- 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

2 1

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

2 5

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 >> > >

2 3

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.

3 3

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 >

3 7

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

2 1

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

2 2

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

2 1

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

2 2

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

3 3

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

2 1

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

2 2

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

2 1

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

2 1

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

2 4

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

3 3

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

2 1

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

2 8

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

3 2

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/

2 1

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!

3 4

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 >

1 0

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!

1 0

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

3 5

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>

2 2

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

2 2

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!

2 2

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/

3 4

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/ >

1 0

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

2 2