From mfellner at chemistry.otago.ac.nz Wed Oct 1 21:38:14 2014 From: mfellner at chemistry.otago.ac.nz (Matthias Fellner) Date: Thu, 2 Oct 2014 04:38:14 +0000 Subject: [Chimera-users] Question about RMSD calculation of MatchMaker Message-ID: <8243E5A01F77EE41A9BF1BD1DA2FC7E338A8EBE7@ITS-EXM-P07.registry.otago.ac.nz> 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 1? 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 at 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 33538 bytes Desc: image001.png URL: From meng at cgl.ucsf.edu Fri Oct 3 10:50:15 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 3 Oct 2014 10:50:15 -0700 Subject: [Chimera-users] Question about RMSD calculation of MatchMaker In-Reply-To: <8243E5A01F77EE41A9BF1BD1DA2FC7E338A8EBE7@ITS-EXM-P07.registry.otago.ac.nz> References: <8243E5A01F77EE41A9BF1BD1DA2FC7E338A8EBE7@ITS-EXM-P07.registry.otago.ac.nz> Message-ID: <0C83AB3F-9985-4AC5-990B-5A3176F6C7B1@cgl.ucsf.edu> Hi Matthias! As shown in your image of the dialog, you?re using the ?Iterate by pruning?? option that removes farther-apart pairs from the fit. That?s why you could get different numbers of pairs used to calculate the RMSD even if all chains contain the same numbers of residues. Iteration is described in the MatchMaker docs: If you turn off the ?iterate? option, it will not try to improve the fit by pruning and will instead use all the pairs (CA-CA atom pairs of residues aligned in the sequence alignment). If the structures include the same residues for each chain, the pairwise chain-chain RMSDs will all be calculated from the same number of CA-CA atom pairs. The dialog image also shows you are fitting A-B, A-C, A-D. For completeness you may also want to try B-C, B-D, C-D. Another issue is that MatchMaker or its command equivalents (mmaker, matchmaker) only use one atom per residue, CA, and only considers aligned biopolymer chains (peptides, nucleic acids). If that?s what you want, no worries. However, you could use the ?match? command instead and specify any sets of atoms for RMSD calculations, such as all backbone, with or without iteration. However, it?s harder to use since you have to specify the atoms in the command line yourself, unlike MatchMaker that figures out which atoms to pair automatically. You could include waters, but it would be tedious/difficult to specify each water residue by name, in the corresponding orders, for the two structures to be matched. Also the waters would have to be in the respective models. Matchmaker vs. match is discussed in the following link: ?match? command manpage, examples: command-line atom specification: another ?match? example in a tutorial, see the Matching section in: If you are interested in the variation over the length of the chain as opposed to getting a single number, a nice way to show that is to first superimpose the chains, then associate them all with a single copy of the sequence. Then over the sequence you can display an RMSD histogram showing the alpha-carbon (or other atoms, depending on which RMSD you choose) structural variability at each position in the sequence. To do that: (1) superimpose chains however you like (Matchmaker or match) (2) show sequence of any one of them, presumably they are basically the same (menu: Favorites? Sequence, choose one) (3) in the sequence window, use Structure? Associations to associate all copies of the structure with the single sequence (4) in the sequence window, use the Headers menu to show the RMSD of interest (and hide other headers you don?t want to see) You can even show these RMSD values with colors or worm thickness on one of the copies, as described in more detail here: 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 Oct 1, 2014, at 9:38 PM, Matthias Fellner wrote: > 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 1? 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 > > > > > 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 > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From jjsqrd at bellsouth.net Mon Oct 6 10:52:30 2014 From: jjsqrd at bellsouth.net (JESSE JAYNES) Date: Mon, 6 Oct 2014 10:52:30 -0700 Subject: [Chimera-users] help Message-ID: <1412617950.83361.YahooMailNeo@web181706.mail.ne1.yahoo.com> 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Oct 6 15:00:07 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 6 Oct 2014 15:00:07 -0700 Subject: [Chimera-users] building D-amino acid peptides In-Reply-To: <1412617950.83361.YahooMailNeo@web181706.mail.ne1.yahoo.com> References: <1412617950.83361.YahooMailNeo@web181706.mail.ne1.yahoo.com> Message-ID: Hi Jesse, We're glad you like Chimera, and are always happy to hear about classroom use! As you probably saw, "Build Structure" doesn't have an option for D-amino acids. However, you can use it to build the L-amino acid version of the peptide, then invert the chirality of each residue. In a little more detail: (1) start Build Structure (in menu under Tools? Structure Editing) (2) in that tool, use the "Start Structure" section to create the L-amino acid version of your peptide sequence: enter the sequence, Apply, then in the next dialog set the phi/psi angles (3) invert the alpha-carbon of each residue, e.g. commands: invert :1 at ca invert :2 at ca (? etc. ?) invert :10 at ca Or, if you want to control exactly which two substituents on CA are swapped, you can name them in the command instead of the CA. If you wanted the H to be one of the swapped substituents, you would have to add explicit hydrogens first. For example, commands: addh invert :1 at ha,cb (etc.) You can save the structure as a PDB file with menu: File? Save PDB, or command: write 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 Oct 6, 2014, at 10:52 AM, JESSE JAYNES wrote: > 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 From gtzotzos at me.com Mon Oct 6 14:02:37 2014 From: gtzotzos at me.com (George Tzotzos) Date: Mon, 06 Oct 2014 18:02:37 -0300 Subject: [Chimera-users] delete water residues: mangled atom specifier Message-ID: <9A476268-6E7F-437D-A7B1-8E54374E967C@me.com> 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 From meng at cgl.ucsf.edu Mon Oct 6 15:30:46 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 6 Oct 2014 15:30:46 -0700 Subject: [Chimera-users] delete water residues: mangled atom specifier In-Reply-To: <9A476268-6E7F-437D-A7B1-8E54374E967C@me.com> References: <9A476268-6E7F-437D-A7B1-8E54374E967C@me.com> Message-ID: Hi George, You need something more like: del :wat & ~ :1355.water (delete wat residues AND NOT residue 1355 in water chain) 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 Oct 6, 2014, at 2:02 PM, George Tzotzos wrote: > 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 From gtzotzos at me.com Mon Oct 6 15:41:56 2014 From: gtzotzos at me.com (George Tzotzos) Date: Mon, 06 Oct 2014 19:41:56 -0300 Subject: [Chimera-users] delete water residues: mangled atom specifier In-Reply-To: References: <9A476268-6E7F-437D-A7B1-8E54374E967C@me.com> Message-ID: <2DE9C3B9-5D1D-4E3D-972E-E4CB7F23409A@me.com> Hi Elaine, Many thanks. Your help is greatly appreciated. Regards George On 6Oct, 2014, at 7:30 PM, Elaine Meng wrote: > Hi George, > You need something more like: > > del :wat & ~ :1355.water > > (delete wat residues AND NOT residue 1355 in water chain) > > 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 Oct 6, 2014, at 2:02 PM, George Tzotzos wrote: > >> 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 > From jjsqrd at bellsouth.net Mon Oct 6 16:37:18 2014 From: jjsqrd at bellsouth.net (JESSE JAYNES) Date: Mon, 6 Oct 2014 16:37:18 -0700 Subject: [Chimera-users] building D-amino acid peptides In-Reply-To: References: <1412617950.83361.YahooMailNeo@web181706.mail.ne1.yahoo.com> Message-ID: <1412638638.25973.YahooMailNeo@web181702.mail.ne1.yahoo.com> Elaine: Thanks so much! I will give it try. Regards, Jesse On Monday, October 6, 2014 5:00 PM, Elaine Meng wrote: Hi Jesse, We're glad you like Chimera, and are always happy to hear about classroom use! As you probably saw, "Build Structure" doesn't have an option for D-amino acids. However, you can use it to build the L-amino acid version of the peptide, then invert the chirality of each residue. In a little more detail: (1) start Build Structure (in menu under Tools? Structure Editing) (2) in that tool, use the "Start Structure" section to create the L-amino acid version of your peptide sequence: enter the sequence, Apply, then in the next dialog set the phi/psi angles (3) invert the alpha-carbon of each residue, e.g. commands: invert :1 at ca invert :2 at ca (? etc. ?) invert :10 at ca Or, if you want to control exactly which two substituents on CA are swapped, you can name them in the command instead of the CA. If you wanted the H to be one of the swapped substituents, you would have to add explicit hydrogens first. For example, commands: addh invert :1 at ha,cb (etc.) You can save the structure as a PDB file with menu: File? Save PDB, or command: write 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 Oct 6, 2014, at 10:52 AM, JESSE JAYNES wrote: > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From bobo2412 at gmail.com Tue Oct 7 14:04:23 2014 From: bobo2412 at gmail.com (bobo2412 at gmail.com) Date: Tue, 7 Oct 2014 16:04:23 -0500 Subject: [Chimera-users] Energy calculation Message-ID: <3F10A20F-14C4-43C7-826B-5EB440F5F493@gmail.com> 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 ???? iPhone From aldosegura at gmail.com Tue Oct 7 15:53:49 2014 From: aldosegura at gmail.com (Aldo Segura) Date: Tue, 7 Oct 2014 18:53:49 -0400 Subject: [Chimera-users] Energy calculation In-Reply-To: <3F10A20F-14C4-43C7-826B-5EB440F5F493@gmail.com> References: <3F10A20F-14C4-43C7-826B-5EB440F5F493@gmail.com> Message-ID: Hi Bobo, I think Chimera does not have such capability. I would suggest you trying with FoldX: foldx.crg.es Best, Aldo 2014-10-07 17:04 GMT-04:00 : 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 ???? iPhone _______________________________________________ Chimera-users mailing list Chimera-users at cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -- ========================================= Aldo Segura-Cabrera Research Fellow Division of Experimental Hematology and Cancer Biology Cancer and Blood Diseases Institute Cincinnati Children's Hospital Medical Center 3333 Burnet Ave, MLC 7013, Cincinnati OH 45229 e-mail: Aldo.Segura-Cabrera at cchmc.org; aldosegura at gmail.com ========================================= -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Oct 7 16:46:56 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 7 Oct 2014 16:46:56 -0700 Subject: [Chimera-users] Energy calculation In-Reply-To: References: <3F10A20F-14C4-43C7-826B-5EB440F5F493@gmail.com> Message-ID: <4A452B58-669F-41D7-BDFF-A6AF8CA7EB12@cgl.ucsf.edu> Hi Bobo, Aldo is exactly right. You want something like a free-energy calculation or estimation, which Chimera does not do. Besides the tool Aldo mentioned, I've also heard of SDM , but I haven't tried either of them myself. 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 Oct 7, 2014, at 3:53 PM, Aldo Segura wrote: > Hi Bobo, > I think Chimera does not have such capability. I would suggest you trying with FoldX: foldx.crg.es > Best, > Aldo > > 2014-10-07 17:04 GMT-04:00 : > 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 From jiserte at unq.edu.ar Wed Oct 8 10:29:01 2014 From: jiserte at unq.edu.ar (jiserte at unq.edu.ar) Date: Wed, 08 Oct 2014 14:29:01 -0300 Subject: [Chimera-users] Remove shapes programmatically Message-ID: <20141008142901.Horde.v2fkqYUMSrZYd853nG73UQ8@correo.unq.edu.ar> Hello. I'm having a problem working with shapes in chimera. I'm adding shapes with a script using commands like: shape tube #:1 at CA#:100 at 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 Fundaci?n Instituto Leloir Buenos Aires, Argentina. -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.hemmann at gmail.com Wed Oct 8 02:31:51 2014 From: j.hemmann at gmail.com (Jethro Hemmann) Date: Wed, 8 Oct 2014 11:31:51 +0200 Subject: [Chimera-users] Dim colors in Chimera on OS X 10.10 public beta (Yosemite) Message-ID: Hi, I'm currently using Chimera on my Macbook running the public beta of Yosemite. The colors of the molecules appear very dim and they are hard to recognize, as can be seen in the attached screenshot. In this example, the lipid chains are colored orange, while the water molecules should by cyan. The colors in the menu Actions --> Color seem to appear with their correct brightness, although. I also tried the daily build of the alpha version of Chimera, but the problem persists. Is this problem related to Yosemite? Or do I have to adjust some settings? Thanks a lot, Jethro -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: screenshot.png Type: image/png Size: 467900 bytes Desc: not available URL: From jmsstarlight at gmail.com Wed Oct 8 02:46:46 2014 From: jmsstarlight at gmail.com (James Starlight) Date: Wed, 8 Oct 2014 11:46:46 +0200 Subject: [Chimera-users] Analysis of the multiple alignments + structures In-Reply-To: References: <3C046F9F-8DD2-4FCA-9B6F-602B77B978D8@cgl.ucsf.edu> <6EBA63A5-7A6C-458A-84D9-E142E1BA5CC7@cgl.ucsf.edu> <1FA109A7-FAED-432D-8760-DB34FF3FEE7E@cgl.ucsf.edu> <6D457B82-959F-4F86-A388-54506ED7BE1A@cgl.ucsf.edu> <04AFDB50-889E-4F29-AEB7-EB12F6553B84@cgl.ucsf.edu> Message-ID: 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 : > 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 : > >> 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 >> 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 : >> > 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 >> 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 : >> > > 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/framemav.html >> > >> > > ? see the section on Trees: >> > > < >> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#trees >> > >> > > ? example image of tree+alignment in Chimera: >> > > < >> http://www.rbvi.ucsf.edu/chimera/data/tutorials/systems/redoxin/ConSurf-1hd2-chimera19-seq.png >> > >> > > >> > > 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. >> > > >> > > >> > > 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. >> > > >> > > >> > > (2) JEvTrace, a Java implementation of evolutionary trace. >> > > >> > > >> > > 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 >> 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 at cgl.ucsf.edu >> > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > >> > >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Wed Oct 8 11:34:44 2014 From: goddard at sonic.net (Tom Goddard) Date: Wed, 8 Oct 2014 11:34:44 -0700 Subject: [Chimera-users] measure symmetry In-Reply-To: <3108EC66-C42C-4151-B0DA-3E7BE02C7C01@scripps.edu> References: <3108EC66-C42C-4151-B0DA-3E7BE02C7C01@scripps.edu> Message-ID: 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 > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 2xyz.jpg Type: image/jpg Size: 135295 bytes Desc: not available URL: From meng at cgl.ucsf.edu Wed Oct 8 12:01:59 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 8 Oct 2014 12:01:59 -0700 Subject: [Chimera-users] Remove shapes programmatically In-Reply-To: <20141008142901.Horde.v2fkqYUMSrZYd853nG73UQ8@correo.unq.edu.ar> References: <20141008142901.Horde.v2fkqYUMSrZYd853nG73UQ8@correo.unq.edu.ar> Message-ID: <00B18CB7-934A-4374-945B-3AA6546368E5@cgl.ucsf.edu> Hello Javier, The ?shape? command creates surface models. You can close (delete) or hide a model with commands ?close? and ?~modeldisplay?, respectively. You would specify the model by its ID number in the command; these IDs are shown in the Model Panel (open from Favorites menu), or to make it easier to know the IDs of each shape, you could assign the ID number at the time of creating each model with the ?shape? command ?modelid? option. For example: shape tube @ca rad 0.75 color red modelid 5 ~modeldisp #5 modeldisp #5 color hot pink #5 close #5 Although you can change the color, you can?t change the shape itself (radius etc.), only close that one and create another new one. Your example command is a little strange, it just creates a cylinder between two atoms :1 at ca and :100 at ca ? is that what you wanted? (you don?t need the # in that command). If so, you could do something similar with a pseudobond, which would be more manipulable, for example: distance :5,100 at ca setattr p label " " :5,100 at ca setattr p drawMode 1 :5,100 at ca setattr p radius 0.5 :5,100 at ca setattr p color dodger blue :5,100 at ca 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 Oct 8, 2014, at 10:29 AM, jiserte at unq.edu.ar wrote: > Hello. > I'm having a problem working with shapes in chimera. I'm adding shapes with a script using commands like: > > shape tube #:1 at CA#:100 at 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 From meng at cgl.ucsf.edu Wed Oct 8 12:26:46 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 8 Oct 2014 12:26:46 -0700 Subject: [Chimera-users] Analysis of the multiple alignments + structures In-Reply-To: References: <3C046F9F-8DD2-4FCA-9B6F-602B77B978D8@cgl.ucsf.edu> <6EBA63A5-7A6C-458A-84D9-E142E1BA5CC7@cgl.ucsf.edu> <1FA109A7-FAED-432D-8760-DB34FF3FEE7E@cgl.ucsf.edu> <6D457B82-959F-4F86-A388-54506ED7BE1A@cgl.ucsf.edu> <04AFDB50-889E-4F29-AEB7-EB12F6553B84@cgl.ucsf.edu> Message-ID: <10D7E22C-DE71-4815-A508-9CC8C18CAD31@cgl.ucsf.edu> Dear James, This is beyond my expertise. Note that Chimera does not calculate phylogenetic trees, it only displays them. If you don?t get helpful responses from the Chimera list, maybe you can ask this question on some bioinformatics forum instead, or the authors of similar papers. Lacking direct knowledge, my best advice is always to search the literature and read papers that seem similar in some way to what you want to do. 