-Bo Li 16 Jul '16

16 Jul '16

Hi, I need to use scipy with Chimera. I like to copy over the scipy folder from my ubuntu's "/usr/lib/python2.7/dist-packages/scipy" directory. This is what I have done in the past, and it works fine. However, when i installed the .bin file for Chimera from Chimera's website (I tried versions 1.11 and 1.8.1), I find that the numpy versions there are 1.7.0b2. The numpy version on my ubuntu computer is 1.11.0. Since my ubuntu python's numpy, and Chimera's numpy are different versions, I can no longer using the scipy folder for Chimera. Can you please update Chimera's numpy version to 1.11.0? XBL

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Re: [Chimera-users] A question about colouring a resmap output file in Chimera.
by Elaine Meng 15 Jul '16

15 Jul '16

Hi Thanos, I’ve never used Resmap myself (it is a separate program from Chimera), but as I understand it, the output file contains the local resolution values calculated from the input map. You would have both that original map and the resmap output map open in Chimera, show an isosurface of the original map, and color it by the values in the resmap map. It is best to send Chimera-related questions to the list CC’d here (chimera-users(a)cgl.ucsf.edu) because often other people know more about something than I do. >From this earlier post to the list, I thought Resmap also output a Chimera script that you could run to perform the coloring: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-October/011679.html> However, even if you didn’t run such a script you could do the coloring using the Surface Color tool or the “scolor” command in Chimera. Finally, there must be more information about how to use Resmap with Chimera, and how it calculates the values, in the Resmap manual and the Resmap paper in Nature Methods, see: <http://resmap.sourceforge.net/#manual> 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 Jul 15, 2016, at 4:47 PM, T-I <ignatiou(a)gmail.com> wrote: > Hello Elaine. > My question today is: > > I have run Resmap on my em-density map (.mrc) to calculate the local resolution > > When i open both the original .mrc file and the _resmap.mrc file in chimera i don't understand how to then colour the map with the values found in the resmap calculation. > > what do i do exactly? > > also i don't understand where the resmap values are?? > many thanks > Thanos >

1 0

Troubleshooting Residue Errors
by Mike Bergman 15 Jul '16

15 Jul '16

Good Morning. I am trying to Dock Prep the kappa1 dimer (PDB ID: 2Q20) in order to run Molecular Dynamics simulation. I keep getting an error that I'm not sure how to solve. I cleared the reply log and tried again so I could attach the reply log to this email. I have not modified the structure at all prior to the dock prep. When I looked at the residues, they seemed fine to me, but maybe you can help me figure out what's wrong. Any help would be appreciated. Thank you very much. Sincerely, Mikey Bergman

2 1

Cannot load trajectory in chimers executed through cytoscape
by Natesh Singh 15 Jul '16

15 Jul '16

Dear Sir/Madam, I am not able to load the MD trajectory, either in PDB or XTC in the chimera that was executed from cytoscape. When I define the path for the files, it says 'reading pdb...' but the trajectory never gets loaded into the screen. and this is happening in both linux and windows. Kindly guide me on this that how can I run the trajectory in chimera from cytoscape to analyze the residue interaction network. Best regards, Natesh

2 1

Re: [Chimera-users] error: more than 63 chains; cannot uniquely identify with single characters
by Elaine Meng 15 Jul '16

15 Jul '16

On Jul 15, 2016, at 7:39 AM, Wu, Weimin (NIH/NIAMS) [E] <weimin.wu(a)nih.gov> wrote: > Dear Elaine, > I have a pdb structure with four chains A, B, C, D. and an icoshedral cryo-EM density map. I fit the pdb into the map, and generate 60 copies. I try to merge all these 60 pdbs into a combination, but without renumbering the residues (choose "retain the name" option). I did this operation before without any error, but now it came with the error "more than 63 chains; cannot uniquely identify with single characters". > > If choose renumber the residues, then the merged is not easy to understand, not easy for comparison either. > > Is there any other way to do it? Thank you, > Weimin On Jul 15, 2016, at 8:43 AM, Wu, Weimin (NIH/NIAMS) [E] <weimin.wu(a)nih.gov> wrote: > Or easy to understand, can we add model number into the pdb as done in biological assembly pdb structure 1qgt.pdb1? Hi Weimin, I’m not sure how you made the copies, but if they are atomic structures I think this will work: Similar to what you said in your second message, instead of merging into a single model, simply keep all the models separate. You can still save to a single “multi-model” PDB file with the main menu: File… Save PDB (or just save the Chimera session for later). Then the copies will still all have chain IDs A,B,C,D which may be easier to work with anyway. I tried this with 1pov (which has chains 0,1,3) and with “sym” made the whole assembly with 59 more copies for 60 total. I looked in the model panel and they were models #0 (original) and #1.1-59 (copies). I saved as single PDB file and read it back in, and again had those same 60 models, each with the original chain IDs 0,1,3. It is recommended you send questions to chimera-users(a)cgl.ucsf.edu (CC’d here) instead of just me because I am not the expert on everything. :-) 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

