- Chimera-users - RBVI Mailing Lists

measuring distance between an atom and centroid of an aromatic ring
by Aswani Kumar Kancherla 10 Oct '14

10 Oct '14

Hello Chimera Users, I need to measure and mark the distances of a few atoms to the center of an aromatic ring. I could define and create a centroid and plane for the ring. However, I am unable to measure or mark the distances of the surrounding atoms from the centroid of the ring (This is an exercise to show the ring current effect of the aromatic ring on the chemical shifts of the neighboring protons). Could anyone please give a hint on how I can go about this? thanking you in advance, best wishes, Aswani -- K.Aswani Kumar Graduate Student Molecular Biophysics Unit Indian Institute of Science Bangalore-560012 Karnataka, India.

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please give advice
by Jane Norman 10 Oct '14

10 Oct '14

Hello I am new to using chimera and I have been struggling with one aspect. I'm trying to mutate one residue in my protein, by using the command swapaa leu :310, this seems to work nicely, To show the amino acid I then go in to "tools" then "sequence" and select this mutated residue and then go to "actions" then "atoms/bond" and "show" and the residue is displayed, however it is displayed as a block colour which I can't seem to change the colour scheme of the amino acid to match other residues which I've displayed nearby (e.g showing different colours (white/blue/red for different groups on the amino acid). i can easily change the block coulr of the whole reside but not to match the helpful scheme of he other displayed residues. However If I just pick an unmutated residue to display it shows it in the same style as the other residues (which is what I want for my mutated one) I hope that makes sense I couldn't find the answer in the help section Thank you very much for your time Jane

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Failed to prepare receptor for AutoDock Vina
by William McDonald 09 Oct '14

09 Oct '14

Hello Chimera users, I am attempting to learn ligand docking using autodock vina in Chimera. I am using a local copy of AutoDock Vina, and Chimera 1.9 (64 bit) for mac os 10.9.5. I have added H atoms to the ligand prior to loading the structure into Chimera. I added H atoms to the protein within Chimera. However, when I run AutpDock Vina I receive the error: ValueError: Could not find atomic number for Ha Ha failed to prepare receptor for AutoDock Vina; please look in Reply Log to see errors. I thought that this could be because of the H atoms added to CA atoms are named HA by default, however if I change the HA atom names to H, I still get the same error. I can verify that there are no atoms named "Ha" in the structure. What am I doing wrong? Thanks for your time. -- William J. McDonald Postdoctoral Scholar Department of Chemistry and Biochemistry University of California, Santa Cruz

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color zones with multiple markers
by Revyakin, Andrey (Dr.) 09 Oct '14

09 Oct '14

Hi Chimera folks, I am a new user of Chimera; trying to simultaneously color different features of a Cryo-EM structure (EMD-2305) with different colors. I select volume tracer and make a marker (looks like a tumour on the structure), and select color zone. The features are large, so I select another marker nearby to expand the color zone (another tumour appears next to the first tumour), but then the color zone associated with the first marker disappears and moves to the next marker. How can I preserve the previously created color zone? I seem to be unable to select multiple markers by holding ctrl and clicking/dragging-- either the whole structure is selected, or only one marker can be selected at a time. I spent an hour looking on the web for a solution, but did not find any. Windows 7, 64 bit. I apologize if this is too trivial of a question. Cheers, Andrey R.

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Energy calculation
by bobo2412＠gmail.com 09 Oct '14

09 Oct '14

Hi, Do you know if chimera can do energy calculation? I have a protein I want to mutate some residues and calculate the energy difference before and after the mutation. Do you know if I can do that in chimera? Thanks, Bobo 发自我的 iPhone

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Re: [Chimera-users] measure symmetry
by Tom Goddard 08 Oct '14