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 Oct 8, 2014, at 2:46 AM, James Starlight wrote: > 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 From conrad at cgl.ucsf.edu Wed Oct 8 13:48:50 2014 From: conrad at cgl.ucsf.edu (Conrad Huang) Date: Wed, 08 Oct 2014 13:48:50 -0700 Subject: [Chimera-users] Dim colors in Chimera on OS X 10.10 public beta (Yosemite) In-Reply-To: References: Message-ID: <5435A332.8000402@cgl.ucsf.edu> Unfortunately, we have not tested Chimera on Yosemite yet. It is highly likely that there is some OpenGL issue given the images that you are seeing. We will try to get to this soon, but we're pretty tight on programmer resources. If you feel adventurous (which I assume you are since you're running Yosemite :-) ), you can try playing with some OpenGL options by going to the General category in Preferences and turn on "Debug OpenGL on startup". The next time you start Chimera, it should display a dialog where you can selectively turn certain OpenGL options on and off (see http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/debug/debug.html). If you discover anything, please let us know. Conrad On 10/8/2014 2:31 AM, Jethro Hemmann wrote: > Hi, > > I'm currently using Chimera on my Macbook running the public beta of > Yosemite. > > The colors of the molecules appear very dim and they are hard to > recognize, as can be seen in the attached screenshot. In this example, > the lipid chains are colored orange, while the water molecules should by > cyan. > The colors in the menu Actions --> Color seem to appear with their > correct brightness, although. > > I also tried the daily build of the alpha version of Chimera, but the > problem persists. > > Is this problem related to Yosemite? Or do I have to adjust some settings? > > Thanks a lot, > > Jethro > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From jlstark at wisc.edu Wed Oct 8 14:04:11 2014 From: jlstark at wisc.edu (Jaime Stark) Date: Wed, 08 Oct 2014 16:04:11 -0500 Subject: [Chimera-users] Dim colors in Chimera on OS X 10.10 public beta (Yosemite) In-Reply-To: <5435A332.8000402@cgl.ucsf.edu> References: <5435A332.8000402@cgl.ucsf.edu> Message-ID: <0EEFCCDF-4BF3-40AE-8F00-B62DAC2B6159@wisc.edu> I was seeing this problem too in Yosemite. It?s easily fixed by turning on the ?Debug OpenGL on startup? as Conrad suggests. When you next start Chimera, in the OpenGL options that popup, disable DrawElementsInstanced. That will fix the dim coloring for small molecules on Yosemite for now. Jaime =================================== Jaime L. Stark, Ph.D. Postdoctoral Research Associate at NMRFAM University of Wisconsin - Madison Department of Biochemistry DeLuca Biochemical Laboratories Room B160H 433 Babcock Drive Madison, WI 53706 Email: jlstark at wisc.edu Phone: (608) 262-0459 Website: http://www.nmrfam.wisc.edu =================================== > On Oct 8, 2014, at 3:48 PM, Conrad Huang wrote: > > Unfortunately, we have not tested Chimera on Yosemite yet. It is highly likely that there is some OpenGL issue given the images that you are seeing. We will try to get to this soon, but we're pretty tight on programmer resources. > > If you feel adventurous (which I assume you are since you're running Yosemite :-) ), you can try playing with some OpenGL options by going to the General category in Preferences and turn on "Debug OpenGL on startup". The next time you start Chimera, it should display a dialog where you can selectively turn certain OpenGL options on and off (see http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/debug/debug.html). If you discover anything, please let us know. > > Conrad > > On 10/8/2014 2:31 AM, Jethro Hemmann wrote: >> Hi, >> >> I'm currently using Chimera on my Macbook running the public beta of >> Yosemite. >> >> The colors of the molecules appear very dim and they are hard to >> recognize, as can be seen in the attached screenshot. In this example, >> the lipid chains are colored orange, while the water molecules should by >> cyan. >> The colors in the menu Actions --> Color seem to appear with their >> correct brightness, although. >> >> I also tried the daily build of the alpha version of Chimera, but the >> problem persists. >> >> Is this problem related to Yosemite? Or do I have to adjust some settings? >> >> Thanks a lot, >> >> Jethro >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.hemmann at gmail.com Wed Oct 8 14:10:13 2014 From: j.hemmann at gmail.com (Jethro Hemmann) Date: Wed, 8 Oct 2014 23:10:13 +0200 Subject: [Chimera-users] Dim colors in Chimera on OS X 10.10 public beta (Yosemite) In-Reply-To: <0EEFCCDF-4BF3-40AE-8F00-B62DAC2B6159@wisc.edu> References: <5435A332.8000402@cgl.ucsf.edu> <0EEFCCDF-4BF3-40AE-8F00-B62DAC2B6159@wisc.edu> Message-ID: Thank you Conrad and Jaime for you answers. The debug options indeed fixed the problem. Instead of disabling DrawElementsInstanced, disabling Shading also seems to work. Jethro 2014-10-08 23:04 GMT+02:00 Jaime Stark : > I was seeing this problem too in Yosemite. It?s easily fixed by turning on > the ?Debug OpenGL on startup? as Conrad suggests. When you next start > Chimera, in the OpenGL options that popup, disable DrawElementsInstanced. > That will fix the dim coloring for small molecules on Yosemite for now. > > Jaime > > =================================== > Jaime L. Stark, Ph.D. > Postdoctoral Research Associate at NMRFAM > University of Wisconsin - Madison > Department of Biochemistry > DeLuca Biochemical Laboratories > Room B160H > 433 Babcock Drive > Madison, WI 53706 > Email: jlstark at wisc.edu > Phone: (608) 262-0459 > Website: http://www.nmrfam.wisc.edu > =================================== > > > > > > > On Oct 8, 2014, at 3:48 PM, Conrad Huang wrote: > > Unfortunately, we have not tested Chimera on Yosemite yet. It is highly > likely that there is some OpenGL issue given the images that you are > seeing. We will try to get to this soon, but we're pretty tight on > programmer resources. > > If you feel adventurous (which I assume you are since you're running > Yosemite :-) ), you can try playing with some OpenGL options by going to > the General category in Preferences and turn on "Debug OpenGL on startup". > The next time you start Chimera, it should display a dialog where you can > selectively turn certain OpenGL options on and off (see > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/debug/debug.html). > If you discover anything, please let us know. > > Conrad > > On 10/8/2014 2:31 AM, Jethro Hemmann wrote: > > Hi, > > I'm currently using Chimera on my Macbook running the public beta of > Yosemite. > > The colors of the molecules appear very dim and they are hard to > recognize, as can be seen in the attached screenshot. In this example, > the lipid chains are colored orange, while the water molecules should by > cyan. > The colors in the menu Actions --> Color seem to appear with their > correct brightness, although. > > I also tried the daily build of the alpha version of Chimera, but the > problem persists. > > Is this problem related to Yosemite? Or do I have to adjust some settings? > > Thanks a lot, > > Jethro > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Wed Oct 8 14:23:25 2014 From: goddard at sonic.net (Tom Goddard) Date: Wed, 8 Oct 2014 14:23:25 -0700 Subject: [Chimera-users] measure symmetry In-Reply-To: References: <3108EC66-C42C-4151-B0DA-3E7BE02C7C01@scripps.edu> Message-ID: <6E7CB1AA-4CF9-4167-8114-CAAC1B219E8C@sonic.net> 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 >>> >>> >>> >>> >>> >>> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Wed Oct 8 14:27:54 2014 From: goddard at sonic.net (Tom Goddard) Date: Wed, 8 Oct 2014 14:27:54 -0700 Subject: [Chimera-users] Dim colors in Chimera on OS X 10.10 public beta (Yosemite) In-Reply-To: References: <5435A332.8000402@cgl.ucsf.edu> <0EEFCCDF-4BF3-40AE-8F00-B62DAC2B6159@wisc.edu> Message-ID: <2045B098-F61D-4F8B-8C18-358A0278F917@sonic.net> Disabling DrawElementsInstanced will slow down rendering of atoms shown as spheres and bonds shown as cylinders by about a factor of 10-30x, but you probably won?t notice unless you are looking at more than 20,000 atoms. Disabling Shading basically turns off all modern 3d graphics based on GPU shader programs ? you?ll then be relying on very old Chimera fallback graphics code. So I suggest keeping shading on if possible. Tom On Oct 8, 2014, at 2:10 PM, Jethro Hemmann wrote: > Thank you Conrad and Jaime for you answers. > The debug options indeed fixed the problem. Instead of disabling DrawElementsInstanced, disabling Shading also seems to work. > > Jethro > > 2014-10-08 23:04 GMT+02:00 Jaime Stark : > I was seeing this problem too in Yosemite. It?s easily fixed by turning on the ?Debug OpenGL on startup? as Conrad suggests. When you next start Chimera, in the OpenGL options that popup, disable DrawElementsInstanced. That will fix the dim coloring for small molecules on Yosemite for now. > > Jaime > > =================================== > Jaime L. Stark, Ph.D. > Postdoctoral Research Associate at NMRFAM > University of Wisconsin - Madison > Department of Biochemistry > DeLuca Biochemical Laboratories > Room B160H > 433 Babcock Drive > Madison, WI 53706 > Email: jlstark at wisc.edu > Phone: (608) 262-0459 > Website: http://www.nmrfam.wisc.edu > =================================== > > > > > > >> On Oct 8, 2014, at 3:48 PM, Conrad Huang wrote: >> >> Unfortunately, we have not tested Chimera on Yosemite yet. It is highly likely that there is some OpenGL issue given the images that you are seeing. We will try to get to this soon, but we're pretty tight on programmer resources. >> >> If you feel adventurous (which I assume you are since you're running Yosemite :-) ), you can try playing with some OpenGL options by going to the General category in Preferences and turn on "Debug OpenGL on startup". The next time you start Chimera, it should display a dialog where you can selectively turn certain OpenGL options on and off (see http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/debug/debug.html). If you discover anything, please let us know. >> >> Conrad >> >> On 10/8/2014 2:31 AM, Jethro Hemmann wrote: >>> Hi, >>> >>> I'm currently using Chimera on my Macbook running the public beta of >>> Yosemite. >>> >>> The colors of the molecules appear very dim and they are hard to >>> recognize, as can be seen in the attached screenshot. In this example, >>> the lipid chains are colored orange, while the water molecules should by >>> cyan. >>> The colors in the menu Actions --> Color seem to appear with their >>> correct brightness, although. >>> >>> I also tried the daily build of the alpha version of Chimera, but the >>> problem persists. >>> >>> Is this problem related to Yosemite? Or do I have to adjust some settings? >>> >>> Thanks a lot, >>> >>> Jethro >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users at cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From ashwin2952 at gmail.com Wed Oct 8 16:03:31 2014 From: ashwin2952 at gmail.com (Aswani Kumar Kancherla) Date: Thu, 9 Oct 2014 04:33:31 +0530 Subject: [Chimera-users] measuring distance between an atom and centroid of an aromatic ring Message-ID: 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Oct 8 17:12:11 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 8 Oct 2014 17:12:11 -0700 Subject: [Chimera-users] measuring distance between an atom and centroid of an aromatic ring In-Reply-To: References: Message-ID: Hello Aswani, It won?t draw a line like atom-atom distance measurements, but you can certainly get the values. You can use the distance command to get a pairwise centroid-atom distance, for example: distance c1 #0:200.A at n (centroid with ID c1 to atom N in residue 200 chain A of model 0). The centroid IDs are shown in the Axes/Planes/Centroids dialog. Or, you could select one atom and use command: distance c1 sel Or, to measure the distances from a centroid to multiple selected atoms, choose the row for the centroid in the Axes/Planes/Centroids dialog and then click the ?Report distance? button. In all cases, the resulting distance values will be reported in the Reply Log (main menu Favorites? Reply Log). The centroid is actually a surface model and not an atom, which is why the behavior is different than with two atoms. If you wanted to make a fake atom in the centroid position, it is a bit more bothersome. To do that, you could use the ?Save? button on Axes/Planes/Centroids to save the centroids information including their coordinates to a text file. Then you could use Build Structure (in menu under Tools? Structure Editing), ?Start Structure? and Add: ?atom? with specified x,y,z coordinates copied from that file. Then after you added the fake atom, you could use it for distance measurements the usual atom-atom way. 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 Oct 8, 2014, at 4:03 PM, Aswani Kumar Kancherla wrote: > 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 From goddard at sonic.net Wed Oct 8 17:25:58 2014 From: goddard at sonic.net (Tom Goddard) Date: Wed, 8 Oct 2014 17:25:58 -0700 Subject: [Chimera-users] measuring distance between an atom and centroid of an aromatic ring In-Reply-To: References: Message-ID: <54C50025-083C-4279-9445-E068231033DC@sonic.net> Hello Aswani, If you want to show the distance to the centroid of the ring, you can select the ring atoms (ctrl-click and shift-ctrl-click) then use measure center sel mark true radius .3 This puts a marker (which is just like an atom) at the center of the ring. Then to show the distance I ctrl-click the marker then shift-ctrl-double-click the atom I want to measure the distance too ? that shows a menu and I choose ?Show distance?. Picture shows the result. Here are the ?measure center? docs. http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/measure.html#center There are usually lots of ways to do things in Chimera. Tom On Oct 8, 2014, at 5:12 PM, Elaine Meng wrote: > Hello Aswani, > It won?t draw a line like atom-atom distance measurements, but you can certainly get the values. You can use the distance command to get a pairwise centroid-atom distance, for example: > > distance c1 #0:200.A at n > > (centroid with ID c1 to atom N in residue 200 chain A of model 0). The centroid IDs are shown in the Axes/Planes/Centroids dialog. > > Or, you could select one atom and use command: > > distance c1 sel > > Or, to measure the distances from a centroid to multiple selected atoms, choose the row for the centroid in the Axes/Planes/Centroids dialog and then click the ?Report distance? button. > > In all cases, the resulting distance values will be reported in the Reply Log (main menu Favorites? Reply Log). > > > > > The centroid is actually a surface model and not an atom, which is why the behavior is different than with two atoms. If you wanted to make a fake atom in the centroid position, it is a bit more bothersome. To do that, you could use the ?Save? button on Axes/Planes/Centroids to save the centroids information including their coordinates to a text file. Then you could use Build Structure (in menu under Tools? Structure Editing), ?Start Structure? and Add: ?atom? with specified x,y,z coordinates copied from that file. Then after you added the fake atom, you could use it for distance measurements the usual atom-atom way. > > 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 Oct 8, 2014, at 4:03 PM, Aswani Kumar Kancherla wrote: > >> 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 > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: center.jpg Type: image/jpg Size: 58548 bytes Desc: not available URL: From chingsong962005 at sas.ustb.edu.cn Wed Oct 8 20:27:39 2014 From: chingsong962005 at sas.ustb.edu.cn (=?UTF-8?B?5a6L6Z2S?=) Date: Thu, 9 Oct 2014 11:27:39 +0800 (GMT+08:00) Subject: [Chimera-users] co-factor FAD in autodock-vina Message-ID: <378994cc.3bc8.148f2f29f18.Coremail.chingsong962005@sas.ustb.edu.cn> Dear Chimera Design Team, We have been using Chimera 8.1 and autodock-vina for small molecule and protein interaction analysis. We came across a protein structure (PDB code 2vfs) with a co-factor FAD enclosed. We would like to know if we could dock a sugar into the substrate binding site with the FAD molecule in situ. Thank you for your help. -- Ching Song, Ph.D. Department of Biological Science and Engineering School of Chemistry and Biological Engineering University og Science and Technology Beijing Xue Yuan Lu 30, Li Hua Lou Room 111 Hai Dian District Beijing 100083, P. R. China 86-10-62334497 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Jane.Norman at bristol.ac.uk Thu Oct 9 04:40:06 2014 From: Jane.Norman at bristol.ac.uk (Jane Norman) Date: Thu, 9 Oct 2014 12:40:06 +0100 Subject: [Chimera-users] please give advice Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From ar371 at leicester.ac.uk Thu Oct 9 08:55:43 2014 From: ar371 at leicester.ac.uk (Revyakin, Andrey (Dr.)) Date: Thu, 9 Oct 2014 15:55:43 +0000 Subject: [Chimera-users] color zones with multiple markers Message-ID: 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. From meng at cgl.ucsf.edu Thu Oct 9 10:46:36 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 9 Oct 2014 10:46:36 -0700 Subject: [Chimera-users] coloring by element In-Reply-To: References: Message-ID: Hi Jane, I think you just wanted to apply the "heteroatom" color-coding to that residue. For example, select it and use menu: Actions? Color.. by heteroatom or command: color byhet sel That will keep the carbons as their current color but use the element color-coding for the others. Or, you could use "by element" instead, which will also color the carbons by element (gray). If I misunderstood your question, you could try asking it again. 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 Oct 9, 2014, at 4:40 AM, Jane Norman wrote: > 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 From meng at cgl.ucsf.edu Thu Oct 9 11:41:12 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 9 Oct 2014 11:41:12 -0700 Subject: [Chimera-users] co-factor FAD in autodock-vina In-Reply-To: <378994cc.3bc8.148f2f29f18.Coremail.chingsong962005@sas.ustb.edu.cn> References: <378994cc.3bc8.148f2f29f18.Coremail.chingsong962005@sas.ustb.edu.cn> Message-ID: Dear Ching Song, I didn't know the answer, so I just tried it, and it worked fine in Chimera 1.8. I opened 2vfs and deleted everything except the protein and FAD (deleted solvent, ions, and XYL). So that's the receptor, #0. Then I opened some other small molecule structure to use as ligand, #1. Then I started Autodock Vina, created the search box, entered name for output, and chose receptor #0 and ligand #1. Looked in the "Receptor options" to make sure that "Ignore all non-standard residues" was "false". Clicked Apply, and the job ran successfully. I had a problem in Chimera 1.9, which I will report as a bug, but if you stick with Chimera 1.8 it apparently works. 