1 0

Distances measurement for NMR ensemble
by James Starlight 15 Jul '16

15 Jul '16

Dear Chimera Users! I wonder to ask whether it possible to calculate distances between two selected atoms by means of the Chimera's Distance measurement tool providing as input NMR-ensemble consisted of 20 snapshots (without any additional files like topology!) or alternatively small md trajectory, obtaining also some elementrary statistics (E.g RMSD etc) Thanks! James

2 2

RMSD of protein-protein interphaces
by James Starlight 12 Jul '16

12 Jul '16

Dear Chimera users! Having several docking poses of 2 proteins I need to estimate RMSD difference between their interphaces (e.g like what I have seen in Capri) Is it possible to do it via some Chimera's plugin e.g in combination with the contact-maps plugin? Thanks! Gleb

2 1

Structural matching of Side-chain selection
by James Starlight 12 Jul '16

12 Jul '16

Dear Chimera users! I need to estimate how the side-chains dynamics are differs in MD compared to X-ray structure. Assuming that I have 2 structures one from md and another from X-ray and I select Sidechains from the both as obj1 and obj02 is it reasonable just to match them using MatchMAker? Thanks! James

2 1

Is it possible to compile python script to an executable file?
by xibei 11 Jul '16

11 Jul '16

Hi, On my computer(debian) I can run "chimera main.py" to run my program. But I also want to submit missions to the server (debian) where only python is installed, chimera is not. Therefore I wonder if it's possible to compile my python script to an executable program so that it can run on another computer without chimera but with python.. Thanks!

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Re: [Chimera-users] Color surface by underlying atom
by Oliver Clarke 08 Jul '16

08 Jul '16

Hi Kyle, Using "Values at Atom Positions" ( http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/density/density.h…) will create an atom attribute corresponding to the density value at each atom position. Then you should be able to use "Select by attribute" to select all atoms above/below the desired threshold. Cheers, Oli. Dear Chimera-dev and users, > > Does anyone now of a way to select only the atoms of a PDB that fall inside the displayed density of a volume? > > Thanks in advance! > > Best wishes, > Kyle > >

1 0

select only PDB atoms that fall inside density
by Morris, Kyle 07 Jul '16

07 Jul '16

Dear Chimera-dev and users, Does anyone now of a way to select only the atoms of a PDB that fall inside the displayed density of a volume? Thanks in advance! Best wishes, Kyle