08 Oct '14

Hi Reggie, You are right that the EMDB 1220 virus capsid has none of the standard icosahedral orientations. It is approximately 3-fold axis along z, and 2-fold axis along x (Chimera orientation 2n3r) but it is maybe 5 degrees off from that. If this capsid was refined with C1 symmetry then there is no reason for it to have a standard orientation. It will be difficult to compute the icosahedral symmetry matrices. I suggest you talk to the author of that map Gabe Lander who has a lab at Scripps, right where you are located. Tom On Oct 8, 2014, at 2:07 PM, Reginald McNulty wrote: > Thanks. It works. > I’m trying to do the same thing now for a virus with a tail. It was refined with C1 symmetry. The icosahedral symmetry in the capsid is evident. But I can’t get the icosahedal surface to match the symmetry exactly. Can you take a look at this map: emd_1220.map? > Reggie > On Oct 8, 2014, at 11:34 AM, Tom Goddard wrote: > >> Hi Reggie, >> >> I used the following Chimera commands to create an icosahedral cage for virus capsid 2xyz and density map for full capsid, image attached. >> >> Tom >> >> open 2xyz >> rainbow chain >> sym #0 surf true >> >> # Used Tools / Higher-Order Structure / Icosahedron Surface to figure out orientation is n25r (no sym on x, 2-fold on y, 5-fold on z, with extra rotation). >> >> shape icos radius 400 orient n25r lattice 2,1 color blue linewidth 5 >> molmap #0 10 sym i,n25r >> >> >> <2xyz.jpg> >> >> On Oct 8, 2014, at 10:40 AM, Reginald McNulty wrote: >> >>> Dear Tom, >>> >>> I’ve imported a virus capsid shell pdb 2xyz to chimera. I want to measure the symmetry and make a cage based on that symmetry. Molmap seems to only produce a map of the asymmetric unit, not the entire capsid. Any thoughts? >>> I’m currently following directions that are here: http://www.cgl.ucsf.edu/chimera/videodoc/IcosWedge/index.html >>> >>> All the best, >>> -Reggie >>> >>> -- >>> Reginald McNulty, Ph.D. >>> Postdoctoral Research Associate >>> The Scripps Research Institute >>> Johnson Lab >>> Department of Integrative Structural and Computational Biology >>> 10550, N. Torrey Pines Road, MB-31 >>> La Jolla, California 92037 >>> >>> >>> >>> >>> >>> >> > >

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Re: [Chimera-users] Analysis of the multiple alignments + structures
by James Starlight 08 Oct '14