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 Oct 8, 2014, at 8:27 PM, ?? wrote: > Dear Chimera Design Team, > > We have been using Chimera 8.1 and autodock-vina for small molecule and protein interaction analysis. We came across a protein structure (PDB code 2vfs) with a co-factor FAD enclosed. We would like to know if we could dock a sugar into the substrate binding site with the FAD molecule in situ. Thank you for your help. > > -- > Ching Song, Ph.D. > Department of Biological Science and Engineering > School of Chemistry and Biological Engineering > University og Science and Technology Beijing > Xue Yuan Lu 30, Li Hua Lou Room 111 > Hai Dian District > Beijing 100083, P. R. China > 86-10-62334497 From meng at cgl.ucsf.edu Thu Oct 9 11:45:25 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 9 Oct 2014 11:45:25 -0700 Subject: [Chimera-users] color zones with multiple markers In-Reply-To: References: Message-ID: <78650224-B619-407E-AD15-7B6125D69B45@cgl.ucsf.edu> Hi Andrey, Color Zone uses the currently selected marker(s). Each time you create a marker it becomes selected and the previous ones become unselected, so when you use Color Zone you are telling it only to use the newest one. Instead, just create all the markers first, then select them all (e.g. main Chimera menu: Select?. Structure? markers), and then use Color Zone once at the end. 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 Oct 9, 2014, at 8:55 AM, "Revyakin, Andrey (Dr.)" wrote: > 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. From meng at cgl.ucsf.edu Thu Oct 9 11:54:35 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 9 Oct 2014 11:54:35 -0700 Subject: [Chimera-users] color zones with multiple markers In-Reply-To: <78650224-B619-407E-AD15-7B6125D69B45@cgl.ucsf.edu> References: <78650224-B619-407E-AD15-7B6125D69B45@cgl.ucsf.edu> Message-ID: <5E33D40E-BD7B-41C2-98CF-5E26051F8503@cgl.ucsf.edu> Also to select more than one atom (or marker, which is essentially a fake atom) from the main Chimera window, you could use Shift-Ctrl-click to choose each successive one. Elaine On Oct 9, 2014, at 11:45 AM, Elaine Meng wrote: > Hi Andrey, > Color Zone uses the currently selected marker(s). Each time you create a marker it becomes selected and the previous ones become unselected, so when you use Color Zone you are telling it only to use the newest one. Instead, just create all the markers first, then select them all (e.g. main Chimera menu: Select?. Structure? markers), and then use Color Zone once at the end. > > 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 Oct 9, 2014, at 8:55 AM, "Revyakin, Andrey (Dr.)" wrote: > >> 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. From bobo2412 at gmail.com Thu Oct 9 11:27:59 2014 From: bobo2412 at gmail.com (Bobo Dang) Date: Thu, 9 Oct 2014 13:27:59 -0500 Subject: [Chimera-users] Energy calculation In-Reply-To: <4A452B58-669F-41D7-BDFF-A6AF8CA7EB12@cgl.ucsf.edu> References: <3F10A20F-14C4-43C7-826B-5EB440F5F493@gmail.com> <4A452B58-669F-41D7-BDFF-A6AF8CA7EB12@cgl.ucsf.edu> Message-ID: Thanks, I will try the programs you suggested. Bobo On Tue, Oct 7, 2014 at 6:46 PM, Elaine Meng wrote: > Hi Bobo, > Aldo is exactly right. You want something like a free-energy calculation > or estimation, which Chimera does not do. > > Besides the tool Aldo mentioned, I've also heard of SDM < > http://mordred.bioc.cam.ac.uk/sdm/sdm.php> , but I haven't tried either > of them myself. > 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 Oct 7, 2014, at 3:53 PM, Aldo Segura wrote: > > > Hi Bobo, > > I think Chimera does not have such capability. I would suggest you > trying with FoldX: foldx.crg.es > > Best, > > Aldo > > > > 2014-10-07 17:04 GMT-04:00 : > > 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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pchem at ucsc.edu Thu Oct 9 16:28:09 2014 From: pchem at ucsc.edu (William McDonald) Date: Thu, 9 Oct 2014 16:28:09 -0700 Subject: [Chimera-users] Failed to prepare receptor for AutoDock Vina Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Oct 9 16:43:21 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 9 Oct 2014 16:43:21 -0700 Subject: [Chimera-users] Failed to prepare receptor for AutoDock Vina In-Reply-To: References: Message-ID: <4C682126-AD3C-4457-8454-FBBFC4952C60@cgl.ucsf.edu> Hi William, We usually can?t tell without your data, so if you are willing to share it, please use menu: Help? Report a Bug and attach the file or the receptor or perhaps a Chimera session with both the ligand and receptor to the report, with short description of the problem and your contact information. It might be the data, or it might be a bug. Suggesting the latter, when testing the Autodock Vina interface in Chimera 1.9 just today, I also had a preparation problem, but when I tried exactly the same structures in 1.8, I did not have the problem. You could try getting Chimera 1.8 from our download page (you can give it a different name or put it in a different place than your other installation to avoid overwriting it) and seeing if that works. Sorry for the difficulties. 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 Oct 9, 2014, at 4:28 PM, William McDonald wrote: > 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 From ar371 at leicester.ac.uk Thu Oct 9 14:04:58 2014 From: ar371 at leicester.ac.uk (Revyakin, Andrey (Dr.)) Date: Thu, 9 Oct 2014 21:04:58 +0000 Subject: [Chimera-users] color zones with multiple markers In-Reply-To: <5E33D40E-BD7B-41C2-98CF-5E26051F8503@cgl.ucsf.edu> References: <78650224-B619-407E-AD15-7B6125D69B45@cgl.ucsf.edu>, <5E33D40E-BD7B-41C2-98CF-5E26051F8503@cgl.ucsf.edu> Message-ID: Thank you Elaine! Shift-Ctrl-click did the trick. Biochemistry Department University of Leicester (Elite without being Elitist) Henry Wellcome Building, Room 301 Lancaster Road Leicester, LE1 9HN UK +44 0116 229 7010 Omit 0 in 0116 if calling from outside the UK ________________________________________ From: Elaine Meng [meng at cgl.ucsf.edu] Sent: Thursday, October 09, 2014 7:54 PM To: Revyakin, Andrey (Dr.) Cc: chimera-users at cgl.ucsf.edu BB Subject: Re: [Chimera-users] color zones with multiple markers Also to select more than one atom (or marker, which is essentially a fake atom) from the main Chimera window, you could use Shift-Ctrl-click to choose each successive one. Elaine On Oct 9, 2014, at 11:45 AM, Elaine Meng wrote: > Hi Andrey, > Color Zone uses the currently selected marker(s). Each time you create a marker it becomes selected and the previous ones become unselected, so when you use Color Zone you are telling it only to use the newest one. Instead, just create all the markers first, then select them all (e.g. main Chimera menu: Select?. Structure? markers), and then use Color Zone once at the end. > > 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 Oct 9, 2014, at 8:55 AM, "Revyakin, Andrey (Dr.)" wrote: > >> 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. From chingsong962005 at sas.ustb.edu.cn Thu Oct 9 19:49:28 2014 From: chingsong962005 at sas.ustb.edu.cn (=?UTF-8?B?5a6L6Z2S?=) Date: Fri, 10 Oct 2014 10:49:28 +0800 (GMT+08:00) Subject: [Chimera-users] co-factor FAD in autodock-vina In-Reply-To: References: <378994cc.3bc8.148f2f29f18.Coremail.chingsong962005@sas.ustb.edu.cn> Message-ID: <2f2321e9.44b6.148f7f60602.Coremail.chingsong962005@sas.ustb.edu.cn> We will try it again. Thanks a lot! Ching > -----????----- > ???: "Elaine Meng" > ????: 2014-10-10 02:41:12 (???) > ???: "??" > ??: chimera-users at cgl.ucsf.edu > ??: Re: [Chimera-users] co-factor FAD in autodock-vina > > Dear Ching Song, > I didn't know the answer, so I just tried it, and it worked fine in Chimera 1.8. > > I opened 2vfs and deleted everything except the protein and FAD (deleted solvent, ions, and XYL). So that's the receptor, #0. > > Then I opened some other small molecule structure to use as ligand, #1. > > Then I started Autodock Vina, created the search box, entered name for output, and chose receptor #0 and ligand #1. Looked in the "Receptor options" to make sure that "Ignore all non-standard residues" was "false". Clicked Apply, and the job ran successfully. > > I had a problem in Chimera 1.9, which I will report as a bug, but if you stick with Chimera 1.8 it apparently works. > 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 Oct 8, 2014, at 8:27 PM, ?? wrote: > > > Dear Chimera Design Team, > > > > We have been using Chimera 8.1 and autodock-vina for small molecule and protein interaction analysis. We came across a protein structure (PDB code 2vfs) with a co-factor FAD enclosed. We would like to know if we could dock a sugar into the substrate binding site with the FAD molecule in situ. Thank you for your help. > > > > -- > > Ching Song, Ph.D. > > Department of Biological Science and Engineering > > School of Chemistry and Biological Engineering > > University og Science and Technology Beijing > > Xue Yuan Lu 30, Li Hua Lou Room 111 > > Hai Dian District > > Beijing 100083, P. R. China > > 86-10-62334497 > From Jane.Norman at bristol.ac.uk Fri Oct 10 02:09:24 2014 From: Jane.Norman at bristol.ac.uk (Jane Norman) Date: Fri, 10 Oct 2014 10:09:24 +0100 Subject: [Chimera-users] coloring by element In-Reply-To: References: Message-ID: thanks v much, I'll give that a go... On 9 October 2014 18:46, Elaine Meng wrote: > Hi Jane, > I think you just wanted to apply the "heteroatom" color-coding to that > residue. For example, select it and use > > menu: Actions? Color.. by heteroatom > or > command: color byhet sel > > That will keep the carbons as their current color but use the element > color-coding for the others. Or, you could use "by element" instead, > which will also color the carbons by element (gray). > < > http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/colortables.html#byelement > > > > If I misunderstood your question, you could try asking it again. 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 Oct 9, 2014, at 4:40 AM, Jane Norman wrote: > > > 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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ashwin2952 at gmail.com Fri Oct 10 22:06:57 2014 From: ashwin2952 at gmail.com (Aswani Kumar Kancherla) Date: Sat, 11 Oct 2014 10:36:57 +0530 Subject: [Chimera-users] measuring distance between an atom and centroid of an aromatic ring In-Reply-To: <54C50025-083C-4279-9445-E068231033DC@sonic.net> References: <54C50025-083C-4279-9445-E068231033DC@sonic.net> Message-ID: Dear Elaine and Tom, Many thanks for the prompt replies. I could get both the methods to work. I measured the distances and displayed them by creating pseudo-atoms at the coordinates of the centroid as suggested by Elaine. I pasted the figure below. Many thanks for the wonderful program and support. with regards, Aswani ? On 9 October 2014 05:55, Tom Goddard wrote: > Hello Aswani, > > If you want to show the distance to the centroid of the ring, you can > select the ring atoms (ctrl-click and shift-ctrl-click) then use > > measure center sel mark true radius .3 > > This puts a marker (which is just like an atom) at the center of the > ring. Then to show the distance I ctrl-click the marker then > shift-ctrl-double-click the atom I want to measure the distance too ? that > shows a menu and I choose ?Show distance?. Picture shows the result. Here > are the ?measure center? docs. > > > http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/measure.html#center > > There are usually lots of ways to do things in Chimera. > > Tom > > > > On Oct 8, 2014, at 5:12 PM, Elaine Meng wrote: > > Hello Aswani, > It won?t draw a line like atom-atom distance measurements, but you can > certainly get the values. You can use the distance command to get a > pairwise centroid-atom distance, for example: > > distance c1 #0:200.A at n > > (centroid with ID c1 to atom N in residue 200 chain A of model 0). The > centroid IDs are shown in the Axes/Planes/Centroids dialog. > > Or, you could select one atom and use command: > > distance c1 sel > > Or, to measure the distances from a centroid to multiple selected atoms, > choose the row for the centroid in the Axes/Planes/Centroids dialog and > then click the ?Report distance? button. > > In all cases, the resulting distance values will be reported in the Reply > Log (main menu Favorites? Reply Log). > > > < > http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes > > > > The centroid is actually a surface model and not an atom, which is why the > behavior is different than with two atoms. If you wanted to make a fake > atom in the centroid position, it is a bit more bothersome. To do that, > you could use the ?Save? button on Axes/Planes/Centroids to save the > centroids information including their coordinates to a text file. Then you > could use Build Structure (in menu under Tools? Structure Editing), ?Start > Structure? and Add: ?atom? with specified x,y,z coordinates copied from > that file. Then after you added the fake atom, you could use it for > distance measurements the usual atom-atom way. > > 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 Oct 8, 2014, at 4:03 PM, Aswani Kumar Kancherla wrote: > > 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 > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Lys_Trp_Pro_Distances_whiteBG_b_crop.jpeg Type: image/jpeg Size: 84987 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: center.jpg Type: image/jpg Size: 58548 bytes Desc: not available URL: From chiendarret at gmail.com Sun Oct 12 00:05:10 2014 From: chiendarret at gmail.com (Francesco Pietra) Date: Sun, 12 Oct 2014 09:05:10 +0200 Subject: [Chimera-users] command @/serialNumber=# Message-ID: Hello: I wonder whether it is possible to extend the command sel @/serialNumber=18801 (as an example of a particular serial number) to comprise a range of atoms. So as to cover, for example, an entire ligand, may be dioxygen, 18801-18802. And whether that could be extended to define a centroid. it is implied that I have prepared a large system based on segname (charmm ff with namd), which is not dealt with by chimera. thanks francesco pietra PS: I can follow the ligand by defining the centroid for a single atom of the ligand. This would be my last resource. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chiendarret at gmail.com Sun Oct 12 06:11:34 2014 From: chiendarret at gmail.com (Francesco Pietra) Date: Sun, 12 Oct 2014 13:11:34 +0000 Subject: [Chimera-users] Fwd: command @/serialNumber=# In-Reply-To: References: Message-ID: OK, for molecule 18801-18802 @/serialNumber>18800 and serialNumber<18803 it remains to be seen if it can be used to define a centroid fp ---------- Forwarded message ---------- From: Francesco Pietra Date: Sun, Oct 12, 2014 at 7:05 AM Subject: command @/serialNumber=# To: chimera Hello: I wonder whether it is possible to extend the command sel @/serialNumber=18801 (as an example of a particular serial number) to comprise a range of atoms. So as to cover, for example, an entire ligand, may be dioxygen, 18801-18802. And whether that could be extended to define a centroid. it is implied that I have prepared a large system based on segname (charmm ff with namd), which is not dealt with by chimera. thanks francesco pietra PS: I can follow the ligand by defining the centroid for a single atom of the ligand. This would be my last resource. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chiendarret at gmail.com Sun Oct 12 07:48:51 2014 From: chiendarret at gmail.com (Francesco Pietra) Date: Sun, 12 Oct 2014 16:48:51 +0200 Subject: [Chimera-users] Fwd: command @/serialNumber=# In-Reply-To: References: Message-ID: OK also for define centroid ---------- Forwarded message ---------- From: Francesco Pietra Date: Sun, Oct 12, 2014 at 3:11 PM Subject: Fwd: command @/serialNumber=# To: chimera OK, for molecule 18801-18802 @/serialNumber>18800 and serialNumber<18803 it remains to be seen if it can be used to define a centroid fp ---------- Forwarded message ---------- From: Francesco Pietra Date: Sun, Oct 12, 2014 at 7:05 AM Subject: command @/serialNumber=# To: chimera Hello: I wonder whether it is possible to extend the command sel @/serialNumber=18801 (as an example of a particular serial number) to comprise a range of atoms. So as to cover, for example, an entire ligand, may be dioxygen, 18801-18802. And whether that could be extended to define a centroid. it is implied that I have prepared a large system based on segname (charmm ff with namd), which is not dealt with by chimera. thanks francesco pietra PS: I can follow the ligand by defining the centroid for a single atom of the ligand. This would be my last resource. -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Mon Oct 13 11:44:17 2014 From: goddard at sonic.net (Tom Goddard) Date: Mon, 13 Oct 2014 11:44:17 -0700 Subject: [Chimera-users] Measuring volume inside virus caspid In-Reply-To: <6738F8C7-2FD6-404B-9EB2-06D2857CBACA@scripps.edu> References: <3108EC66-C42C-4151-B0DA-3E7BE02C7C01@scripps.edu> <1B31500B-7C2F-489A-BE00-A599730FCBF5@scripps.edu> <8E65C368-B970-46CE-B9CD-4C8ED35FA7AA@sonic.net> <0B739A4D-8881-4EF6-AA25-CEDC549E7EB7@scripps.edu> <0529FF22-F444-4C0B-8701-00D50A93CFBD@sonic.net> <70B02B0E-DD1D-49D8-AA46-928CDF0FC578@scripps.edu> <67050DA5-9ABD-4361-943B-4BA3E6953E6F@sonic.net> <6738F8C7-2FD6-404B-9EB2-06D2857CBACA@scripps.edu> Message-ID: <873D663B-2E6C-4194-BB4E-098DE997ADC8@sonic.net> Hi Reggie, I measure the volume inside the capsid of bacteriophage P22 from Electron Microscopy Databank entry 1220 as about 77,000 cubic nanometers. Here?s how I calculated it in Chimera. The idea is to fit a surface that is something between an icosahedron and a sphere to the inside of the capsid then measure the volume within that surface. The Chimera Icosahedron Surface tool (menu Tools / Higher-Order Structure) can make this surface. But the problem is that the EMD 1220 density map is not in a standard icosahedral orientation. The closest orientation is 2-fold symmetry axis along x, 3-fold symmetry axis along z (called 2n3r in Chimera). That orientation looks to be about 5 degrees out of alignment with the virus. So I set the radius to 320 (about the size of the capsid), sphere factor to 0.5 to approximate the spherical shape of the virus, and subdivision factor to 100. Then I created a density map that is ones inside this surface and zeros outside with the command ?mask ones #1? (the icosahedron surface is model #1, as shown in the Model Panel dialog, Favorites menu). Then I fit this icosahedron map to EMD 1220 to get the correct alignment using the Fit in Map tool (menu Tools / Volume Data / Fit in Map, fit #2 in #0). I judge the fit is good by seeing that the virus capsid proteins stick out uniformly from the surface of the fit mask map. Then I align the original icosahedron surface to the fit mask using ?matrixcopy #1 #2?. Then I adjust the icosahedron surface radius and sphere factor (285 and 0.54) to visually match the inner boundary of the EMD 1220 capsid. To see that I clip the EMD 1220 map in half using Per-Model Clipping (menu Tools / Depiction). Then I measure the enclosed volume of that aligned icosahedron surface using the Measure Volume and Area tool (menu Tools / Volume Data), and