1 0

About findclash in detecting overlap of atoms
by xibei 06 Jul '16

06 Jul '16

Hi, I'm trying to use command "findclash" to check the excluded volume effect by detecting overlaps between atoms. The command I use is "findclash #0 test #0" or "findclash #0 overlapCutoff value test #0", but I found that two close atoms (14C,16C, dis=0.8) are not identified as "overlaped" while another two atoms (11C, 16C, dis=1.8) whose distance is larger are overlaped... Is there anything wrong about understanding the overlap? Example molecular (init.mol2): @<TRIPOS>MOLECULE init.mol2 20 19 20 0 0 NUCLEIC_ACID NO_CHARGES @<TRIPOS>ATOM 1 C 14.7888 10.0072 -5.6663 C.3 1 DA 0.0000 2 C 15.4013 8.5150 -3.5012 C.3 2 DA 0.0000 3 C 13.7388 8.7698 -5.6133 C.3 3 DA 0.0000 4 C 14.6414 7.5770 -3.3654 C.3 4 DA 0.0000 5 C 12.9675 5.9273 -2.0359 C.3 5 DA 0.0000 6 C 13.6457 4.0155 -0.2544 C.3 6 DA 0.0000 7 C 12.8822 2.8588 2.0634 C.3 7 DA 0.0000 8 C 11.7541 3.3958 4.4562 C.3 8 DA 0.0000 9 C 11.2290 4.5854 6.8231 C.3 9 DA 0.0000 10 C 13.8907 4.6510 7.2730 C.3 10 DA 0.0000 11 C 15.5581 5.2490 9.3114 C.3 11 DA 0.0000 12 C 17.8150 4.7800 10.7177 C.3 12 DA 0.0000 13 C 18.0666 2.1205 10.3271 C.3 13 DA 0.0000 14 C 16.9288 4.4119 9.4640 C.3 14 DA 0.0000 15 C 14.9471 3.0788 10.7232 C.3 15 DA 0.0000 16 C 16.7345 3.9070 8.8773 C.3 16 DA 0.0000 17 C 15.5384 2.3512 10.7314 C.3 17 DA 0.0000 18 C 16.0476 1.4159 8.2501 C.3 18 DA 0.0000 19 C 17.5152 1.5369 5.9877 C.3 19 DA 0.0000 20 C 17.5650 3.1811 3.8468 C.3 20 DA 0.0000 @<TRIPOS>BOND 1 1 2 1 2 2 3 1 3 3 4 1 4 4 5 1 5 5 6 1 6 6 7 1 7 7 8 1 8 8 9 1 9 9 10 1 10 10 11 1 11 11 12 1 12 12 13 1 13 13 14 1 14 14 15 1 15 15 16 1 16 16 17 1 17 17 18 1 18 18 19 1 19 19 20 1 @<TRIPOS>SUBSTRUCTURE 1 DA 1 RESIDUE 4 A DA 1 ROOT 2 DA 2 RESIDUE 4 A DA 2 3 DA 3 RESIDUE 4 A DA 2 4 DA 4 RESIDUE 4 A DA 2 5 DA 5 RESIDUE 4 A DA 2 6 DA 6 RESIDUE 4 A DA 2 7 DA 7 RESIDUE 4 A DA 2 8 DA 8 RESIDUE 4 A DA 2 9 DA 9 RESIDUE 4 A DA 2 10 DA 10 RESIDUE 4 A DA 2 11 DA 11 RESIDUE 4 A DA 2 12 DA 12 RESIDUE 4 A DA 2 13 DA 13 RESIDUE 4 A DA 2 14 DA 14 RESIDUE 4 A DA 2 15 DA 15 RESIDUE 4 A DA 2 16 DA 16 RESIDUE 4 A DA 2 17 DA 17 RESIDUE 4 A DA 2 18 DA 18 RESIDUE 4 A DA 2 19 DA 19 RESIDUE 4 A DA 2 20 DA 20 RESIDUE 4 A DA 1 Best Wishes! Jiying Jia

2 2

Color surface by underlying atom
by Tom Zhang 06 Jul '16

06 Jul '16

Hello, I have a question about surface coloring. I've noticed that when I create surfaces in a session for the first time, the surface are colored based on the colors of the underlying atoms. However, after setting the surface colors manually, I couldn’t find a way to change the colors back. I have tried settings in surface attributes, but none of them work. So my question is, how do I change the surface color back so that it is based on the underlying atoms? Many thanks, Tom