08 Oct '14

Dear Chimera users! I've been interested in the possibility to make some sort of evolutional analysis in Chimera using MSA of the protein under study, its X-ray structures and its superimpositions as well as obtained projections of the sequence conservation in key (functionally-important) hot spots made by means of mutalign plugin. For my particular case I have MSA for the big number of olfactory receptors sequences (including receptors from different sub-groups associated with different specificity towards different odors). As the result I should to find possibility to sort these sequences of each ORs based on some phylogenetic study (I thinks to obtain tree-like view of the sequences) considering explicitly residues of the receptor's binding site. One of the possible idea is to keep only those residues of interest (from the ligand binding cavity) and rerun the alignment on these mini sequences to make prediction of new family of Or that may interact with the same kind of odorants. Would this idea is better realized by means of differential evolutional tracing method (because In fact we need to subtract conservative residues of one sub-branch of the whole phylogeny tree from those of all (root) OR) or there are any trivial alternatives? Thanks for help, James 2014-09-19 22:04 GMT+02:00 James Starlight <jmsstarlight(a)gmail.com>: > Dear Elaine, > > thanks you very much for the suggestions! It's always a big pleasure to > get advise from the experienced person :) BTW may be the next question will > be more in connection with your present job (Chimera software developer). I > wounder whether it *in principle* possible to find an academic post-doc job > focused mainly on molecular visualization and animation (as the trivial > example os such job in my mind is to make a pictures and movies of the > proteins and it's complexes using data from different resolution's > experimental techniques and modelling). How do you think will it be easily > to obtain such job for the person who's PhD was based on structural biology > (experimentalist) or alternatively focused on molecular modeling and > bioinformatics ? > > Kind regards, > > Gleb > > 2014-09-16 23:36 GMT+04:00 Elaine Meng <meng(a)cgl.ucsf.edu>: > >> Dear Gleb, >> I really don't know the answer! I've never searched for such a position >> myself. I could only guess that you would try to search for "teaching" in >> addition to the keywords about molecular modeling and structural >> bioinformatics. >> >> For postdocs at least, most people are looking for research lab positions >> rather than teaching. In that case they identify research papers that >> describe the types of work that they want to do, then contact the labs of >> the authors about possible postdoc opportunities. >> >> The only other idea I have is to try to figure out (by online searching) >> what institutions offer classes in chemistry and biology that include >> structures/modeling, then see if they have openings for instructors. >> >> I'm sorry, I don't think these are very bright ideas, or anything that >> you wouldn't have thought of yourself already. >> 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 Sep 16, 2014, at 12:09 PM, James Starlight <jmsstarlight(a)gmail.com> >> wrote: >> >> > Hi Elaine, >> > >> > thank you for the suggestions again! By that time I've noticed that to >> find structural bioinformatics position is much complicated than to find >> positions in fields of theoretical biophysics, computational biology or >> even genome bioinformatics. BTW according to your experience what keywords >> might be to seek position focused rather not to the research but to make >> some teaching practice, workshops and tutorials (focused on structural >> bioinformatics and modeling)? >> > >> > Kind regards, >> > >> > Gleb >> > >> > 2014-09-10 2:52 GMT+04:00 Elaine Meng <meng(a)cgl.ucsf.edu>: >> > Glad it was useful! I don't know if there is a specific name other >> than "structural bioinformatics," but especially now that more and more >> structures are known (in combination with perhaps too many sequences!), it >> should be a fruitful and interesting area of research. >> > Best, >> > Elaine >> > >> > On Sep 6, 2014, at 12:00 AM, James Starlight <jmsstarlight(a)gmail.com> >> wrote: >> > >> > > Hi Elaine, >> > > >> > > thank you very much It was really useful for me! I plan to look for >> the post-doc for myself on next year switching from the modeling and >> theoretical chemistry to structural bioinformatics coupled with the >> phylogenetic analysis (I don't know yet precise name of this discipline in >> the computational biology) so It will be very helpful! >> > > >> > > All the best, >> > > >> > > James >> > > >> > > >> > > 2014-09-05 20:59 GMT+04:00 Elaine Meng <meng(a)cgl.ucsf.edu>: >> > > HI James, >> > > Sorry, Chimera does not do evolutionary trace calculations. I would >> definitely have mentioned it if it did! In Chimera, if you input a tree >> along with your alignment, you can click a node on the tree and easily >> extract only the sequences for that node, but there is nothing to compare >> the residues from one set of sequences with those from another set of >> sequences, other than looking at the separate alignment windows yourself. >> Also, Chimera cannot create the tree, it must be read in from a file. >> > > < >> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/f… >> > >> > > … see the section on Trees: >> > > < >> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m… >> > >> > > … example image of tree+alignment in Chimera: >> > > < >> http://www.rbvi.ucsf.edu/chimera/data/tutorials/systems/redoxin/ConSurf-1hd… >> > >> > > >> > > Although I’m still very interested in GPCRs, I have not actively >> worked on them for >10 years, so I’m not the best person to ask for >> current information. I know there is a GPCRdb, but I don’t know if it has >> been kept up to date. You could try googling or pubmed-searching for “gpcr >> alignments” or similar terms. >> > > >> > > Two ideas for evolutionary trace: >> > > >> > > (1) The Lichtarge group has an evolutionary trace server. >> > > <http://mammoth.bcm.tmc.edu/ETserver.html> >> > > >> > > At first I thought you could only put in a PDB ID and not have any >> control over what sequences are used (which might not be useful for your >> research), but then I noticed a “GPCRs” link on the left-hand side. Click >> that and it lets you choose specific GPCR subsets, which sounds exactly >> like the kind of calculation you wanted. I don’t know if it includes your >> specific groups of interest, however, and I don’t see a way to use your >> own alignments. >> > > <http://mammoth.bcm.tmc.edu/gpcr/diff_GPCRA.html> >> > > >> > > (2) JEvTrace, a Java implementation of evolutionary trace. >> > > <http://compbio.berkeley.edu/people/marcin/jevtrace/> >> > > >> > > I have one correction to that page. It says you can show results >> using the MSF Viewer tool in Chimera, which no longer exists. You can >> still use Chimera, just the Multalign Viewer tool instead (Multalign Viewer >> menu: "File… Load SCF/Seqsel File” will open the file from JEvTrace). I’ll >> email the author and tell him to update that information. >> > > >> > > Those are all my ideas. If neither helps you, you may have to >> continue searching for programs or other tools and instructions on how to >> do the steps of the analysis yourself. >> > > 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 4, 2014, at 11:39 PM, James Starlight <jmsstarlight(a)gmail.com> >> wrote: >> > > >> > > > Elaine, >> > > > >> > > > onequestion about your 2003 GPCRs study: in this paper you've used >> the method called differential evolution tracing to detect >> functionally-relevant amino acids for rhodopsin only (substration of the >> conservative residues found in rhodopsin from those found in whole set of >> A-class GPCRs). I wounder if there any possibility for this method in >> Chimera's mutalign (in case where I have big alignment with thesequences of >> all olfactory receptors) to substract residues found in one philogenetic >> branch (corresponded to specified sub-class or group of those receptors) >> from the residues common to all olfactory receptors or (ii) substract >> residues common for the all olfactory receptors from those common to all >> A-class GPCRs? BTW do you know open-access data-bases consisted of the >> evolutional (alignments) information to the GPCRs? it's intresting to >> compare my alignment with some references. >> > > > >> > > > Thanks for help, >> > > > >> > > > James >> > > >> > > >> > > _______________________________________________ >> > > Chimera-users mailing list >> > > Chimera-users(a)cgl.ucsf.edu >> > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > >> > >> >> >