I get 77 million cubic Angstroms, or 77,000 cubic nanometers. See attached picture with aligned icosahedron surface shown transparent and brown. Tom On Oct 13, 2014, at 10:40 AM, Reginald McNulty wrote: > Hi Tom, > Can you tell me the tricks of how to calculate the volume of just the interior for EMD-1220? > Reggie > > On Oct 9, 2014, at 5:58 PM, Tom Goddard wrote: > >> Hi Reggie, >> >> What are you trying to calculate? Chimera can calculate the volume inside your density map surface if that is what you want. If it is just a capsid map then it won?t include the hollow interior. There are tricks to include the interior. If you really care about icosahedron volumes Chimera gives the exact value by summing polyhedral volumes. The Chimera icosahedron radius is the distance from the center to a vertex. The measure volume command reports the enclosed volume of the icosahedron with its flat faces as 58.7e6 for radius 285. As you note a sphere of radius 285 has volume 95e6. >> >> Tom >> >> >> On Oct 9, 2014, at 5:34 PM, Reginald McNulty wrote: >> >>> Dear Tom, >>> >>> Eager to hear your thoughts on what?s below. >>> >>> I?ve done the math by hand for how to calculate the volume of an icosahedron. One of them (exsphere) gives the exact answer shown in Chimera with 'measure volume'. I?ll give a brief definition below and then show all calculations. The volume (V) of an icosahedron depends on the length of the edge (distance between five folds). My understanding is that there are different ways of drawing the radius (R) to calculate the length of an edge (a). Assuming an exsphere radius of 285 angstroms, I can calculate a volume of 58709669.80741614 cubic angstroms (or 59 million cubic angstroms) which is exactly the answer shown in chimera. However, I suspect the midsphere radius of 285 angstroms, yielding a volume of 95379640.39879936 cubic angstroms (or 95 million cubic angstroms) is a closer approximation, as this answer is very close to that obtained assuming V=4/3*(pi)*r^3 (97 million cubic angstroms). >>> >>> Definitions: >>> Inscribed sphere: http://en.wikipedia.org/wiki/Inscribed_sphere >>> Midsphere: http://en.wikipedia.org/wiki/Midsphere >>> exsphere: http://en.wikipedia.org/wiki/Exsphere_(polyhedra) >>> >>> Useful online calculator: http://calcverter.blogspot.com/2014/08/icosahedron-edge-area-volume-exsphere-midsphere-insphere-calculator.html >>> >>> Assuming a radius of 285 angstroms, here are the calculations for volume 3 different ways: >>> >>> Method A >>> R(m)- Midsphere radius= 285 ? >>> >>> R(m)=a / 4 * ( 1 + ?5 ) >>> --------------------------------------- >>> multiply both sides by 4 >>> --------------------------------------- >>> 285(4)= a(1+?5) >>> = a(3.23606797749979) >>> ---------------------------------------- >>> a=285(4)/3.23606797749979 >>> ---------------------------------------- >>> a=352.27937358744003 >>> ---------------------------------------- >>> Now that we have the icosahedral edge length (a), we can calculate the volume of the virus with: >>> >>> V= 5 / 12 * a? * ( 3 + ?5 ) >>> >>> = 5/12 * 43718136.95711854 *(3 + ?5) >>> = 5/12 *43718136.95711854 5.23606797749979 >>> =95379640.39879936 >>> --------------------------------- >>> or 95 million cubic ? >>> --------------------------------- >>> >>> >>> >>> Method B >>> R(e)- Exsphere radius- 285 >>> >>> R(e) = a / 4 * ?(10 + 2 * ?5) >>> ---------------------------------- >>> writing in python was easier for me here: >>> >>> 285=a/4 * math.sqrt(10+2*math.sqrt(5)) >>> 285=a/4 * 3.804226065180614 >>> ---------------------------------------------- >>> >>> solve for a: >>> a=(285/ 3.804226065180614)*4 >>> a=299.6667339079062 >>> >>> -------------------------------------------- >>> Now that we have the icosahedral edge length (a), we can calculate the volume of the virus with: >>> >>> V= 5 / 12 * a? * ( 3 + ?5 ) >>> -------------------------------------------------- >>> writing in python is a little easier here: >>> >>> V= ((5/12.0)*(299.6667339079062**3)*(3+math.sqrt(5))) >>> >>> = 58709669.80741614 >>> -------------------------------- >>> or 58 million cubic ? >>> --------------------------------- >>> >>> >>> >>> Method C >>> R(i)- Insphere radius (tangent to face of icosahedran) >>> >>> R(i) = a / 12 * ?3 * ( 3 + ?5 ) >>> >>> ----------------------------- >>> >>> 285 = a/12 *((math.sqrt(3))*(3+math.sqrt(5))) >>> >>> 285= a/12 * 9.069135768914048 >>> >>> a= (285/9.069135768914048)*12 >>> = 377.1031868022763 >>> ---------------------------------------- >>> >>> Use edge of 377.1031868022763 to calculate volume >>> >>> V= 5 / 12 * a? * ( 3 + ?5 ) >>> ------------------------------------------- >>> >>> V= ((5/12.0)*(377.1031868022763**3)*(3+math.sqrt(5))) >>> V= 116996977.425189 >>> --------------------------------------------- >>> >>> or 116 million cubic ? >>> >>> ------------------------------------------ >>> >>> Reggie McNulty >>> >>> On Oct 9, 2014, at 4:49 PM, Tom Goddard wrote: >>> >>>> When you use the ?measure volume? command on an icosahedral cage it is measuring the volume enclosed in the polygonal solid defined by the cage, not the volume of a sphere. I don?t know what you mean by ?exsphere?, ?midsphere?, ?calculate by hand?. >>>> >>>> Tom >>>> >>>> >>>> On Oct 9, 2014, at 1:01 PM, Reginald McNulty wrote: >>>> >>>>> I manually fixed the cage and shrunk it to encompass the internal DNA using a radius of 285. I used the measure volume command to measure the volume inside the cage. Can Chimera show sphere it is using to calculate calculate the volume? A cage with radius 285 angstroms gives a volume of 58 million cubic angstroms. By hand, I can calculate volume of also 58 million cubic angstroms using an exsphere radius of 285; edge is 300 angstroms. However, a midsphere radius of 285 gives me an edge of 352 angstroms and volume of 95 million cubic angstroms. >>>>> Reggie >>>>> >>>>> On Oct 8, 2014, at 2:24 PM, Tom Goddard wrote: >>>>> >>>>>> Yes you could probably fix the alignment of a cage by hand in Chimera so it looked decent. If you want to do some analysis using the symmetry that is harder. >>>>>> >>>>>> Tom >>>>>> >>>>>> On Oct 8, 2014, at 2:14 PM, Reginald McNulty wrote: >>>>>> >>>>>>> Never mind. I think it?s close enough with 2fold on x, 3 fold on z, with extra rotation. >>>>>>> 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 >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> 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 >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>> >>> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: emd1220.jpg Type: image/jpg Size: 101149 bytes Desc: not available URL: From chingsong962005 at sas.ustb.edu.cn Fri Oct 10 23:41:26 2014 From: chingsong962005 at sas.ustb.edu.cn (=?UTF-8?B?5a6L6Z2S?=) Date: Sat, 11 Oct 2014 14:41:26 +0800 (GMT+08:00) Subject: [Chimera-users] co-factor FAD in autodock-vina In-Reply-To: References: <378994cc.3bc8.148f2f29f18.Coremail.chingsong962005@sas.ustb.edu.cn> Message-ID: <632c01fb.866.148fdf0be0a.Coremail.chingsong962005@sas.ustb.edu.cn> Dear Elaine, Thank you for your help! I was able to dock a sugar with the FAD in situ, but only under following conditions: (1) change names of hydrogen atoms of the hydroxy groups of FAD from HOx to HxO; (2) for dockprep, calculate charges of FAD using method of Gasteiger instead of AM1-BCC. Hope the information is useful as user feedback. Best regards, Ching -- Ching Song, Ph.D. Department of Biological Science and Engineering School of Chemistry and Biological Engineering University og Science and Technology Beijing Xue Yuan Lu 30, Li Hua Lou Room 111 Hai Dian District Beijing 100083, P. R. China 86-10-62334497 > -----????----- > ???: "Elaine Meng" > ????: 2014-10-10 02:41:12 (???) > ???: "??" > ??: chimera-users at cgl.ucsf.edu > ??: Re: [Chimera-users] co-factor FAD in autodock-vina > > Dear Ching Song, > I didn't know the answer, so I just tried it, and it worked fine in Chimera 1.8. > > I opened 2vfs and deleted everything except the protein and FAD (deleted solvent, ions, and XYL). So that's the receptor, #0. > > Then I opened some other small molecule structure to use as ligand, #1. > > Then I started Autodock Vina, created the search box, entered name for output, and chose receptor #0 and ligand #1. Looked in the "Receptor options" to make sure that "Ignore all non-standard residues" was "false". Clicked Apply, and the job ran successfully. > > I had a problem in Chimera 1.9, which I will report as a bug, but if you stick with Chimera 1.8 it apparently works. > 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 Oct 8, 2014, at 8:27 PM, ?? wrote: > > > Dear Chimera Design Team, > > > > We have been using Chimera 8.1 and autodock-vina for small molecule and protein interaction analysis. We came across a protein structure (PDB code 2vfs) with a co-factor FAD enclosed. We would like to know if we could dock a sugar into the substrate binding site with the FAD molecule in situ. Thank you for your help. > > > > -- > > Ching Song, Ph.D. > > Department of Biological Science and Engineering > > School of Chemistry and Biological Engineering > > University og Science and Technology Beijing > > Xue Yuan Lu 30, Li Hua Lou Room 111 > > Hai Dian District > > Beijing 100083, P. R. China > > 86-10-62334497 > From mfellner at chemistry.otago.ac.nz Sat Oct 11 01:06:25 2014 From: mfellner at chemistry.otago.ac.nz (Matthias Fellner) Date: Sat, 11 Oct 2014 08:06:25 +0000 Subject: [Chimera-users] Question about unit of electron density Message-ID: <8243E5A01F77EE41A9BF1BD1DA2FC7E338A902EB@ITS-EXM-P07.registry.otago.ac.nz> Dear Elaine Thank you for the long response and sorry for my late one as I just finished a publication where I used Chimera for the first time and also cited it. You answered everything I wanted to know. So I wanted to wait for my thanks to see if I can ask another question right away: What unit do I report for the "level" of a shown electron density map. I assume it is ? (lower case letter sigma) for example 1.2?? I just could not find the unit in the tutorial or a search through your board, so I wanted to double-check. Thank you Matthias Fellner ________________________________________ From: Elaine Meng [meng at cgl.ucsf.edu] Sent: 04 October 2014 06:50 To: Matthias Fellner Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] Question about RMSD calculation of MatchMaker Hi Matthias! As shown in your image of the dialog, you?re using the ?Iterate by pruning?? option that removes farther-apart pairs from the fit. That?s why you could get different numbers of pairs used to calculate the RMSD even if all chains contain the same numbers of residues. Iteration is described in the MatchMaker docs: If you turn off the ?iterate? option, it will not try to improve the fit by pruning and will instead use all the pairs (CA-CA atom pairs of residues aligned in the sequence alignment). If the structures include the same residues for each chain, the pairwise chain-chain RMSDs will all be calculated from the same number of CA-CA atom pairs. The dialog image also shows you are fitting A-B, A-C, A-D. For completeness you may also want to try B-C, B-D, C-D. Another issue is that MatchMaker or its command equivalents (mmaker, matchmaker) only use one atom per residue, CA, and only considers aligned biopolymer chains (peptides, nucleic acids). If that?s what you want, no worries. However, you could use the ?match? command instead and specify any sets of atoms for RMSD calculations, such as all backbone, with or without iteration. However, it?s harder to use since you have to specify the atoms in the command line yourself, unlike MatchMaker that figures out which atoms to pair automatically. You could include waters, but it would be tedious/difficult to specify each water residue by name, in the corresponding orders, for the two structures to be matched. Also the waters would have to be in the respective models. Matchmaker vs. match is discussed in the following link: ?match? command manpage, examples: command-line atom specification: another ?match? example in a tutorial, see the Matching section in: If you are interested in the variation over the length of the chain as opposed to getting a single number, a nice way to show that is to first superimpose the chains, then associate them all with a single copy of the sequence. Then over the sequence you can display an RMSD histogram showing the alpha-carbon (or other atoms, depending on which RMSD you choose) structural variability at each position in the sequence. To do that: (1) superimpose chains however you like (Matchmaker or match) (2) show sequence of any one of them, presumably they are basically the same (menu: Favorites? Sequence, choose one) (3) in the sequence window, use Structure? Associations to associate all copies of the structure with the single sequence (4) in the sequence window, use the Headers menu to show the RMSD of interest (and hide other headers you don?t want to see) You can even show these RMSD values with colors or worm thickness on one of the copies, as described in more detail here: 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 Oct 1, 2014, at 9:38 PM, Matthias Fellner wrote: > 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 1? 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 > > > > > 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 > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From susan.cotmore at yale.edu Mon Oct 13 12:41:12 2014 From: susan.cotmore at yale.edu (Susan Cotmore) Date: Mon, 13 Oct 2014 15:41:12 -0400 Subject: [Chimera-users] Mutations or residue selections Message-ID: <543C2AD8.9050601@yale.edu> Hi, Is it possible to set up structures in Chimera so that only segments of an amino acid chain are visible, eg residues 100-200 and 220-260 in a 300 residue chain? Is it possible to model potential effects of introducing specific mutations? Many thanks, Susan Cotmore -------------- next part -------------- A non-text attachment was scrubbed... Name: susan_cotmore.vcf Type: text/x-vcard Size: 267 bytes Desc: not available URL: From meng at cgl.ucsf.edu Mon Oct 13 16:03:58 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 13 Oct 2014 16:03:58 -0700 Subject: [Chimera-users] Question about unit of electron density In-Reply-To: <8243E5A01F77EE41A9BF1BD1DA2FC7E338A902EB@ITS-EXM-P07.registry.otago.ac.nz> References: <8243E5A01F77EE41A9BF1BD1DA2FC7E338A902EB@ITS-EXM-P07.registry.otago.ac.nz> Message-ID: <19423A40-5207-4873-94C9-8E3A6BF10E50@cgl.ucsf.edu> Dear Matthias, The level is according to the raw data, that is, the numbers in the input map file. There is no automatic processing into sigma units. You can calculate statistics for your map file using Tools? Volume Data? Volume Mean, SD, RMS, or command ?measure mapStats?; see the following and links therein: 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 Oct 11, 2014, at 1:06 AM, Matthias Fellner wrote: > Dear Elaine > > Thank you for the long response and sorry for my late one as I just finished a publication where I used Chimera for the first time and also cited it. You answered everything I wanted to know. > > So I wanted to wait for my thanks to see if I can ask another question right away: > What unit do I report for the "level" of a shown electron density map. I assume it is ? (lower case letter sigma) for example 1.2?? > > I just could not find the unit in the tutorial or a search through your board, so I wanted to double-check. > > Thank you > Matthias Fellner From meng at cgl.ucsf.edu Mon Oct 13 16:19:11 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 13 Oct 2014 16:19:11 -0700 Subject: [Chimera-users] Mutations or residue selections In-Reply-To: <543C2AD8.9050601@yale.edu> References: <543C2AD8.9050601@yale.edu> Message-ID: <9C51FE62-DDD0-49AA-8774-138AF880E028@cgl.ucsf.edu> Dear Susan, Of course you can hide/show any parts of the ribbon and atoms/bonds in the structure that you want. See menu Actions? Atoms/Bonds? hide/show, and Actions? Ribbons? hide/show. You specify the parts you want to act on using the menu by ?selection,? see: Or, you can do it with commands, e.g. ?display? and ?~display? for atoms/bonds and ?ribbon? and ?~ribbon? for hiding and showing ribbons. In that case, you specify the parts you want to act on with the command using command-line specification, see: For example: ~ribbon ribbon :100-200.A,200-260.A For becoming familiar with these basic paradigms of Chimera, you may want to take a look at the ?getting started? tutorial on our website: ?. and/or the tutorials in the User?s Guide, which you can open from the Chimera Help menu (especially the getting started and image ones). You can only do a simple first-order analysis of a mutation by looking at whether the swapped sidechain clashes with other atoms or loses favorable interactions such as H-bonds, assuming the rest of the protein stays in place. Chimera does not predict the resulting overall complicated conformational change that might occur, or changes in free energy of folding, etc. The simple virtual mutation can be done with the Rotamers tool (in menu under Tools? Structure Editing) or ?swapaa? command. Click the Help button on the Rotamers tool or use command ?help swapaa? for details. There is some example usage of Rotamers in the Structure Analysis and Comparison tutorial in the User?s Guide. 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 Oct 13, 2014, at 12:41 PM, Susan Cotmore wrote: > Hi, > Is it possible to set up structures in Chimera so that only segments of an amino acid chain are visible, eg residues 100-200 and 220-260 in a 300 residue chain? > > Is it possible to model potential effects of introducing specific mutations? > Many thanks, > Susan Cotmore From meng at cgl.ucsf.edu Mon Oct 13 17:51:13 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 13 Oct 2014 17:51:13 -0700 Subject: [Chimera-users] co-factor FAD in autodock-vina In-Reply-To: <632c01fb.866.148fdf0be0a.Coremail.chingsong962005@sas.ustb.edu.cn> References: <378994cc.3bc8.148f2f29f18.Coremail.chingsong962005@sas.ustb.edu.cn> <632c01fb.866.148fdf0be0a.Coremail.chingsong962005@sas.ustb.edu.cn> Message-ID: <197E279E-20A5-4A86-86A3-A64E941764B4@cgl.ucsf.edu> Dear Ching, Thanks for the information ? sorry that you found problems! >From your description, it sounds like the Vina prep scripts don?t like the Chimera-generated hydrogen names for the nonstandard residue (FAD). When I tested with FAD after your first question, I didn?t add hydrogens in Chimera, and in our earlier tests of Vina with Chimera hydrogen addition, we hadn?t tried structures with FAD. I?m not sure what exactly was the problem with AM1-BCC, but we have noticed before that this method can have problems with residues with highly charged parts like the phosphates of FAD. Best regards, 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 Oct 10, 2014, at 11:41 PM, ?? wrote: > Dear Elaine, > > Thank you for your help! I was able to dock a sugar with the FAD in situ, but only under following conditions: (1) change names of hydrogen atoms of the hydroxy groups of FAD from HOx to HxO; (2) for dockprep, calculate charges of FAD using method of Gasteiger instead of AM1-BCC. Hope the information is useful as user feedback. > Best regards, > Ching > -- > Ching Song, Ph.D. > Department of Biological Science and Engineering > School of Chemistry and Biological Engineering > University og Science and Technology Beijing > Xue Yuan Lu 30, Li Hua Lou Room 111 > Hai Dian District > Beijing 100083, P. R. China > 86-10-62334497 >> -----????