2 2

About findclash in detecting overlap of atoms
by xibei 06 Jul '16

06 Jul '16

Hi, I'm trying to use command "findclash" to check the excluded volume effect by detecting overlaps between atoms. The command I use is "findclash #0 test #0" or "findclash #0 overlapCutoff value test #0", but I found that two close atoms (14C,16C, dis=0.8) are not identified as "overlaped" while another two atoms (11C, 16C, dis=1.8) whose distance is larger are overlaped... Is there anything wrong about understanding the overlap? Example molecular (init.mol2): @<TRIPOS>MOLECULE init.mol2 20 19 20 0 0 NUCLEIC_ACID NO_CHARGES @<TRIPOS>ATOM 1 C 14.7888 10.0072 -5.6663 C.3 1 DA 0.0000 2 C 15.4013 8.5150 -3.5012 C.3 2 DA 0.0000 3 C 13.7388 8.7698 -5.6133 C.3 3 DA 0.0000 4 C 14.6414 7.5770 -3.3654 C.3 4 DA 0.0000 5 C 12.9675 5.9273 -2.0359 C.3 5 DA 0.0000 6 C 13.6457 4.0155 -0.2544 C.3 6 DA 0.0000 7 C 12.8822 2.8588 2.0634 C.3 7 DA 0.0000 8 C 11.7541 3.3958 4.4562 C.3 8 DA 0.0000 9 C 11.2290 4.5854 6.8231 C.3 9 DA 0.0000 10 C 13.8907 4.6510 7.2730 C.3 10 DA 0.0000 11 C 15.5581 5.2490 9.3114 C.3 11 DA 0.0000 12 C 17.8150 4.7800 10.7177 C.3 12 DA 0.0000 13 C 18.0666 2.1205 10.3271 C.3 13 DA 0.0000 14 C 16.9288 4.4119 9.4640 C.3 14 DA 0.0000 15 C 14.9471 3.0788 10.7232 C.3 15 DA 0.0000 16 C 16.7345 3.9070 8.8773 C.3 16 DA 0.0000 17 C 15.5384 2.3512 10.7314 C.3 17 DA 0.0000 18 C 16.0476 1.4159 8.2501 C.3 18 DA 0.0000 19 C 17.5152 1.5369 5.9877 C.3 19 DA 0.0000 20 C 17.5650 3.1811 3.8468 C.3 20 DA 0.0000 @<TRIPOS>BOND 1 1 2 1 2 2 3 1 3 3 4 1 4 4 5 1 5 5 6 1 6 6 7 1 7 7 8 1 8 8 9 1 9 9 10 1 10 10 11 1 11 11 12 1 12 12 13 1 13 13 14 1 14 14 15 1 15 15 16 1 16 16 17 1 17 17 18 1 18 18 19 1 19 19 20 1 @<TRIPOS>SUBSTRUCTURE 1 DA 1 RESIDUE 4 A DA 1 ROOT 2 DA 2 RESIDUE 4 A DA 2 3 DA 3 RESIDUE 4 A DA 2 4 DA 4 RESIDUE 4 A DA 2 5 DA 5 RESIDUE 4 A DA 2 6 DA 6 RESIDUE 4 A DA 2 7 DA 7 RESIDUE 4 A DA 2 8 DA 8 RESIDUE 4 A DA 2 9 DA 9 RESIDUE 4 A DA 2 10 DA 10 RESIDUE 4 A DA 2 11 DA 11 RESIDUE 4 A DA 2 12 DA 12 RESIDUE 4 A DA 2 13 DA 13 RESIDUE 4 A DA 2 14 DA 14 RESIDUE 4 A DA 2 15 DA 15 RESIDUE 4 A DA 2 16 DA 16 RESIDUE 4 A DA 2 17 DA 17 RESIDUE 4 A DA 2 18 DA 18 RESIDUE 4 A DA 2 19 DA 19 RESIDUE 4 A DA 2 20 DA 20 RESIDUE 4 A DA 1 Best Wishes! Jiying Jia

1 0

Visulaizing maps from COOT in Chimera
by Cedric Govaerts 05 Jul '16

05 Jul '16

Hi all, I would like to use Chimera to show a 2FO-FC or FO-FC electron density map (actually a tiny part of it) obtained from COOT (or directly from the refinement program). If I open both the PDB file and the .map file, they are correctly open except that the bounding box from chimera truncate the map way to early. That's because my PDB absolute coordinate sit in the origin and it seem I cannot use negative value for the boundaries of the volume/map. How can I get the map to extend entirely over my protein ? Thanks ! Cedric -- Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77 Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium http://govaertslab.ulb.ac.be/

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molecular surface el. potential data
by Marek Maly 05 Jul '16

05 Jul '16

Hello, Chimera has capability to color molecular surface by electrostatic potential (including solvent, ions effect) using data calculated on relevant volume grid (eventually saved in *.dx file) by apbs module. My question is, is/could be possible simply to export el. potential values which are on the molecular surface (that which are using for surface coloring) to *.txt file for consequent processing - e.g. calculation of the average value of the el. potential on the molecular surface, standard deviation ... ? Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

2 1

Re: [Chimera-users] Visulaizing maps from COOT in Chimera
by Oliver Clarke 05 Jul '16