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Remove shapes programmatically
by jiserte＠unq.edu.ar 08 Oct '14

08 Oct '14

Hello. I'm having a problem working with shapes in chimera. I'm adding shapes with a script using commands like: shape tube #:1@CA#:100@CA radius 0.1 I want to remove some of the shapes later in the script, however i can not find the proper way to do it. I know is posible to do it using the GUI (picking the shape with control key and then "Actions>Surfce>Hide" in the menu bar), but i dont know how to do the same with the command line. Also, i can not find the way to manipulate existing shapes (increase radius, change color, etc). There is a way to delele, hide or manipualte shapes? Thank you all. Javier Iserte PhD Fundación Instituto Leloir Buenos Aires, Argentina.

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Re: [Chimera-users] measure symmetry
by Tom Goddard 08 Oct '14

08 Oct '14

Hi Reggie, I used the following Chimera commands to create an icosahedral cage for virus capsid 2xyz and density map for full capsid, image attached. Tom open 2xyz rainbow chain sym #0 surf true # Used Tools / Higher-Order Structure / Icosahedron Surface to figure out orientation is n25r (no sym on x, 2-fold on y, 5-fold on z, with extra rotation). shape icos radius 400 orient n25r lattice 2,1 color blue linewidth 5 molmap #0 10 sym i,n25r On Oct 8, 2014, at 10:40 AM, Reginald McNulty wrote: > Dear Tom, > > I’ve imported a virus capsid shell pdb 2xyz to chimera. I want to measure the symmetry and make a cage based on that symmetry. Molmap seems to only produce a map of the asymmetric unit, not the entire capsid. Any thoughts? > I’m currently following directions that are here: http://www.cgl.ucsf.edu/chimera/videodoc/IcosWedge/index.html > > All the best, > -Reggie > > -- > Reginald McNulty, Ph.D. > Postdoctoral Research Associate > The Scripps Research Institute > Johnson Lab > Department of Integrative Structural and Computational Biology > 10550, N. Torrey Pines Road, MB-31 > La Jolla, California 92037 > > > > > >

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help
by JESSE JAYNES 06 Oct '14

06 Oct '14

I am a long time user of Chimra and greatly appreciate the software. I am also a professor at Tuskegee university and I use it in the classroom. I am Mac user. I have a question. How can I model an all D-form of a 10 amino acid peptide and generate its pdb? Thank you! Jesse M. Jaynes

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delete water residues: mangled atom specifier
by George Tzotzos 06 Oct '14

06 Oct '14

I’m running an amber trajectory and in particular snapshots I’d like to delete all water molecules but one. If I do del :WAT !1355.water I get a “mangled atom specifier”. Obviously I got the wrong syntax. Your help will be much appreciated Regards George