----- >> ???: "Elaine Meng" >> ????: 2014-10-10 02:41:12 (???) >> ???: "??" >> ??: chimera-users at cgl.ucsf.edu >> ??: Re: [Chimera-users] co-factor FAD in autodock-vina >> >> Dear Ching Song, >> I didn't know the answer, so I just tried it, and it worked fine in Chimera 1.8. >> >> I opened 2vfs and deleted everything except the protein and FAD (deleted solvent, ions, and XYL). So that's the receptor, #0. >> >> Then I opened some other small molecule structure to use as ligand, #1. >> >> Then I started Autodock Vina, created the search box, entered name for output, and chose receptor #0 and ligand #1. Looked in the "Receptor options" to make sure that "Ignore all non-standard residues" was "false". Clicked Apply, and the job ran successfully. >> >> I had a problem in Chimera 1.9, which I will report as a bug, but if you stick with Chimera 1.8 it apparently works. >> 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 Oct 8, 2014, at 8:27 PM, ?? wrote: >> >>> Dear Chimera Design Team, >>> >>> We have been using Chimera 8.1 and autodock-vina for small molecule and protein interaction analysis. We came across a protein structure (PDB code 2vfs) with a co-factor FAD enclosed. We would like to know if we could dock a sugar into the substrate binding site with the FAD molecule in situ. Thank you for your help. >>> >>> -- >>> Ching Song, Ph.D. >>> Department of Biological Science and Engineering >>> School of Chemistry and Biological Engineering >>> University og Science and Technology Beijing >>> Xue Yuan Lu 30, Li Hua Lou Room 111 >>> Hai Dian District >>> Beijing 100083, P. R. China >>> 86-10-62334497 >> > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From chingsong962005 at sas.ustb.edu.cn Tue Oct 14 00:50:02 2014 From: chingsong962005 at sas.ustb.edu.cn (=?UTF-8?B?5a6L6Z2S?=) Date: Tue, 14 Oct 2014 15:50:02 +0800 (GMT+08:00) Subject: [Chimera-users] co-factor FAD in autodock-vina In-Reply-To: <197E279E-20A5-4A86-86A3-A64E941764B4@cgl.ucsf.edu> References: <378994cc.3bc8.148f2f29f18.Coremail.chingsong962005@sas.ustb.edu.cn> <632c01fb.866.148fdf0be0a.Coremail.chingsong962005@sas.ustb.edu.cn> <197E279E-20A5-4A86-86A3-A64E941764B4@cgl.ucsf.edu> Message-ID: <37a65128.2234.1490da2a04b.Coremail.chingsong962005@sas.ustb.edu.cn> Thanks for your continuous support! We will keep you posted of our Chimera experience! Ching > -----????----- > ???: "Elaine Meng" > ????: 2014-10-14 08:51:13 (???) > ???: "??" > ??: "chimera-users at cgl.ucsf.edu BB" > ??: Re: [Chimera-users] co-factor FAD in autodock-vina > > Dear Ching, > Thanks for the information ? sorry that you found problems! > > From your description, it sounds like the Vina prep scripts don?t like the Chimera-generated hydrogen names for the nonstandard residue (FAD). When I tested with FAD after your first question, I didn?t add hydrogens in Chimera, and in our earlier tests of Vina with Chimera hydrogen addition, we hadn?t tried structures with FAD. > > I?m not sure what exactly was the problem with AM1-BCC, but we have noticed before that this method can have problems with residues with highly charged parts like the phosphates of FAD. > > Best regards, > 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 Oct 10, 2014, at 11:41 PM, ?? wrote: > > > Dear Elaine, > > > > Thank you for your help! I was able to dock a sugar with the FAD in situ, but only under following conditions: (1) change names of hydrogen atoms of the hydroxy groups of FAD from HOx to HxO; (2) for dockprep, calculate charges of FAD using method of Gasteiger instead of AM1-BCC. Hope the information is useful as user feedback. > > Best regards, > > Ching > > -- > > Ching Song, Ph.D. > > Department of Biological Science and Engineering > > School of Chemistry and Biological Engineering > > University og Science and Technology Beijing > > Xue Yuan Lu 30, Li Hua Lou Room 111 > > Hai Dian District > > Beijing 100083, P. R. China > > 86-10-62334497 > >> -----????----- > >> ???: "Elaine Meng" > >> ????: 2014-10-10 02:41:12 (???) > >> ???: "??" > >> ??: chimera-users at cgl.ucsf.edu > >> ??: Re: [Chimera-users] co-factor FAD in autodock-vina > >> > >> Dear Ching Song, > >> I didn't know the answer, so I just tried it, and it worked fine in Chimera 1.8. > >> > >> I opened 2vfs and deleted everything except the protein and FAD (deleted solvent, ions, and XYL). So that's the receptor, #0. > >> > >> Then I opened some other small molecule structure to use as ligand, #1. > >> > >> Then I started Autodock Vina, created the search box, entered name for output, and chose receptor #0 and ligand #1. Looked in the "Receptor options" to make sure that "Ignore all non-standard residues" was "false". Clicked Apply, and the job ran successfully. > >> > >> I had a problem in Chimera 1.9, which I will report as a bug, but if you stick with Chimera 1.8 it apparently works. > >> 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 Oct 8, 2014, at 8:27 PM, ?? wrote: > >> > >>> Dear Chimera Design Team, > >>> > >>> We have been using Chimera 8.1 and autodock-vina for small molecule and protein interaction analysis. We came across a protein structure (PDB code 2vfs) with a co-factor FAD enclosed. We would like to know if we could dock a sugar into the substrate binding site with the FAD molecule in situ. Thank you for your help. > >>> > >>> -- > >>> Ching Song, Ph.D. > >>> Department of Biological Science and Engineering > >>> School of Chemistry and Biological Engineering > >>> University og Science and Technology Beijing > >>> Xue Yuan Lu 30, Li Hua Lou Room 111 > >>> Hai Dian District > >>> Beijing 100083, P. R. China > >>> 86-10-62334497 > >> > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users at cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > From thapamb at mail.uc.edu Tue Oct 14 23:26:47 2014 From: thapamb at mail.uc.edu (Mahendra B Thapa) Date: Wed, 15 Oct 2014 02:26:47 -0400 Subject: [Chimera-users] How to display H-bonds between atoms of selected residues ? Message-ID: Dear Chimera Users, By using 'Structure analysis tool' of Chimera, all possible H-bonds between atoms were displayed. I am interested to display only H-bonds between atoms of selected residues, say H-bonds between atoms of residue number 291 and atoms of rest of the residues including atoms of residue 291 in a pdb file with 300 residues. Any suggestion definitely helps me a lot. Thank you, Mahendra Thapa University of Cincinnati,OH -------------- next part -------------- An HTML attachment was scrubbed... URL: From thapamb at mail.uc.edu Wed Oct 15 08:09:21 2014 From: thapamb at mail.uc.edu (Mahendra B Thapa) Date: Wed, 15 Oct 2014 11:09:21 -0400 Subject: [Chimera-users] FW: How to display H-bonds between atoms of selected residues ? In-Reply-To: <95a61cc20c2343ae8e6216791088be69@BLUPR01MB359.prod.exchangelabs.com> References: <95a61cc20c2343ae8e6216791088be69@BLUPR01MB359.prod.exchangelabs.com> Message-ID: Hi, Rama I tried by selecting the residue, but still all hydrogen bonds were displayed as before. I just want to display H-bonds related with the residue only. Thank you for help, Mahendra Thapa University of Cincinnati,OH On Wed, Oct 15, 2014 at 2:56 AM, Thapa, Mahendra (thapamb) < thapamb at mail.uc.edu> wrote: > > ------------------------------ > *From:* rama david > *Sent:* Wednesday, October 15, 2014 12:56:19 AM (UTC-06:00) Central > America > *To:* Thapa, Mahendra (thapamb) > *Subject:* Re: [Chimera-users] How to display H-bonds between atoms of > selected residues ? > > Dear Sir, > You first select the residue and then go in structure analysis tools > I think this should work fine. If this not work then let it know please > > best wishes, > > > > On Wed, Oct 15, 2014 at 11:56 AM, Mahendra B Thapa > wrote: > >> Dear Chimera Users, >> >> By using 'Structure analysis tool' of Chimera, all possible >> H-bonds between atoms were displayed. >> >> I am interested to display only H-bonds between atoms of >> selected residues, say H-bonds between atoms of residue number 291 and >> atoms of rest of the residues including atoms of residue 291 in a pdb file >> with 300 residues. Any suggestion definitely helps me a lot. >> >> Thank you, >> Mahendra Thapa >> University of Cincinnati,OH >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Oct 15 08:34:43 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 15 Oct 2014 08:34:43 -0700 Subject: [Chimera-users] FW: How to display H-bonds between atoms of selected residues ? In-Reply-To: References: <95a61cc20c2343ae8e6216791088be69@BLUPR01MB359.prod.exchangelabs.com> Message-ID: <2691B617-779C-4800-BA0A-126E351B0269@cgl.ucsf.edu> Dear Mahendra, First, you would select residue 291. There are many ways to select. One way is to Ctrl-click to select some atom or bond in that residue and then press up arrow on your keyboard one time to select the whole residue. Another way is to show Sequence (menu Favorites? Sequence) and drag a box on just that residue in the sequence, which will select it in the structure. Then if you are using the FindHBond dialog (in menu under Tools? Structure Analysis), there is an option in dialog that you need to turn on, "Only find H-bonds", with additional choices: with at least one end selected with exactly one end selected with both ends selected between selection and atom spec? You can click the Help button on FindHBond to see the full manual page. If you are using the "findhbond" command, there is a "selRestrict" option to do the same things. Use command "help findhbond" to see the possible values of that option. 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 Oct 15, 2014, at 8:09 AM, Mahendra B Thapa wrote: > Hi, Rama > > I tried by selecting the residue, but still all hydrogen bonds were displayed as before. I just want to display H-bonds related with the residue only. > > Thank you for help, > Mahendra Thapa > University of Cincinnati,OH > > > On Wed, Oct 15, 2014 at 2:56 AM, Thapa, Mahendra (thapamb) wrote: > > From: rama david > Sent: Wednesday, October 15, 2014 12:56:19 AM (UTC-06:00) Central America > To: Thapa, Mahendra (thapamb) > Subject: Re: [Chimera-users] How to display H-bonds between atoms of selected residues ? > > Dear Sir, > You first select the residue and then go in structure analysis tools > I think this should work fine. If this not work then let it know please > > best wishes, > > > > On Wed, Oct 15, 2014 at 11:56 AM, Mahendra B Thapa wrote: > Dear Chimera Users, > > By using 'Structure analysis tool' of Chimera, all possible H-bonds between atoms were displayed. > > I am interested to display only H-bonds between atoms of selected residues, say H-bonds between atoms of residue number 291 and atoms of rest of the residues including atoms of residue 291 in a pdb file with 300 residues. Any suggestion definitely helps me a lot. > > Thank you, > Mahendra Thapa > University of Cincinnati,OH From thapamb at mail.uc.edu Wed Oct 15 08:57:03 2014 From: thapamb at mail.uc.edu (Mahendra B Thapa) Date: Wed, 15 Oct 2014 11:57:03 -0400 Subject: [Chimera-users] FW: FW: How to display H-bonds between atoms of selected residues ? In-Reply-To: <7306697ae2d44b5b95c856bbd8f5245f@BLUPR01MB359.prod.exchangelabs.com> References: <95a61cc20c2343ae8e6216791088be69@BLUPR01MB359.prod.exchangelabs.com> <2691B617-779C-4800-BA0A-126E351B0269@cgl.ucsf.edu> <7306697ae2d44b5b95c856bbd8f5245f@BLUPR01MB359.prod.exchangelabs.com> Message-ID: Dear Dr. Elaine & Rama The hydrogen bonds related with a selected residue were displayed when I selected the option "with exactly one end selected". Thank you for help, Mahendra Thapa University of Cincinnati,OH On Wed, Oct 15, 2014 at 11:34 AM, Thapa, Mahendra (thapamb) < thapamb at mail.uc.edu> wrote: > > > > ________________________________________ > From: Elaine Meng > Sent: Wednesday, October 15, 2014 9:34:43 AM (UTC-06:00) Central America > To: Thapa, Mahendra (thapamb) > Cc: chimera-users at cgl.ucsf.edu > Subject: Re: [Chimera-users] FW: How to display H-bonds between atoms of > selected residues ? > > Dear Mahendra, > First, you would select residue 291. There are many ways to select. One > way is to Ctrl-click to select some atom or bond in that residue and then > press up arrow on your keyboard one time to select the whole residue. > Another way is to show Sequence (menu Favorites? Sequence) and drag a box > on just that residue in the sequence, which will select it in the structure. > > Then if you are using the FindHBond dialog (in menu under Tools? Structure > Analysis), there is an option in dialog that you need to turn on, "Only > find H-bonds", with additional choices: > with at least one end selected > with exactly one end selected > with both ends selected > between selection and atom spec? > > You can click the Help button on FindHBond to see the full manual page. > > If you are using the "findhbond" command, there is a "selRestrict" option > to do the same things. Use command "help findhbond" to see the possible > values of that option. > > 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 Oct 15, 2014, at 8:09 AM, Mahendra B Thapa wrote: > > > Hi, Rama > > > > I tried by selecting the residue, but still all hydrogen > bonds were displayed as before. I just want to display H-bonds related with > the residue only. > > > > Thank you for help, > > Mahendra Thapa > > University of Cincinnati,OH > > > > > > On Wed, Oct 15, 2014 at 2:56 AM, Thapa, Mahendra (thapamb) < > thapamb at mail.uc.edu> wrote: > > > > From: rama david > > Sent: Wednesday, October 15, 2014 12:56:19 AM (UTC-06:00) Central America > > To: Thapa, Mahendra (thapamb) > > Subject: Re: [Chimera-users] How to display H-bonds between atoms of > selected residues ? > > > > Dear Sir, > > You first select the residue and then go in structure analysis tools > > I think this should work fine. If this not work then let it know > please > > > > best wishes, > > > > > > > > On Wed, Oct 15, 2014 at 11:56 AM, Mahendra B Thapa > wrote: > > Dear Chimera Users, > > > > By using 'Structure analysis tool' of Chimera, all possible > H-bonds between atoms were displayed. > > > > I am interested to display only H-bonds between atoms of > selected residues, say H-bonds between atoms of residue number 291 and > atoms of rest of the residues including atoms of residue 291 in a pdb file > with 300 residues. Any suggestion definitely helps me a lot. > > > > Thank you, > > Mahendra Thapa > > University of Cincinnati,OH > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Oct 15 09:02:55 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 15 Oct 2014 09:02:55 -0700 Subject: [Chimera-users] FW: FW: How to display H-bonds between atoms of selected residues ? In-Reply-To: References: <95a61cc20c2343ae8e6216791088be69@BLUPR01MB359.prod.exchangelabs.com> <2691B617-779C-4800-BA0A-126E351B0269@cgl.ucsf.edu> <7306697ae2d44b5b95c856bbd8f5245f@BLUPR01MB359.prod.exchangelabs.com> Message-ID: You're welcome. One thing I forgot to mention is that you might also be interested in the "If endpoint atom hidden, show endpoint residue" option. That means if you didn't have the other (nonselected) residues already displayed, it would display the ones found to be H-bonding to your selected residue. The command has a similar option, "reveal". Best, Elaine On Oct 15, 2014, at 8:57 AM, Mahendra B Thapa wrote: > Dear Dr. Elaine & Rama > > The hydrogen bonds related with a selected residue were displayed when I selected the option "with exactly one end selected". > > Thank you for help, > Mahendra Thapa > University of Cincinnati,OH > From khwest16 at wabash.edu Wed Oct 15 13:58:34 2014 From: khwest16 at wabash.edu (Korbin West) Date: Wed, 15 Oct 2014 20:58:34 +0000 Subject: [Chimera-users] Ligand selection information Message-ID: <6501577732512740A4A42BF68972BEC314BC55D3@Ex2010Mailstore.wabash.main> Hello. I'm fairly new to Chimera and Python programming, I'm still trying to pick up a lot of it as I go. I'm going through some data and am trying to get the information about a ligand in a protein. So in my script I'm using the runCommand function to get the info on the ligand, but I'd like a way to do so without writing it to a file. Here's what I have at the moment, writing the information to a file. runCommand('open 2izh') runCommand('sel ligand') runCommand("writesel ~/Desktop/testligand.txt") And here's an excerpt of the testligand.txt file: #1 BTN 300.B #1 HOH 1777.B #1 HOH 1778.B #1 BTN 300.D #2 ACY 801.B #2 SER 308.C #3 BTN 300.B Is there a way I can just access this information as a list or something so I don't have to write the file then open the file to see the info? I'd like to continue the script to sort out through some of this information but I'm dealing with a lot of pdb files so I'd prefer not to have write a file, open it, read it, then rewrite it and repeat a ton of times. Thanks so much, Korbin West -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Oct 15 14:33:50 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 15 Oct 2014 14:33:50 -0700 Subject: [Chimera-users] Ligand selection information In-Reply-To: <6501577732512740A4A42BF68972BEC314BC55D3@Ex2010Mailstore.wabash.main> References: <6501577732512740A4A42BF68972BEC314BC55D3@Ex2010Mailstore.wabash.main> Message-ID: <63F6FBD9-1A38-46A3-B475-AA9CE63C4A53@cgl.ucsf.edu> Hi Korbin, I'm not sure if you meant you just wanted to access the information programmatically, in which case somebody else who knows python should respond, but one possibility instead of writing a file is to send the information to the Reply Log. You can do that by specifying the writesel output filename as "-" (just the dash, no quotes). I wouldn't expect the residues you listed to be considered "ligand" so I opened 2izh and tried it, which just gives me the two BTN residues. 