05 Jul '16

Hi Cedric, Chimera cannot extend the map to cover your molecule - it does not have the symmetry expansion features available in coot. I have an extension for Coot (available as part of this script: https://www.dropbox.com/s/0b4bebwxw0p9x0e/oli_custom.py?dl=0) which will open the region of the map(s) currently displayed in coot in Chimera, perhaps this will be useful for you. Alternatively, when you are calculating the map, make sure you calculate it to cover your entire molecule (there are options in both phenix and refmac for this purpose). Cheers, Oli. > Date: Mon, 4 Jul 2016 15:11:56 +0200 > From: Cedric Govaerts <cgovaert(a)ulb.ac.be> > To: chimera-users(a)cgl.ucsf.edu > Subject: [Chimera-users] Visulaizing maps from COOT in Chimera > Message-ID: <6db1dd6b-2fc9-9fd9-158c-34db965d5a8f(a)ulb.ac.be> > Content-Type: text/plain; charset="utf-8"; Format="flowed" > > Hi all, > > I would like to use Chimera to show a 2FO-FC or FO-FC electron density > map (actually a tiny part of it) obtained from COOT (or directly from > the refinement program). > > If I open both the PDB file and the .map file, they are correctly open > except that the bounding box from chimera truncate the map way to early. > > That's because my PDB absolute coordinate sit in the origin and it seem > I cannot use negative value for the boundaries of the volume/map. > > How can I get the map to extend entirely over my protein ? > > > Thanks ! > > > Cedric > > > -- > Cedric Govaerts, Ph.D. > Universite Libre de Bruxelles > Campus Plaine. Phone :+32 2 650 53 77 > Building BC, Room 1C4 203 > Boulevard du Triomphe, Acces 2 > 1050 Brussels > Belgium > http://govaertslab.ulb.ac.be/ >

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How to detect bond cross
by Jiying Jia 01 Jul '16

01 Jul '16

Hi, Is there a way to detect whether there's bond cross in the conformation? Or check whether it's self-avoiding? The command "findclash" seems not to be able to do this. ------------------ Best Wishes! Jiying Jia

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

30 Jun '16

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

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

30 Jun '16

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

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

30 Jun '16

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

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

30 Jun '16

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

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

29 Jun '16

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

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

29 Jun '16

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

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vector from atom
by Fabian gmail 29 Jun '16

29 Jun '16

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

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

29 Jun '16

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

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

28 Jun '16

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

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

27 Jun '16

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

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opening large xyz file
by Michał Kadlof 27 Jun '16

27 Jun '16

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

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(no subject)
by Nicole Mckinney 27 Jun '16

27 Jun '16

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

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Chimera question
by Smart Biology 24 Jun '16

24 Jun '16

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

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

24 Jun '16

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

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

24 Jun '16

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

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Module import error
by Subha Kalyaanamoorthy 23 Jun '16

23 Jun '16

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

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

23 Jun '16

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

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assistance
by A G Szabo 23 Jun '16

23 Jun '16

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

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

23 Jun '16

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

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volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