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Question about RMSD calculation of MatchMaker
by Matthias Fellner 03 Oct '14

03 Oct '14

Good day I am a PhD student at the University of Otago New Zealand. First I would like to thank you for this very useful software, I use it for all my protein crystallography pictures and a lot of analysis as well, I will use a citation for sure when I publish using your software. A current analysis of mine involves a crystal structure that has 4 chains in the asymmetric unit. They chains are very similar when aligned and I would like to have a statistic to show this. I assume the RMSD is the way to go. So I saved each chain as its own pdb, loaded them in Chimera and used your MatchMaker to align chain B,C and D to chain A (randomly chosen because of notation of chains). The chains have an identical amino acid sequence (~200 residues), I just build 1-5 residues more or less at each end of the chain but otherwise they should all be the same. Now the reply log gives out the RMSD and the number is under 1Å as I expected and I can quote that. But my question would be why did it use a different numbers of atom pairs for the different chains (191 or 188 or 193) and which atom pairs are those. I assume it picks one atom from the main chain of each residue and the different number comes from the difference residue number at the end of the chains. I searched through your help files and with google through your board but could not find the answer to what atoms are paired and if you can change the pair for example to include all atoms of the mainchain or even all atoms all together. Sorry for the long question but I wanted to give all the details, attached also the (default) options I had for the MatchMaker and the reply log. In addition a small question which I guess wont be possible - is there any way to also align water molecules adjacent to the chains although all water molecules are saved in chain S together? Thank you Matthias [cid:image001.png@01CFDE66.FDAB5BD0] Matchmaker chainA.pdb, chain A (#0) with chainD.pdb, chain D (#3), sequence alignment score = 999.7 with these parameters: chain pairing: bb Needleman-Wunsch using BLOSUM-62 ss fraction: 0.3 gap open (HH/SS/other) 18/18/6, extend 1 ss matrix: (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4 iteration cutoff: 2 RMSD between 191 atom pairs is 0.506 angstroms Matchmaker chainA.pdb, chain A (#0) with chainC.pdb, chain C (#2), sequence alignment score = 999.1 with these parameters: chain pairing: bb Needleman-Wunsch using BLOSUM-62 ss fraction: 0.3 gap open (HH/SS/other) 18/18/6, extend 1 ss matrix: (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4 iteration cutoff: 2 RMSD between 188 atom pairs is 0.551 angstroms Matchmaker chainA.pdb, chain A (#0) with chainB.pdb, chain B (#1), sequence alignment score = 987.2 with these parameters: chain pairing: bb Needleman-Wunsch using BLOSUM-62 ss fraction: 0.3 gap open (HH/SS/other) 18/18/6, extend 1 ss matrix: (O, S): -6 (H, O): -6 (H, H): 6 (S, S): 6 (H, S): -9 (O, O): 4 iteration cutoff: 2 RMSD between 193 atom pairs is 0.336 angstroms

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Reg: Peptide Dimer
by Amit Jaiswal 30 Sep '14

30 Sep '14

Hi, I would like to know if is it possible to prepare peptide dimer In Chimera. If yes, how and if no what are the possible ways to prepare it? Thanks in advance. With kind regards, Amit Jaiswal -- *Yours Sincerely,* *~~~~~~~~~~~~~~~~~~~~~~~~**~~~* *Amit Jaiswal,* *A.T. Road, Tarajan,* *Jorhat - 785001,* *Assam.-------------------------------------------* *Centre for Bioinformatics,Pondicherry Central University,* *Pondicherry - 605014,* *Pondicherry. * *~~~~~~~~~~~~~~~~~~~~~~~~**~~~**~*

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Proposal to add ability to load CATH domains in Chimera
by Tony Lewis 30 Sep '14

30 Sep '14

Dear Chimera people, Many thanks to all Chimera contributors. Please may I propose an addition to allow users to access our CATH domains in the same way that they can currently access SCOP domains ( https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/scop.html )? PDBs for CATH domains can be loaded from URI's of the form: http://data.cathdb.info/latest_release/pdb/1cukA01 For information, CATH domain IDs contain 7 digits: - 1-4 : (eg 1cuk ) : PDB code - 5 : (eg A ) : chain code - 6-7 : (eg 01 ) : 2-digit domain number ( '00' for whole chain domains ) We here at CATH would be very happy to provide any other information required to implement this. Many thanks for your help. Kind regards, Tony Dr Tony Lewis Orengo Group UCL