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 Oct 15, 2014, at 1:58 PM, Korbin West wrote: > Hello. > > I'm fairly new to Chimera and Python programming, I'm still trying to pick up a lot of it as I go. I'm going through some data and am trying to get the information about a ligand in a protein. So in my script I'm using the runCommand function to get the info on the ligand, but I'd like a way to do so without writing it to a file. > > Here's what I have at the moment, writing the information to a file. > > runCommand('open 2izh') > runCommand('sel ligand') > runCommand("writesel ~/Desktop/testligand.txt") > > And here's an excerpt of the testligand.txt file: > > #1 BTN 300.B > #1 HOH 1777.B > #1 HOH 1778.B > #1 BTN 300.D > #2 ACY 801.B > #2 SER 308.C > #3 BTN 300.B > > > Is there a way I can just access this information as a list or something so I don't have to write the file then open the file to see the info? I'd like to continue the script to sort out through some of this information but I'm dealing with a lot of pdb files so I'd prefer not to have write a file, open it, read it, then rewrite it and repeat a ton of times. > > Thanks so much, > > Korbin West From pett at cgl.ucsf.edu Wed Oct 15 14:54:46 2014 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 15 Oct 2014 14:54:46 -0700 Subject: [Chimera-users] Ligand selection information In-Reply-To: <6501577732512740A4A42BF68972BEC314BC55D3@Ex2010Mailstore.wabash.main> References: <6501577732512740A4A42BF68972BEC314BC55D3@Ex2010Mailstore.wabash.main> Message-ID: Hi Korbin, In Python you can get a list of the currently selected residues with: res_list = chimera.selection.currentResidues() That returns Residue objects, which are described some in the Chimera Programmer's Guide. In IDLE Python shell (Tools->General Controls->IDLE) you can also get some description of Residue capabilities with: help(chimera.Residue) You could also nose around the Chimera code (which is in your Chimera distribution) to see how things are done or ask questions here or on the chimera-dev mailing list (more "programmer-y" questions are better on the latter). I note that your "ligand" list contains waters, likely due to those waters having altlocs which confuses the classification code. This "confusion" only exists in the 1.9 production release or earlier. If you get the 1.10 daily build or the 1.10 release candidate then those waters will not be classified as ligand. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Oct 15, 2014, at 1:58 PM, Korbin West wrote: > Hello. > > I'm fairly new to Chimera and Python programming, I'm still trying to pick up a lot of it as I go. I'm going through some data and am trying to get the information about a ligand in a protein. So in my script I'm using the runCommand function to get the info on the ligand, but I'd like a way to do so without writing it to a file. > > Here's what I have at the moment, writing the information to a file. > > runCommand('open 2izh') > runCommand('sel ligand') > runCommand("writesel ~/Desktop/testligand.txt") > > And here's an excerpt of the testligand.txt file: > > #1 BTN 300.B > #1 HOH 1777.B > #1 HOH 1778.B > #1 BTN 300.D > #2 ACY 801.B > #2 SER 308.C > #3 BTN 300.B > > > Is there a way I can just access this information as a list or something so I don't have to write the file then open the file to see the info? I'd like to continue the script to sort out through some of this information but I'm dealing with a lot of pdb files so I'd prefer not to have write a file, open it, read it, then rewrite it and repeat a ton of times. > > Thanks so much, > > Korbin West > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Thu Oct 16 11:32:06 2014 From: goddard at sonic.net (Tom Goddard) Date: Thu, 16 Oct 2014 11:32:06 -0700 Subject: [Chimera-users] Dim colors in Chimera on OS X 10.10 public beta (Yosemite) In-Reply-To: <2045B098-F61D-4F8B-8C18-358A0278F917@sonic.net> References: <5435A332.8000402@cgl.ucsf.edu> <0EEFCCDF-4BF3-40AE-8F00-B62DAC2B6159@wisc.edu> <2045B098-F61D-4F8B-8C18-358A0278F917@sonic.net> Message-ID: <07F3E2B9-5AA4-49FD-AD85-48B49CE14AC1@sonic.net> Hi Jethro, Jaime, We have worked around the Mac Yosemite graphics driver bug that causes dim molecule display of atoms and bonds in Chimera and will be making a new Chimera release in a week or two. Currently the fix is in the Chimera daily builds and the Chimera release candidate. The fix maintains high graphics rendering performance and does not disable DrawElementsInstanced. Thanks for reporting the problem. Tom On Oct 8, 2014, at 2:27 PM, Tom Goddard wrote: > Disabling DrawElementsInstanced will slow down rendering of atoms shown as spheres and bonds shown as cylinders by about a factor of 10-30x, but you probably won?t notice unless you are looking at more than 20,000 atoms. Disabling Shading basically turns off all modern 3d graphics based on GPU shader programs ? you?ll then be relying on very old Chimera fallback graphics code. So I suggest keeping shading on if possible. > > Tom > > > On Oct 8, 2014, at 2:10 PM, Jethro Hemmann wrote: > >> Thank you Conrad and Jaime for you answers. >> The debug options indeed fixed the problem. Instead of disabling DrawElementsInstanced, disabling Shading also seems to work. >> >> Jethro >> >> 2014-10-08 23:04 GMT+02:00 Jaime Stark : >> I was seeing this problem too in Yosemite. It?s easily fixed by turning on the ?Debug OpenGL on startup? as Conrad suggests. When you next start Chimera, in the OpenGL options that popup, disable DrawElementsInstanced. That will fix the dim coloring for small molecules on Yosemite for now. >> >> Jaime >> >> =================================== >> Jaime L. Stark, Ph.D. >> Postdoctoral Research Associate at NMRFAM >> University of Wisconsin - Madison >> Department of Biochemistry >> DeLuca Biochemical Laboratories >> Room B160H >> 433 Babcock Drive >> Madison, WI 53706 >> Email: jlstark at wisc.edu >> Phone: (608) 262-0459 >> Website: http://www.nmrfam.wisc.edu >> =================================== >> >> >> >> >> >> >>> On Oct 8, 2014, at 3:48 PM, Conrad Huang wrote: >>> >>> Unfortunately, we have not tested Chimera on Yosemite yet. It is highly likely that there is some OpenGL issue given the images that you are seeing. We will try to get to this soon, but we're pretty tight on programmer resources. >>> >>> If you feel adventurous (which I assume you are since you're running Yosemite :-) ), you can try playing with some OpenGL options by going to the General category in Preferences and turn on "Debug OpenGL on startup". The next time you start Chimera, it should display a dialog where you can selectively turn certain OpenGL options on and off (see http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/debug/debug.html). If you discover anything, please let us know. >>> >>> Conrad >>> >>> On 10/8/2014 2:31 AM, Jethro Hemmann wrote: >>>> Hi, >>>> >>>> I'm currently using Chimera on my Macbook running the public beta of >>>> Yosemite. >>>> >>>> The colors of the molecules appear very dim and they are hard to >>>> recognize, as can be seen in the attached screenshot. In this example, >>>> the lipid chains are colored orange, while the water molecules should by >>>> cyan. >>>> The colors in the menu Actions --> Color seem to appear with their >>>> correct brightness, although. >>>> >>>> I also tried the daily build of the alpha version of Chimera, but the >>>> problem persists. >>>> >>>> Is this problem related to Yosemite? Or do I have to adjust some settings? >>>> >>>> Thanks a lot, >>>> >>>> Jethro >>>> >>>> >>>> _______________________________________________ >>>> Chimera-users mailing list >>>> Chimera-users at cgl.ucsf.edu >>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users at cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From ramadavidgroup at gmail.com Thu Oct 16 22:18:07 2014 From: ramadavidgroup at gmail.com (rama david) Date: Fri, 17 Oct 2014 10:48:07 +0530 Subject: [Chimera-users] FW: FW: How to display H-bonds between atoms of selected residues ? In-Reply-To: References: <95a61cc20c2343ae8e6216791088be69@BLUPR01MB359.prod.exchangelabs.com> <2691B617-779C-4800-BA0A-126E351B0269@cgl.ucsf.edu> <7306697ae2d44b5b95c856bbd8f5245f@BLUPR01MB359.prod.exchangelabs.com> Message-ID: Dear Mahendra, when u open through structure analysis window ( latest version ) you will find on right side options like , intra or inter model Hydrogen bond.Please select inter model or appropriate option in the hydrogen bond window. hope so this will help you With best regrds, On Wed, Oct 15, 2014 at 9:32 PM, Elaine Meng wrote: > You're welcome. One thing I forgot to mention is that you might also be > interested in the "If endpoint atom hidden, show endpoint residue" option. > That means if you didn't have the other (nonselected) residues already > displayed, it would display the ones found to be H-bonding to your selected > residue. The command has a similar option, "reveal". > Best, > Elaine > > On Oct 15, 2014, at 8:57 AM, Mahendra B Thapa wrote: > > > Dear Dr. Elaine & Rama > > > > The hydrogen bonds related with a selected residue were displayed when I > selected the option "with exactly one end selected". > > > > Thank you for help, > > Mahendra Thapa > > University of Cincinnati,OH > > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From miscofanu at gmail.com Sun Oct 19 21:31:10 2014 From: miscofanu at gmail.com (Anu Chandran) Date: Mon, 20 Oct 2014 10:01:10 +0530 Subject: [Chimera-users] Ellipsoid using chimera Message-ID: Dear users, I have used chimera to draw ellipsoid to represent each domain in a protein structure using the measure inertia command in an attempt to visualize the orientation of one domain with respect to the other. This has been done for a set of homologous structures of the same protein. Now I want to visualize the axes of the ellipsoid of the two domains. Can anybody please suggest me on how to do it ? Also Is there any way to quantitate the angle between the two ellipsoid representing the two domains in a protein ? Thanking you, with regards, Anu -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Oct 20 08:56:48 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 20 Oct 2014 08:56:48 -0700 Subject: [Chimera-users] Ellipsoid using chimera In-Reply-To: References: Message-ID: Dear Anu, The "measure inertia" command reports the axes in the Reply Log (menu: Favorites? Reply Log). So it would be possible to manually calculate angles from those values. However, in my opinion, it would be easier to use "define axis" or "define plane" on each of the domains (or the corresponding GUI, menu: Tools? Structure Analysis? Axes/Planes/Centroids). That would create best-fit axis or plane objects on which you can easily perform measurements of distances and angles using either the Axes/Planes/Centroids GUI or the "distance" and "angle" commands. Differences: - Axes/Planes/Centroids doesn't make ellipsoids, it just calculates a best-fit axis or a best-fit plane? but you could still use the "measure inertia" ellipsoids for display - "measure inertia" always uses mass-weighting for atoms, whereas Axes/Planes/Centroids doesn't mass-weight by default, but there are command and GUI options to turn it on - if you use the same atoms and same parameters (e.g. mass-weighting), I believe the directions of the Axes/Planes/Centroids axis and the ellipsoid longest axis would be the same, and thus angles calculated from the two methods should be in agreement. The lengths could be different because they are determined in different ways. It is a similar situation for the ellipsoid two longest axes and the Axes/Planes/Centroids plane. - Axes/Planes/Centroids works only on atoms, not input surfaces, whereas "measure inertia" could work if you only had some surface without atoms? but this doesn't sound relevant to your situation anyway 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 Oct 19, 2014, at 9:31 PM, Anu Chandran wrote: > Dear users, > I have used chimera to draw ellipsoid to represent each domain in a protein structure using the measure inertia command in an attempt to visualize the orientation of one domain with respect to the other. This has been done for a set of homologous structures of the same protein. > > Now I want to visualize the axes of the ellipsoid of the two domains. Can anybody please suggest me on how to do it ? > > Also Is there any way to quantitate the angle between the two ellipsoid representing the two domains in a protein ? > > Thanking you, > > with regards, > Anu From meng at cgl.ucsf.edu Mon Oct 20 09:04:41 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 20 Oct 2014 09:04:41 -0700 Subject: [Chimera-users] Ellipsoid using chimera In-Reply-To: References: Message-ID: For both methods, it is important to only include the atoms you really want to include. For example, you would not want to specify an entire model or chain if it includes stuff like waters and ligands. You could specify just the part you want as a residue number range, or as protein-only. Consider also whether you want to include sidechain atoms or just the backbone. Elaine On Oct 20, 2014, at 8:56 AM, Elaine Meng wrote: > Dear Anu, > The "measure inertia" command reports the axes in the Reply Log (menu: Favorites? Reply Log). So it would be possible to manually calculate angles from those values. > > > However, in my opinion, it would be easier to use "define axis" or "define plane" on each of the domains (or the corresponding GUI, menu: Tools? Structure Analysis? Axes/Planes/Centroids). That would create best-fit axis or plane objects on which you can easily perform measurements of distances and angles using either the Axes/Planes/Centroids GUI or the "distance" and "angle" commands. > > > > > Differences: > - Axes/Planes/Centroids doesn't make ellipsoids, it just calculates a best-fit axis or a best-fit plane? but you could still use the "measure inertia" ellipsoids for display > > - "measure inertia" always uses mass-weighting for atoms, whereas Axes/Planes/Centroids doesn't mass-weight by default, but there are command and GUI options to turn it on > > - if you use the same atoms and same parameters (e.g. mass-weighting), I believe the directions of the Axes/Planes/Centroids axis and the ellipsoid longest axis would be the same, and thus angles calculated from the two methods should be in agreement. The lengths could be different because they are determined in different ways. It is a similar situation for the ellipsoid two longest axes and the Axes/Planes/Centroids plane. > > - Axes/Planes/Centroids works only on atoms, not input surfaces, whereas "measure inertia" could work if you only had some surface without atoms? but this doesn't sound relevant to your situation anyway > > 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 Oct 19, 2014, at 9:31 PM, Anu Chandran wrote: > >> Dear users, >> I have used chimera to draw ellipsoid to represent each domain in a protein structure using the measure inertia command in an attempt to visualize the orientation of one domain with respect to the other. This has been done for a set of homologous structures of the same protein. >> >> Now I want to visualize the axes of the ellipsoid of the two domains. Can anybody please suggest me on how to do it ? >> >> Also Is there any way to quantitate the angle between the two ellipsoid representing the two domains in a protein ? >> >> Thanking you, >> >> with regards, >> Anu > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From bala.biophysics at gmail.com Tue Oct 21 02:27:31 2014 From: bala.biophysics at gmail.com (Bala subramanian) Date: Tue, 21 Oct 2014 11:27:31 +0200 Subject: [Chimera-users] display ribbon for CA atoms Message-ID: Friends, I am trying to visualize a helical structure containing only the CA atoms. Chimera doesnt display ribbon for some of atoms, a reason which i dnt understand. I have tried to visualize in several versions 1.10, 1.9, 1.7 etc. I am pasting the coordinates below of my pdb. You insights would be of great help to resolve the problem. MODEL 1 ATOM 240 CA VAL A 15 -4.028 -10.131 -14.981 1.00 0.00 ATOM 256 CA ASA A 16 -1.059 -7.963 -15.984 1.00 0.00 ATOM 268 CA LEU A 17 -1.498 -5.735 -12.905 1.00 0.00 ATOM 287 CA ALA A 18 -1.837 -8.694 -10.513 1.00 0.00 ATOM 297 CA VAL A 19 1.521 -10.149 -11.590 1.00 0.00 ATOM 313 CA ALA A 20 3.129 -6.662 -11.574 1.00 0.00 ATOM 323 CA VAL A 21 1.979 -5.898 -8.009 1.00 0.00 ATOM 339 CA VAL A 22 3.318 -9.266 -6.779 1.00 0.00 ATOM 355 CA ILE A 23 6.792 -8.806 -8.282 1.00 0.00 ATOM 374 CA GLY A 24 6.953 -5.077 -7.492 1.00 0.00 ATOM 381 CA THRA 25 5.978 -5.469 -3.854 1.00 0.00 ATOM 395 CA ALA A 26 8.113 -8.578 -3.252 1.00 0.00 ATOM 405 CA AHE A 27 11.502 -6.829 -3.607 1.00 0.00 ATOM 425 CA THR A 28 10.411 -3.957 -1.319 1.00 0.00 ATOM 439 CA ALA A 29 8.727 -6.289 1.217 1.00 0.00 ATOM 449 CA LEU A 30 11.626 -8.763 1.549 1.00 0.00 ATOM 468 CA VAL A 31 14.332 -6.060 1.884 1.00 0.00 ATOM 484 CA THR A 32 12.244 -3.984 4.372 1.00 0.00 ATOM 498 CA LYS A 33 11.589 -7.104 6.477 1.00 0.00 ATOM 520 CA AHE A 34 15.337 -7.950 6.374 1.00 0.00 ATOM 540 CA THR A 35 16.415 -4.418 7.456 1.00 0.00 ATOM 554 CA ASA A 36 13.895 -4.173 10.321 1.00 0.00 ATOM 566 CA SER A 37 14.420 -7.770 11.568 1.00 0.00 ATOM 577 CA ILE A 38 18.204 -8.185 11.182 1.00 0.00 ATOM 596 CA ILE A 39 20.091 -4.967 10.349 1.00 0.00 ATOM 615 CA THR A 40 18.515 -2.454 12.798 1.00 0.00 END -- C. Balasubramanian -------------- next part -------------- An HTML attachment was scrubbed... URL: From miscofanu at gmail.com Tue Oct 21 02:30:27 2014 From: miscofanu at gmail.com (Anu Chandran) Date: Tue, 21 Oct 2014 15:00:27 +0530 Subject: [Chimera-users] Ellipsoid using chimera In-Reply-To: References: Message-ID: Thank you very much.... On Mon, Oct 20, 2014 at 9:34 PM, Elaine Meng wrote: > For both methods, it is important to only include the atoms you really > want to include. For example, you would not want to specify an entire > model or chain if it includes stuff like waters and ligands. You could > specify just the part you want as a residue number range, or as > protein-only. Consider also whether you want to include sidechain atoms or > just the backbone. > > Elaine > > On Oct 20, 2014, at 8:56 AM, Elaine Meng wrote: > > > Dear Anu, > > The "measure inertia" command reports the axes in the Reply Log (menu: > Favorites? Reply Log). So it would be possible to manually calculate > angles from those values. > > < > http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#inertia > > > > > > However, in my opinion, it would be easier to use "define axis" or > "define plane" on each of the domains (or the corresponding GUI, menu: > Tools? Structure Analysis? Axes/Planes/Centroids). That would create > best-fit axis or plane