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

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

21 Jun '16

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

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

20 Jun '16

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

2 2

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

20 Jun '16

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

2 4

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

19 Jun '16

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

2 1

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

15 Jun '16

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

2 1

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

15 Jun '16

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

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

15 Jun '16

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

1 0

RR distance plot export
by Toshiki Nakashige 14 Jun '16

14 Jun '16

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

2 1

Paper viruses
by David Bhella 14 Jun '16

14 Jun '16

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

2 1

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

14 Jun '16

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

2 1

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

13 Jun '16

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

1 0

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

13 Jun '16

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

2 1

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

13 Jun '16

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

2 4

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

10 Jun '16

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

2 2

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

10 Jun '16

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

2 1

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

09 Jun '16

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

3 2

query regarding volume viewer
by Nidhi Batra 09 Jun '16

09 Jun '16

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

2 4

renumbering missing residues
by Charles, Fiorella 08 Jun '16

08 Jun '16

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

2 2

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

07 Jun '16

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

2 1

Trouble starting Chimera
by Janet Iwasa 07 Jun '16

07 Jun '16

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

2 1

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

07 Jun '16

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

1 0

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

07 Jun '16

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

2 1

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

07 Jun '16

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

2 2

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

06 Jun '16

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

2 1

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

06 Jun '16

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

2 3

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

06 Jun '16

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

2 1

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

06 Jun '16

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

2 2

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

03 Jun '16

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

2 3

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

03 Jun '16

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

2 3

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

03 Jun '16

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

2 1

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

03 Jun '16

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

3 7

mask
by Dougherty, Matthew T 02 Jun '16

02 Jun '16

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

2 1

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

01 Jun '16

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

1 0

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

01 Jun '16

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

3 2

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

01 Jun '16

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

2 1

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

01 Jun '16

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

3 14

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

31 May '16

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

1 0

Rotamers in Chimera
by Lew Jacobson 31 May '16

31 May '16

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

2 1

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

31 May '16

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

3 8

broken lines
by shazia sabir 29 May '16

29 May '16

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

2 1

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

26 May '16

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

2 2

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

25 May '16

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

2 1

PDB post-processing
by James Starlight 25 May '16

25 May '16

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

2 1

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

25 May '16

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

2 1

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

23 May '16

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

1 0

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

23 May '16

Hi guys, just to let you know that mesa-11.2.2 is messing with Chimera startup sequence.: $ chimera --debug initializing general preferences loading Tix initializing graphics libGL error: unable to load driver: i965_dri.so libGL error: driver pointer missing libGL error: failed to load driver: i965 libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 154 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 1410 Current serial number in output stream: 1411 $ `chimera --root`/bin/linuxdist /etc/os-release: NAME="Antergos Linux" VERSION="2015.11-ISO-Rolling" ID="antergos" ID_LIKE="arch" PRETTY_NAME="Antergos Linux" CPE_NAME="cpe:/o:antergosproject:antergos:2015.11" ANSI_COLOR="1;34;40" HOME_URL="https://antergos.com/" SUPPORT_URL="https://forum.antergos.com/" BUG_REPORT_URL="https://github.com/antergos" /etc/arch-release: Antergos Linux release 2015.11 (ISO-Rolling) /proc/cpuinfo: cpu: 8 GenuineIntel Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz (x86_64) cpu MHz: 3884.625 cache: 8192 KB /proc/meminfo: MemTotal: 16296392 kB Graphics: 00:02.0 VGA compatible controller: Intel Corporation Xeon E3-1200 v3/4th Gen Core Processor Integrated Graphics Controller (rev 06) 01:00.0 VGA compatible controller: NVIDIA Corporation GM204 [GeForce GTX 970] (rev a1) I had to rollback to mesa-11.2.1 to make it work again. Cheers, Jaime Rodríguez-Guerra Pedregal Molecular modeling of transition metal systems group Department of Chemistry, Faculty of Sciences Edif. C · C7/153 Campus de la UAB · 08193 Bellaterra (Cerdanyola del Vallès) · Barcelona · Spain +34 93 581 28 57 www.uab.cat<http://www.uab.cat/> [http://www.uab.cat/vcard/Logo_ORCID_0.png] <http://orcid.org/0000-0001-8974-1566> [http://www.uab.cat/vcard/Logo_LinkedIn_0.png] <https://www.linkedin.com/in/jaimergp> This message may contain private or confidential information, and is addressed exclusively to its intended recipient. If you have received it in error, please notify the sender and delete it. Please bear in mind that you are not authorized to use it for any purposes. Please consider the environment before printing this email.

1 0

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

19 May '16

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

1 1

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

16 May '16

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

2 5

question
by zona cat 14 May '16

14 May '16

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

2 5

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

13 May '16

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

2 1

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

12 May '16

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

2 1

Averaging multiple structures
by Yehuda Halfon 11 May '16

11 May '16

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

2 4

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

11 May '16

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

2 3

Join models
by shazia sabir 10 May '16

10 May '16

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

2 3

surfaces
by A G Szabo 10 May '16

10 May '16

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

2 1

repeat question
by A G Szabo 10 May '16

10 May '16

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

2 2

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

10 May '16

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

1 0

rainbow color scheme
by Shreeramesh 09 May '16

09 May '16

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

2 1

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

09 May '16

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

2 1

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

09 May '16

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

3 3

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

05 May '16

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

2 1

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

04 May '16

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

3 2

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

04 May '16

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

2 1

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

02 May '16

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

2 1

Solicitud Información
by luz Martinez 02 May '16

02 May '16

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

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

01 May '16

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

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Manually adjusting alignment
by Visvaldas K. 30 Apr '16

30 Apr '16

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

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

28 Apr '16

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

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Labeling and coloring chains
by Elaine Meng 28 Apr '16

28 Apr '16

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

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

28 Apr '16

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

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The question about fitting
by Zhongjun Hu 28 Apr '16

28 Apr '16

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

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electron density map
by 陈柳青 28 Apr '16

28 Apr '16

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

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

28 Apr '16

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

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

28 Apr '16

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

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

27 Apr '16

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

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

27 Apr '16

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

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

27 Apr '16

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

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

26 Apr '16

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

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

26 Apr '16

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

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

26 Apr '16

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

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