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Regarding organic molecule minimization
by Satheesh G 29 Sep '14

29 Sep '14

Dear Sir, The azo compounds (organic molecule) minimization using Chimera software giving linear form (R-N=N-R to R-N=N-R (180 degrees bong angle between R-N=N instead R-N=N- 120 degrees). Which is not true. I have used the gasteiger and amber ff12sb force field. Please suggest me to solve this problem. Thanking you. Satheesh. [image: Inline image 1]

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Select next residue
by Tom Goddard 29 Sep '14

29 Sep '14

Hi Yanyan, I added three new keyboard shortcuts. “rn” selects the next residue after the currently selected one and the currently selected one gets unselected — basically it just moves the selection down by one residue. This applies even if a several residues are selected, the whole selection just gets moved down the chain by one position. “rp” selects the previous residue, and “ri” selects all residues between two currently selected residues. These should help you move the selection along in a quick way. Chimera keyboard shortcuts are not enabled by default. To enable them use the Chimera command “ac” (stands for accelerators) or use menu entry Tools / General Controls / Keyboard Shortcuts and click “Enable keyboard shortcuts”. If you use that menu entry then it will be remembered and shortcuts will be enabled when you start Chimera the next time. Shortcuts are all 2 letters and you don’t hit return after typing one. To get back to typing a command instead of a shortcut use the shortcut “cl” (command line). Here’s the list of shortcuts from the Chimera documentation. http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/ali… The new ones will be in tomorrow’s daily build (dated Sept 27, 2014). Tom On Sep 26, 2014, at 7:10 AM, Zhao, Yanyan wrote: > Hi, Tom. > > Thank you so much for the chimera lecture yesterday. It is very helpful. > I'm Yanyan from Baylor college of Medicine and is a rotation student in Wah's lab now. I'm using this software now. But I have a problem finding the keyboard shortcuts for selecting residues. I want to select residue one by one along the whole chain. But Ctl+left mouse click is a pain when dealing wit so many residues. Is there any shortcuts that I don't need to click the mouse and still can flow through the chain? > > Thanks. > > Best regards, > Yanyan

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running chimera on FC20
by David Roberts 29 Sep '14

29 Sep '14

Hi all, I just did a clean install of FC20 on an AMD dual core system. I opted for the 32 bit version, as these workstations are used for multiple things (and I find that it’s just easier most of the time, though 64 bit may be where I need to go eventually). I installed Chimera Version 1.9, Build 39798 on Fedora FC20. When running chimera, my computer constantly freezes. Obviously I’m missing something. I’m not doing anything fancy - I use Zalman monitors connected to generic video cards. I can run coot fine - I don’t know about ccp4i (it seems to run, but I haven’t challenged it in any way). As long as Chimera is not running, my computer runs nicely. I have flash/etc… working fine. Any thoughts on where I should start here? This happens on 3 separate systems (that are essentially the same, but not identical clones). I’m assuming I missed something obvious in the install. Thanks Dave

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How to load PDB data inline in Chimera script/command files
by Tony Lewis 29 Sep '14

29 Sep '14

Dear Chimera people, Many thanks to all Chimera contributors. Please can anyone tell me if there's a way to include PDB data *inline* in Chimera script / command / Chimerax files? PyMOL's read_pdbstr() command loads PDB data from an inline string, which means one file can contain both the structural data and the associated commands. That's rather convenient. I would much appreciate any help on how to do the same with Chimera. Apologies if the answer is obvious. Many thanks and kind regards, Tony Dr Tony Lewis Orengo Group UCL

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Angle
by Jian Guan 25 Sep '14

25 Sep '14

Hi All, I made two axes for two molecule, and want to measure the angle between them. Let's say, #1 and #2 are the two axes. I used command line of "angle #1 #2" to do that. Question: What is the default angle measurement? The #1 rotate clockwise or anti-clockwise to reach #2? Thanks, Jian