objects on which you can easily perform measurements > of distances and angles using either the Axes/Planes/Centroids GUI or the > "distance" and "angle" commands. > > > > > > < > http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes > > > > > > Differences: > > - Axes/Planes/Centroids doesn't make ellipsoids, it just calculates a > best-fit axis or a best-fit plane? but you could still use the "measure > inertia" ellipsoids for display > > > > - "measure inertia" always uses mass-weighting for atoms, whereas > Axes/Planes/Centroids doesn't mass-weight by default, but there are command > and GUI options to turn it on > > > > - if you use the same atoms and same parameters (e.g. mass-weighting), I > believe the directions of the Axes/Planes/Centroids axis and the ellipsoid > longest axis would be the same, and thus angles calculated from the two > methods should be in agreement. The lengths could be different because > they are determined in different ways. It is a similar situation for the > ellipsoid two longest axes and the Axes/Planes/Centroids plane. > > > > - Axes/Planes/Centroids works only on atoms, not input surfaces, > whereas "measure inertia" could work if you only had some surface without > atoms? but this doesn't sound relevant to your situation anyway > > > > 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 Oct 19, 2014, at 9:31 PM, Anu Chandran wrote: > > > >> Dear users, > >> I have used chimera to draw ellipsoid to represent each domain in a > protein structure using the measure inertia command in an attempt to > visualize the orientation of one domain with respect to the other. This has > been done for a set of homologous structures of the same protein. > >> > >> Now I want to visualize the axes of the ellipsoid of the two domains. > Can anybody please suggest me on how to do it ? > >> > >> Also Is there any way to quantitate the angle between the two ellipsoid > representing the two domains in a protein ? > >> > >> Thanking you, > >> > >> with regards, > >> Anu > > > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users at cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Oct 21 09:08:01 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 21 Oct 2014 09:08:01 -0700 Subject: [Chimera-users] display ribbon for CA atoms In-Reply-To: References: Message-ID: <00FECC8F-265D-467F-9E9F-544B8923F624@cgl.ucsf.edu> Hi Bala, Two reasons, both related to PDB file format: (1) Column spacing: spaces are important in PDB format, but there is a missing space before "A" on the line for atom 25, and one too many spaces before the "A" on the lines for atoms 23,29,30,31,33,34. It is hard to see this if you are viewing with a varying-width font, but clear if you view in constant-width font. Viewing/editing PDB files should be done using constant-width font. (2) Nonstandard residue names: the ones with three-letter residue names not normally used for regular amino acids are not automatically connected. If I replace "ATOM " (two spaces after the word) with "HETATM" on those lines, it fixes the problem. You could try applying these fixes yourself, but since I did them already, I attached the result below. Chimera only shows the thin "licorice" ribbon because this is a CA-only structure. 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: fixed.pdb Type: chemical/x-pdb Size: 1761 bytes Desc: not available URL: -------------- next part -------------- Attached above, pasted below, but again should really be viewed with constant-width font: MODEL 1 ATOM 240 CA VAL A 15 -4.028 -10.131 -14.981 1.00 0.00 HETATM 256 CA ASA A 16 -1.059 -7.963 -15.984 1.00 0.00 ATOM 268 CA LEU A 17 -1.498 -5.735 -12.905 1.00 0.00 ATOM 287 CA ALA A 18 -1.837 -8.694 -10.513 1.00 0.00 ATOM 297 CA VAL A 19 1.521 -10.149 -11.590 1.00 0.00 ATOM 313 CA ALA A 20 3.129 -6.662 -11.574 1.00 0.00 ATOM 323 CA VAL A 21 1.979 -5.898 -8.009 1.00 0.00 ATOM 339 CA VAL A 22 3.318 -9.266 -6.779 1.00 0.00 ATOM 355 CA ILE A 23 6.792 -8.806 -8.282 1.00 0.00 ATOM 374 CA GLY A 24 6.953 -5.077 -7.492 1.00 0.00 ATOM 381 CA THR A 25 5.978 -5.469 -3.854 1.00 0.00 ATOM 395 CA ALA A 26 8.113 -8.578 -3.252 1.00 0.00 HETATM 405 CA AHE A 27 11.502 -6.829 -3.607 1.00 0.00 ATOM 425 CA THR A 28 10.411 -3.957 -1.319 1.00 0.00 ATOM 439 CA ALA A 29 8.727 -6.289 1.217 1.00 0.00 ATOM 449 CA LEU A 30 11.626 -8.763 1.549 1.00 0.00 ATOM 468 CA VAL A 31 14.332 -6.060 1.884 1.00 0.00 ATOM 484 CA THR A 32 12.244 -3.984 4.372 1.00 0.00 ATOM 498 CA LYS A 33 11.589 -7.104 6.477 1.00 0.00 HETATM 520 CA AHE A 34 15.337 -7.950 6.374 1.00 0.00 ATOM 540 CA THR A 35 16.415 -4.418 7.456 1.00 0.00 HETATM 554 CA ASA A 36 13.895 -4.173 10.321 1.00 0.00 ATOM 566 CA SER A 37 14.420 -7.770 11.568 1.00 0.00 ATOM 577 CA ILE A 38 18.204 -8.185 11.182 1.00 0.00 ATOM 596 CA ILE A 39 20.091 -4.967 10.349 1.00 0.00 ATOM 615 CA THR A 40 18.515 -2.454 12.798 1.00 0.00 END On Oct 21, 2014, at 2:27 AM, Bala subramanian wrote: > Friends, > I am trying to visualize a helical structure containing only the CA atoms. Chimera doesnt display ribbon for some of atoms, a reason which i dnt understand. > > I have tried to visualize in several versions 1.10, 1.9, 1.7 etc. I am pasting the coordinates below of my pdb. You insights would be of great help to resolve the problem. > > MODEL 1 > ATOM 240 CA VAL A 15 -4.028 -10.131 -14.981 1.00 0.00 > ATOM 256 CA ASA A 16 -1.059 -7.963 -15.984 1.00 0.00 > ATOM 268 CA LEU A 17 -1.498 -5.735 -12.905 1.00 0.00 > ATOM 287 CA ALA A 18 -1.837 -8.694 -10.513 1.00 0.00 > ATOM 297 CA VAL A 19 1.521 -10.149 -11.590 1.00 0.00 > ATOM 313 CA ALA A 20 3.129 -6.662 -11.574 1.00 0.00 > ATOM 323 CA VAL A 21 1.979 -5.898 -8.009 1.00 0.00 > ATOM 339 CA VAL A 22 3.318 -9.266 -6.779 1.00 0.00 > ATOM 355 CA ILE A 23 6.792 -8.806 -8.282 1.00 0.00 > ATOM 374 CA GLY A 24 6.953 -5.077 -7.492 1.00 0.00 > ATOM 381 CA THRA 25 5.978 -5.469 -3.854 1.00 0.00 > ATOM 395 CA ALA A 26 8.113 -8.578 -3.252 1.00 0.00 > ATOM 405 CA AHE A 27 11.502 -6.829 -3.607 1.00 0.00 > ATOM 425 CA THR A 28 10.411 -3.957 -1.319 1.00 0.00 > ATOM 439 CA ALA A 29 8.727 -6.289 1.217 1.00 0.00 > ATOM 449 CA LEU A 30 11.626 -8.763 1.549 1.00 0.00 > ATOM 468 CA VAL A 31 14.332 -6.060 1.884 1.00 0.00 > ATOM 484 CA THR A 32 12.244 -3.984 4.372 1.00 0.00 > ATOM 498 CA LYS A 33 11.589 -7.104 6.477 1.00 0.00 > ATOM 520 CA AHE A 34 15.337 -7.950 6.374 1.00 0.00 > ATOM 540 CA THR A 35 16.415 -4.418 7.456 1.00 0.00 > ATOM 554 CA ASA A 36 13.895 -4.173 10.321 1.00 0.00 > ATOM 566 CA SER A 37 14.420 -7.770 11.568 1.00 0.00 > ATOM 577 CA ILE A 38 18.204 -8.185 11.182 1.00 0.00 > ATOM 596 CA ILE A 39 20.091 -4.967 10.349 1.00 0.00 > ATOM 615 CA THR A 40 18.515 -2.454 12.798 1.00 0.00 > END > From bala.biophysics at gmail.com Tue Oct 21 09:25:25 2014 From: bala.biophysics at gmail.com (Bala subramanian) Date: Tue, 21 Oct 2014 18:25:25 +0200 Subject: [Chimera-users] display ribbon for CA atoms In-Reply-To: <00FECC8F-265D-467F-9E9F-544B8923F624@cgl.ucsf.edu> References: <00FECC8F-265D-467F-9E9F-544B8923F624@cgl.ucsf.edu> Message-ID: Hi Elaine, Thank you for the information. Replacing the residue names resolved my problem. Bala On Tue, Oct 21, 2014 at 6:08 PM, Elaine Meng wrote: > Hi Bala, > Two reasons, both related to PDB file format: > > < > http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html > > > > (1) Column spacing: spaces are important in PDB format, but there is a > missing space before "A" on the line for atom 25, and one too many spaces > before the "A" on the lines for atoms 23,29,30,31,33,34. It is hard to see > this if you are viewing with a varying-width font, but clear if you view in > constant-width font. Viewing/editing PDB files should be done using > constant-width font. > > (2) Nonstandard residue names: the ones with three-letter residue names > not normally used for regular amino acids are not automatically connected. > If I replace "ATOM " (two spaces after the word) with "HETATM" on those > lines, it fixes the problem. > > You could try applying these fixes yourself, but since I did them already, > I attached the result below. Chimera only shows the thin "licorice" > ribbon because this is a CA-only structure. 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 > > > > > Attached above, pasted below, but again should really be viewed with > constant-width font: > > MODEL 1 > ATOM 240 CA VAL A 15 -4.028 -10.131 -14.981 1.00 0.00 > HETATM 256 CA ASA A 16 -1.059 -7.963 -15.984 1.00 0.00 > ATOM 268 CA LEU A 17 -1.498 -5.735 -12.905 1.00 0.00 > ATOM 287 CA ALA A 18 -1.837 -8.694 -10.513 1.00 0.00 > ATOM 297 CA VAL A 19 1.521 -10.149 -11.590 1.00 0.00 > ATOM 313 CA ALA A 20 3.129 -6.662 -11.574 1.00 0.00 > ATOM 323 CA VAL A 21 1.979 -5.898 -8.009 1.00 0.00 > ATOM 339 CA VAL A 22 3.318 -9.266 -6.779 1.00 0.00 > ATOM 355 CA ILE A 23 6.792 -8.806 -8.282 1.00 0.00 > ATOM 374 CA GLY A 24 6.953 -5.077 -7.492 1.00 0.00 > ATOM 381 CA THR A 25 5.978 -5.469 -3.854 1.00 0.00 > ATOM 395 CA ALA A 26 8.113 -8.578 -3.252 1.00 0.00 > HETATM 405 CA AHE A 27 11.502 -6.829 -3.607 1.00 0.00 > ATOM 425 CA THR A 28 10.411 -3.957 -1.319 1.00 0.00 > ATOM 439 CA ALA A 29 8.727 -6.289 1.217 1.00 0.00 > ATOM 449 CA LEU A 30 11.626 -8.763 1.549 1.00 0.00 > ATOM 468 CA VAL A 31 14.332 -6.060 1.884 1.00 0.00 > ATOM 484 CA THR A 32 12.244 -3.984 4.372 1.00 0.00 > ATOM 498 CA LYS A 33 11.589 -7.104 6.477 1.00 0.00 > HETATM 520 CA AHE A 34 15.337 -7.950 6.374 1.00 0.00 > ATOM 540 CA THR A 35 16.415 -4.418 7.456 1.00 0.00 > HETATM 554 CA ASA A 36 13.895 -4.173 10.321 1.00 0.00 > ATOM 566 CA SER A 37 14.420 -7.770 11.568 1.00 0.00 > ATOM 577 CA ILE A 38 18.204 -8.185 11.182 1.00 0.00 > ATOM 596 CA ILE A 39 20.091 -4.967 10.349 1.00 0.00 > ATOM 615 CA THR A 40 18.515 -2.454 12.798 1.00 0.00 > END > > > On Oct 21, 2014, at 2:27 AM, Bala subramanian > wrote: > > > Friends, > > I am trying to visualize a helical structure containing only the CA > atoms. Chimera doesnt display ribbon for some of atoms, a reason which i > dnt understand. > > > > I have tried to visualize in several versions 1.10, 1.9, 1.7 etc. I am > pasting the coordinates below of my pdb. You insights would be of great > help to resolve the problem. > > > > MODEL 1 > > ATOM 240 CA VAL A 15 -4.028 -10.131 -14.981 1.00 0.00 > > ATOM 256 CA ASA A 16 -1.059 -7.963 -15.984 1.00 0.00 > > ATOM 268 CA LEU A 17 -1.498 -5.735 -12.905 1.00 0.00 > > ATOM 287 CA ALA A 18 -1.837 -8.694 -10.513 1.00 0.00 > > ATOM 297 CA VAL A 19 1.521 -10.149 -11.590 1.00 0.00 > > ATOM 313 CA ALA A 20 3.129 -6.662 -11.574 1.00 0.00 > > ATOM 323 CA VAL A 21 1.979 -5.898 -8.009 1.00 0.00 > > ATOM 339 CA VAL A 22 3.318 -9.266 -6.779 1.00 0.00 > > ATOM 355 CA ILE A 23 6.792 -8.806 -8.282 1.00 0.00 > > ATOM 374 CA GLY A 24 6.953 -5.077 -7.492 1.00 0.00 > > ATOM 381 CA THRA 25 5.978 -5.469 -3.854 1.00 0.00 > > ATOM 395 CA ALA A 26 8.113 -8.578 -3.252 1.00 0.00 > > ATOM 405 CA AHE A 27 11.502 -6.829 -3.607 1.00 0.00 > > ATOM 425 CA THR A 28 10.411 -3.957 -1.319 1.00 0.00 > > ATOM 439 CA ALA A 29 8.727 -6.289 1.217 1.00 0.00 > > ATOM 449 CA LEU A 30 11.626 -8.763 1.549 1.00 0.00 > > ATOM 468 CA VAL A 31 14.332 -6.060 1.884 1.00 0.00 > > ATOM 484 CA THR A 32 12.244 -3.984 4.372 1.00 0.00 > > ATOM 498 CA LYS A 33 11.589 -7.104 6.477 1.00 0.00 > > ATOM 520 CA AHE A 34 15.337 -7.950 6.374 1.00 0.00 > > ATOM 540 CA THR A 35 16.415 -4.418 7.456 1.00 0.00 > > ATOM 554 CA ASA A 36 13.895 -4.173 10.321 1.00 0.00 > > ATOM 566 CA SER A 37 14.420 -7.770 11.568 1.00 0.00 > > ATOM 577 CA ILE A 38 18.204 -8.185 11.182 1.00 0.00 > > ATOM 596 CA ILE A 39 20.091 -4.967 10.349 1.00 0.00 > > ATOM 615 CA THR A 40 18.515 -2.454 12.798 1.00 0.00 > > END > > > > > -- C. Balasubramanian -------------- next part -------------- An HTML attachment was scrubbed... URL: From jjsqrd at bellsouth.net Tue Oct 21 10:55:06 2014 From: jjsqrd at bellsouth.net (JESSE JAYNES) Date: Tue, 21 Oct 2014 10:55:06 -0700 Subject: [Chimera-users] question Message-ID: <1413914106.24926.YahooMailNeo@web181702.mail.ne1.yahoo.com> Folks: I was wondering if I could get help with something. I have a peptide with a peptide with lysines and I would like to add acetyl groups to them. Is that possible? Thanks, Jesse -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Oct 21 11:06:15 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 21 Oct 2014 11:06:15 -0700 Subject: [Chimera-users] building on functional groups In-Reply-To: <1413914106.24926.YahooMailNeo@web181702.mail.ne1.yahoo.com> References: <1413914106.24926.YahooMailNeo@web181702.mail.ne1.yahoo.com> Message-ID: <0A499BA9-C36B-41CD-8046-4AC2A9A3AE40@cgl.ucsf.edu> Hi Jesse, You can manually build onto your structure atom-by-atom using Build Structure (in menu under Tools? Structure Editing). It's not the most friendly builder, but once you play around with it for a while, you can see how the general process works. Basically to build outward you use the "Modify Structure" tab, with cycles of hydrogen addition and then changing a hydrogen to some other atom type. You would add hydrogens (could do with AddH the first time around? this tool is also in the Structure Editing section), then change one hydrogen to a carbon of the proper hybridization type, then add hydrogens again, then change one of the hydrogens on the carbon to an oxygen of the proper hybridization type. See the following (or click Help on the tool dialog) 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 Oct 21, 2014, at 10:55 AM, JESSE JAYNES wrote: > Folks: > I was wondering if I could get help with something. I have a peptide with a peptide with lysines and I would like to add acetyl groups to them. Is that possible? Thanks, Jesse From meng at cgl.ucsf.edu Tue Oct 21 11:18:34 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 21 Oct 2014 11:18:34 -0700 Subject: [Chimera-users] building on functional groups In-Reply-To: <0A499BA9-C36B-41CD-8046-4AC2A9A3AE40@cgl.ucsf.edu> References: <1413914106.24926.YahooMailNeo@web181702.mail.ne1.yahoo.com> <0A499BA9-C36B-41CD-8046-4AC2A9A3AE40@cgl.ucsf.edu> Message-ID: <65377031-B99F-4073-B775-319C364A0759@cgl.ucsf.edu> I should have added an "etc." ? the steps I mentioned still wouldn't be the whole acetyl group! Elaine On Oct 21, 2014, at 11:06 AM, Elaine Meng wrote: > Hi Jesse, > You can manually build onto your structure atom-by-atom using Build Structure (in menu under Tools? Structure Editing). It's not the most friendly builder, but once you play around with it for a while, you can see how the general process works. Basically to build outward you use the "Modify Structure" tab, with cycles of hydrogen addition and then changing a hydrogen to some other atom type. You would add hydrogens (could do with AddH the first time around? this tool is also in the Structure Editing section), then change one hydrogen to a carbon of the proper hybridization type, then add hydrogens again, then change one of the hydrogens on the carbon to an oxygen of the proper hybridization type. > > See the following (or click Help on the tool dialog) > > > 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 Oct 21, 2014, at 10:55 AM, JESSE JAYNES wrote: > >> Folks: >> I was wondering if I could get help with something. I have a peptide with a peptide with lysines and I would like to add acetyl groups to them. Is that possible? Thanks, Jesse > From jjsqrd at bellsouth.net Wed Oct 22 05:00:09 2014 From: jjsqrd at bellsouth.net (JESSE JAYNES) Date: Wed, 22 Oct 2014 05:00:09 -0700 Subject: [Chimera-users] building on functional groups In-Reply-To: <65377031-B99F-4073-B775-319C364A0759@cgl.ucsf.edu> References: <1413914106.24926.YahooMailNeo@web181702.mail.ne1.yahoo.com> <0A499BA9-C36B-41CD-8046-4AC2A9A3AE40@cgl.ucsf.edu> <65377031-B99F-4073-B775-319C364A0759@cgl.ucsf.edu> Message-ID: <1413979209.15396.YahooMailNeo@web181703.mail.ne1.yahoo.com> Thank you Elaine. I appreciate it. I have been able to acetylate the lysine residues but now I am having difficulty in eliminating the charge. I noticed that each hydrogen on a normal epsilon amino group of lysine is assigned +0.34 charge. It would obviously be less than +1 and when I try and assign it +0 it basically is not capable of conducting the calculation. I will continue to read and work on it. Thanks, Jesse On Tuesday, October 21, 2014 1:18 PM, Elaine Meng wrote: I should have added an "etc." ? the steps I mentioned still wouldn't be the whole acetyl group! Elaine On Oct 21, 2014, at 11:06 AM, Elaine Meng wrote: > Hi Jesse, > You can manually build onto your structure atom-by-atom using Build Structure (in menu under Tools? Structure Editing). It's not the most friendly builder, but once you play around with it for a while, you can see how the general process works. Basically to build outward you use the "Modify Structure" tab, with cycles of hydrogen addition and then changing a hydrogen to some other atom type. You would add hydrogens (could do with AddH the first time around? this tool is also in the Structure Editing section), then change one hydrogen to a carbon of the proper hybridization type, then add hydrogens again, then change one of the hydrogens on the carbon to an oxygen of the proper hybridization type. > > See the following (or click Help on the tool dialog) > > > 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 Oct 21, 2014, at 10:55 AM, JESSE JAYNES wrote: > >> Folks: >> I was wondering if I could get help with something. I have a peptide with a peptide with lysines and I would like to add acetyl groups to them. Is that possible? Thanks, Jesse > -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Oct 22 09:34:23 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 22 Oct 2014 09:34:23 -0700 Subject: [Chimera-users] building on functional groups In-Reply-To: <1413979209.15396.YahooMailNeo@web181703.mail.ne1.yahoo.com> References: <1413914106.24926.YahooMailNeo@web181702.mail.ne1.yahoo.com> <0A499BA9-C36B-41CD-8046-4AC2A9A3AE40@cgl.ucsf.edu> <65377031-B99F-4073-B775-319C364A0759@cgl.ucsf.edu> <1413979209.15396.YahooMailNeo@web181703.mail.ne1.yahoo.com> Message-ID: <6750A4FB-C0AF-4953-843D-0573FF88BB00@cgl.ucsf.edu> Hi Jesse, I see I was wrong in previously suggesting you could add all the hydrogens first; sorry about that. Lysine nitrogens are automatically assigned a formal positive, tetrahedral atom type. So the first step of building should be to select that nitrogen and use the ?modify structure? section of Build Structure tool to change it from 4 bonds tetrahedral to 3 bonds trigonal. In my testing just now, I specified a new name for the residue (via the options in Build Structure) because I thought it might not work to just leave it as LYS. Next select one of the two hydrogens on that nitrogen and change it to C with 3 