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Castp volume and surface area
by Felipe Vasquez 24 Sep '14

24 Sep '14

Hi, I am using CASTp plugin from Chimera in order to calculate both the volume and surface area of a specific pocket. I noticed that the 'mouth' atoms can be excluded from the visualization, and even the surface area is reported separately for both the pocket and the mouths by CASTp. However, there is only one reported volume. Is that volume considering both the pocket and mouth atoms to make just one general calculation? In addition, where can I find more info about the criteria to define a pocket's mouth? Thanks in advance for your help. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN +57 (1) 2207700 ext. 1419 Bogotá, D.C., Colombia

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opening a .dx format file as a volume file?
by David A Case 24 Sep '14

24 Sep '14

Hi: Is there a way for chimera to open a .dx file, but to treat the data as volume (density) data, rather than as an electrostatic potential? That is, I'd like the data in the .dx file to be rendered by the Volume Viewer, as if I had opened a CNS/XPLOR or CCP4 map file. Or, do you know of programs that will convert these file formats? (I've written one of my own, but am looking for confirmation that my code is actually correct, and doesn't have some off-by-one grid point or other mistake.) ....thanks!....dave case

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code or psuedo code for unit cell packing
by Bennion, Brian 24 Sep '14

24 Sep '14

Hello I found the unit cell gui to be very useful recently. However I am curious about how the "pack into unit cell" option works. What information in the pdb header is used to translate/rotate a set of monomers each in an individual unit cell and pack them back into the "original cell". Thanks for any help Brian

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soft roll off edges with Zone masks
by Adam Frost 23 Sep '14

23 Sep '14

hi Chimera users We have determined a pseudo-atomic resolution cryoEM density of a helical co-polymer (two unique chains for the repeating hetero-dimer). We would like to compute map-versus-model FSC curves for each of the unique chains. We'd like to use the Zone tool to mask out the relevant density per chain within ~3A or so of the atoms in our atomic model, but we would like the edges of this mask to be appropriately "soft" (whereas right now zone masking appears to employ a hard edge). has anyone already solved this problem? ~Adam

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Swapping aminoacid to a non-standard residue
by Rui Almeida 23 Sep '14

23 Sep '14

Hello all I am trying to change one aminoacid on a PDB file to a nonstandard residue: TYR to nitrotyroine (PDB ligand code: NIY). I tried modifying the structure of the existing aminoacid in the coordinate file to include an NO2 group in the meta position (Structure Editing --> Build Structure --> Modify Structure...), but ANTECHAMBER cannot assign the correct charges afterwards. Command "swapaa" was also ineffective. Is there anyway to modify the residue and assign the correct charges? Thank you in advance, Rui Almeida. -- Rui Almeida Ph.D., Biochemistry REQUIMTE/CQFB - BioInorganic Chemistry Lab Dep. Quimica, Faculdade de Ciencias e Tecnologia, UNL 2829-516 Caparica, PORTUGAL E-mail: rui.almeida(a)fct.unl.pt

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Find Clashes/Contact (or FindHBond) after splitting chains?
by Mark Girvin 19 Sep '14

19 Sep '14

(Apologies if this arrives twice - on rechecking it, the email address that I tried first looked wrong) Hello, A student in our Biochem class (we have them use Chimera, and tell them that this choice is because it is such a well-done program, and has such active support from the developers and mailing list -- thank you all!) was trying to use Tools->Structure Analysis->Find Contacts/Clashes (and FindHBonds, with the same problem) after running split to simplify displaying and hiding the 14 chains in the coordinate file of the oligomer (1avo) that he was working on. Selecting the residues in one chain (now one model), designating them as the first set within Find Clash/Contacts, checking against all other atoms, choosing "contacts" and applying (Find Contacts) gives no contacts (0 contacts on Reply log). But if run before splitting (selecting chain A and running Find Clash/Contact with the same settings) finds many contacts. The same holds true when using FindHBond - works pre-split, but not post-split. I was wondering whether we were doing something wrong, or if this is the expected behaviour? Thanks, - Mark (our work-around was to delete different subsets of chains and save the resulting coordinates as "HeteroDimerDimer.pdb" & "HeteroDimer.pdb" and then work with those, which went fine) - Mark

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