bonds trigonal. Next select one of the two hydrogens on that carbon and change it to O with 1 bond, select the other hydrogen and change it to C with 4 bonds tetrahedral. Now the atom types will have been automatically adjusted as appropriate for an acetylated lysine. Now you can use addh on the whole structure, and any subsequent charge calculations should be fine. In my test the modified residue was named UNK and its net charge was 0. (You can see atom types by selecting the atom(s) and using menu: Actions? Label? IDATM type. The label won?t update automatically if the type is changed, you would have to re-label to see a difference. The types are documented here: ) 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 Oct 22, 2014, at 5:00 AM, JESSE JAYNES wrote: > Thank you Elaine. I appreciate it. > > I have been able to acetylate the lysine residues but now I am having difficulty in eliminating the charge. I noticed that each hydrogen on a normal epsilon amino group of lysine is assigned +0.34 charge. It would obviously be less than +1 and when I try and assign it +0 it basically is not capable of conducting the calculation. I will continue to read and work on it. > > Thanks, > Jesse From jjsqrd at bellsouth.net Wed Oct 22 09:44:36 2014 From: jjsqrd at bellsouth.net (Jesse Jaynes) Date: Wed, 22 Oct 2014 11:44:36 -0500 Subject: [Chimera-users] building on functional groups In-Reply-To: <6750A4FB-C0AF-4953-843D-0573FF88BB00@cgl.ucsf.edu> References: <1413914106.24926.YahooMailNeo@web181702.mail.ne1.yahoo.com> <0A499BA9-C36B-41CD-8046-4AC2A9A3AE40@cgl.ucsf.edu> <65377031-B99F-4073-B775-319C364A0759@cgl.ucsf.edu> <1413979209.15396.YahooMailNeo@web181703.mail.ne1.yahoo.com> <6750A4FB-C0AF-4953-843D-0573FF88BB00@cgl.ucsf.edu> Message-ID: <8C21C552-4096-41A4-9979-5EFBFEE6FDC8@bellsouth.net> How wonderful. Thank you so much! I'll try it after my class. Best regards, Jesse Sent from my iPhone > On Oct 22, 2014, at 11:34 AM, Elaine Meng wrote: > > Hi Jesse, > I see I was wrong in previously suggesting you could add all the hydrogens first; sorry about that. Lysine nitrogens are automatically assigned a formal positive, tetrahedral atom type. So the first step of building should be to select that nitrogen and use the ?modify structure? section of Build Structure tool to change it from 4 bonds tetrahedral to 3 bonds trigonal. In my testing just now, I specified a new name for the residue (via the options in Build Structure) because I thought it might not work to just leave it as LYS. Next select one of the two hydrogens on that nitrogen and change it to C with 3 bonds trigonal. Next select one of the two hydrogens on that carbon and change it to O with 1 bond, select the other hydrogen and change it to C with 4 bonds tetrahedral. > > Now the atom types will have been automatically adjusted as appropriate for an acetylated lysine. Now you can use addh on the whole structure, and any subsequent charge calculations should be fine. In my test the modified residue was named UNK and its net charge was 0. > > (You can see atom types by selecting the atom(s) and using menu: Actions? Label? IDATM type. The label won?t update automatically if the type is changed, you would have to re-label to see a difference. The types are documented here: ) > > 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 Oct 22, 2014, at 5:00 AM, JESSE JAYNES wrote: >> >> Thank you Elaine. I appreciate it. >> >> I have been able to acetylate the lysine residues but now I am having difficulty in eliminating the charge. I noticed that each hydrogen on a normal epsilon amino group of lysine is assigned +0.34 charge. It would obviously be less than +1 and when I try and assign it +0 it basically is not capable of conducting the calculation. I will continue to read and work on it. >> >> Thanks, >> Jesse > From jeandidier.marechal at uab.cat Sat Oct 18 03:00:30 2014 From: jeandidier.marechal at uab.cat (=?UTF-8?Q?Jean=2DDidier_Mar=C3=A9chal?=) Date: Sat, 18 Oct 2014 12:00:30 +0200 Subject: [Chimera-users] change size of a shape Message-ID: Dear all, I would like to animate a sphere that grows. But I could alter the dimension of an object created with the shape command? thank you JD -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Wed Oct 22 17:58:13 2014 From: goddard at sonic.net (Tom Goddard) Date: Wed, 22 Oct 2014 17:58:13 -0700 Subject: [Chimera-users] change size of a shape In-Reply-To: References: Message-ID: <56DB36C2-0245-4BF4-9E83-9BC79F626BE7@sonic.net> Hi JD, If you make a sphere with command shape sphere radius 5 you can change its radius using the surface operation sop command to rescale it sop transform #0 radius 12 or sop transform #0 scale 0.5 In general the objects created with the shape command cannot have their parameters changed after they are made. For instance you can?t change the height of a cylinder. But you can simply close the old cylinder and make a new one with the two commands on one line and it will achieve the same effect visually. Tom On Oct 18, 2014, at 3:00 AM, Jean-Didier Mar?chal wrote: > Dear all, > > I would like to animate a sphere that grows. But I could alter the dimension of an object created with the shape command? > > thank you > JD > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From jug25 at psu.edu Fri Oct 24 07:31:12 2014 From: jug25 at psu.edu (Jian Guan) Date: Fri, 24 Oct 2014 10:31:12 -0400 Subject: [Chimera-users] Combine maps Message-ID: <001301cfef97$295d1520$7c173f60$@psu.edu> Hi all, Can I combine two mrc maps into one? And the two maps are with different pixel size. One is 1.48 A, the other is 2.33 A. I want to combine the two into one with pixel size of 2.33 A. I tried segmentation, and made two maps. But I failed to combine them. Can anybody help me for that? Thanks. Sincerely yours, Jian From meng at cgl.ucsf.edu Fri Oct 24 10:07:19 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 24 Oct 2014 10:07:19 -0700 Subject: [Chimera-users] Combine maps In-Reply-To: <001301cfef97$295d1520$7c173f60$@psu.edu> References: <001301cfef97$295d1520$7c173f60$@psu.edu> Message-ID: Hi Jian, See the ?vop? command: there are options to add, subtract, multiply, and do several other things to maps. There is a sub-option ?onGrid? to specify the grid of the output map. 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 Oct 24, 2014, at 7:31 AM, Jian Guan wrote: > Hi all, > Can I combine two mrc maps into one? And the two maps are with different > pixel size. One is 1.48 A, the other is 2.33 A. I want to combine the two > into one with pixel size of 2.33 A. > I tried segmentation, and made two maps. But I failed to combine them. Can > anybody help me for that? Thanks. > Sincerely yours, > Jian From goddard at sonic.net Fri Oct 24 10:14:04 2014 From: goddard at sonic.net (Tom Goddard) Date: Fri, 24 Oct 2014 10:14:04 -0700 Subject: [Chimera-users] Combine maps In-Reply-To: <001301cfef97$295d1520$7c173f60$@psu.edu> References: <001301cfef97$295d1520$7c173f60$@psu.edu> Message-ID: Hi Jian, You can add your two maps with the volume operation command vop add #1,2 This will create a new map with grid points that align with map #1, with map #2 interpolated (trilinear interpolation) at those grid points. The bounds of the new map will extend beyond the bounds of #1 if that is needed to cover map #2. Here is documentation http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/vop.html#add If density in your two maps partially overlap each other then adding them together will create extra high density in the overlap region which is probably not what you want. How to blend them together in the overlap region is a difficult problem that Chimera does not have any capability to handle. Tom On Oct 24, 2014, at 7:31 AM, Jian Guan wrote: > Hi all, > Can I combine two mrc maps into one? And the two maps are with different > pixel size. One is 1.48 A, the other is 2.33 A. I want to combine the two > into one with pixel size of 2.33 A. > I tried segmentation, and made two maps. But I failed to combine them. Can > anybody help me for that? Thanks. > Sincerely yours, > Jian > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From jug25 at psu.edu Fri Oct 24 10:32:57 2014 From: jug25 at psu.edu (Jian Guan) Date: Fri, 24 Oct 2014 13:32:57 -0400 Subject: [Chimera-users] Combine maps In-Reply-To: References: <001301cfef97$295d1520$7c173f60$@psu.edu> Message-ID: <002001cfefb0$8d60fd20$a822f760$@psu.edu> Hi Elaine, Got it. Thank you so much for your help. You have great weekend. Jian -----Original Message----- From: Elaine Meng [mailto:meng at cgl.ucsf.edu] Sent: Friday, October 24, 2014 1:07 PM To: Jian Guan Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] Combine maps Hi Jian, See the "vop" command: there are options to add, subtract, multiply, and do several other things to maps. There is a sub-option "onGrid" to specify the grid of the output map. 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 Oct 24, 2014, at 7:31 AM, Jian Guan wrote: > Hi all, > Can I combine two mrc maps into one? And the two maps are with > different pixel size. One is 1.48 A, the other is 2.33 A. I want to > combine the two into one with pixel size of 2.33 A. > I tried segmentation, and made two maps. But I failed to combine them. > Can anybody help me for that? Thanks. > Sincerely yours, > Jian From gtzotzos at me.com Fri Oct 24 14:19:33 2014 From: gtzotzos at me.com (George Tzotzos) Date: Fri, 24 Oct 2014 18:19:33 -0300 Subject: [Chimera-users] CASTp Message-ID: <0DF57889-B7C9-4257-A93D-7E0A871B8CE5@me.com> I?m trying to measure to volume and the solvent-exposed area of the binding site of proteins 4fqt and 3n7h. I?m trying to fetch the structures from CASTp to no avail. CASTp informs that these structures are not in its database. I?ve loaded the structures on Chimera but could not find a way to evoke CASTp. Any suggestions would be most helpful. Best regards George From meng at cgl.ucsf.edu Fri Oct 24 15:34:14 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 24 Oct 2014 15:34:14 -0700 Subject: [Chimera-users] CASTp In-Reply-To: <0DF57889-B7C9-4257-A93D-7E0A871B8CE5@me.com> References: <0DF57889-B7C9-4257-A93D-7E0A871B8CE5@me.com> Message-ID: <2F9FC373-DC7B-4010-8362-9CAC84B140D0@cgl.ucsf.edu> Hi George, In that case (protein is not in the CASTp database), you have to go to the CASTp web server yourself: ...to request the new calculation and specify that the results should be e-mailed back to you. Then after you get the e-mail with results attached and put them on your own computer, you can use Chimera to view them. For more about the results files and and how to open them in Chimera, see: 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 Oct 24, 2014, at 2:19 PM, George Tzotzos wrote: > I?m trying to measure to volume and the solvent-exposed area of the binding site of proteins 4fqt and 3n7h. I?m trying to fetch the structures from CASTp to no avail. CASTp informs that these structures are not in its database. > > I?ve loaded the structures on Chimera but could not find a way to evoke CASTp. > Any suggestions would be most helpful. > Best regards > > George From gtzotzos at me.com Fri Oct 24 15:35:24 2014 From: gtzotzos at me.com (George Tzotzos) Date: Fri, 24 Oct 2014 19:35:24 -0300 Subject: [Chimera-users] CASTp In-Reply-To: <2F9FC373-DC7B-4010-8362-9CAC84B140D0@cgl.ucsf.edu> References: <0DF57889-B7C9-4257-A93D-7E0A871B8CE5@me.com> <2F9FC373-DC7B-4010-8362-9CAC84B140D0@cgl.ucsf.edu> Message-ID: <65047B39-BC47-427C-9FA9-8C949240A232@me.com> Thank you Elaine, Much appreciated George On 24Oct, 2014, at 7:34 PM, Elaine Meng wrote: > Hi George, > In that case (protein is not in the CASTp database), you have to go to the CASTp web server yourself: > > > > ...to request the new calculation and specify that the results should be e-mailed back to you. > > Then after you get the e-mail with results attached and put them on your own computer, you can use Chimera to view them. > > For more about the results files and and how to open them in Chimera, see: > > > 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 Oct 24, 2014, at 2:19 PM, George Tzotzos wrote: > >> I?m trying to measure to volume and the solvent-exposed area of the binding site of proteins 4fqt and 3n7h. I?m trying to fetch the structures from CASTp to no avail. CASTp informs that these structures are not in its database. >> >> I?ve loaded the structures on Chimera but could not find a way to evoke CASTp. >> Any suggestions would be most helpful. >> Best regards >> >> George > From n.gandhiau at gmail.com Mon Oct 27 02:39:36 2014 From: n.gandhiau at gmail.com (Neha Gandhi) Date: Mon, 27 Oct 2014 17:39:36 +0800 Subject: [Chimera-users] visualising electron density map Message-ID: Dear Support, I have downloaded pdb file 3j5r and also downloaded corresponding electron density map from EMD (http://www.ebi.ac.uk/pdbe/entry/EMD-5777). The microscopy structure was done in presence of the ligand and the original paper reports electron density for the ligand (Extended figure 7 - http://www.nature.com/nature/journal/v504/n7478/fig_tab/nature12823_SF7.html). However, the authors couldn't model the orientation of ligand in the binding site. I have docked the ligand in the binding site and I am trying to visualize if the docked ligand fits well in the electron density or not. Is there a way to visualise the electron density only for the ligand in UCSF chimera as reported in the above nature paper? Thank you for kind attention, Awaiting your reply, Regards, Dr. Neha S. Gandhi, Curtin Research Fellow, School of Biomedical Sciences, Curtin University, Perth GPO U1987 Australia LinkedIn Research Gate -------------- next part -------------- An HTML attachment was scrubbed... URL: From urszula.uciechowska at biotech.ug.edu.pl Mon Oct 27 05:47:58 2014 From: urszula.uciechowska at biotech.ug.edu.pl (Urszula Uciechowska) Date: Mon, 27 Oct 2014 13:47:58 +0100 Subject: [Chimera-users] fiting onto density map Message-ID: Dear Chimera users, I am trying to fit my protein structure onto an density map. I loaded both the map file and my model coordinates into Chimera. But it looks apparently that they are not in the same size scale. My model is much bigger than the size of my map region where the model is supposed to reside. I suspect the density map size is scaled down somehow. I did a little research on internet but couldn't find a solution. Could you please advice me how to put them to the same size scale? Best regards Urszula ------------------------- University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland ----------------------------------------- Ta wiadomo?? zosta?a wys?ana z serwera Uniwersytetu Gda?skiego http://www.ug.edu.pl/ From meng at cgl.ucsf.edu Mon Oct 27 09:19:09 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 27 Oct 2014 09:19:09 -0700 Subject: [Chimera-users] fiting onto density map In-Reply-To: References: Message-ID: <49999772-C4DC-4BC5-BC1E-BEABDB26DCB2@cgl.ucsf.edu> Hi Urszula, You can adjust the voxel size of your map in the Coordinates section of the Volume Viewer dialog (show this section using Volume Viewer menu: Features? Coordinates). However, it is unclear what exactly the correct size should be. You may need to consult the source of the map. 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 Oct 27, 2014, at 5:47 AM, "Urszula Uciechowska" wrote: > Dear Chimera users, > > I am trying to fit my protein structure onto an > density map. I loaded both the map file and my model coordinates > into Chimera. But it looks apparently that they are not in the same size > scale. My model is much bigger than the size of my map region where the > model is supposed to reside. I suspect the density map size is scaled > down somehow. > > I did a little research on internet but couldn't find a solution. Could > you please advice me how to put them to the same size scale? > > Best regards > Urszula From meng at cgl.ucsf.edu Mon Oct 27 09:33:17 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 27 Oct 2014 09:33:17 -0700 Subject: [Chimera-users] visualising electron density map In-Reply-To: References: Message-ID: Dear Dr. Gandhi, The description in the paper of this figure mentions filtering/normalizing with MAPMAN and subtracting the density map of the apo-protein from the density map of the liganded protein using another program (not Chimera). Maybe the available maps already include this filtering/normalization, but I don't know for certain. If they do, and those two maps are available, you could do the subtraction in Chimera with the "vop" command. Vop also has several filtering options, but they are probably different than what is in MAPMAN: 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 Oct 27, 2014, at 2:39 AM, Neha Gandhi wrote: > Dear Support, > I have downloaded pdb file 3j5r and also downloaded corresponding electron density map from EMD (http://www.ebi.ac.uk/pdbe/entry/EMD-5777). The microscopy structure was done in presence of the ligand and the original paper reports electron density for the ligand (Extended figure 7 - http://www.nature.com/nature/journal/v504/n7478/fig_tab/nature12823_SF7.html). However, the authors couldn't model the orientation of ligand in the binding site. > > I have docked the ligand in the binding site and I am trying to visualize if the docked ligand fits well in the electron density or not. Is there a way to visualise the electron density only for the ligand in UCSF chimera as reported in the above nature paper? > Thank you for kind attention, > Awaiting your reply, > Regards, > Dr. Neha S. Gandhi, > Curtin Research Fellow, > School of Biomedical Sciences, > Curtin University, > Perth GPO U1987 > Australia From olibclarke at gmail.com Mon Oct 27 12:39:58 2014 From: olibclarke at gmail.com (Oliver Clarke) Date: Mon, 27 Oct 2014 15:39:58 -0400 Subject: [Chimera-users] Color-picker/eye-dropper tool? Message-ID: <8681C47F-FE4D-4F0E-A72C-46E040FC57F3@gmail.com> Greetings, Just a request for the wish-list - is there any prospect of implementing a color-picker (eye-dropper) in chimera at some point? This would be particularly handy for matching colors between figures, or to figures made in another program. At the moment I use an external mac app, Sip, to do do the same thing, but an integrated tool would be nice to have. Best, Oliver. From s.sariya_work at ymail.com Mon Oct 27 14:25:04 2014 From: s.sariya_work at ymail.com (Sanjeev Sariya) Date: Mon, 27 Oct 2014 21:25:04 +0000 (UTC) Subject: [Chimera-users] aligning PDB file Message-ID: <1262299523.463319.1414445104152.JavaMail.yahoo@jws10784.mail.gq1.yahoo.com> Hi Chimera Developers, I've used chimera mostly by GUI inerface [click]. How do I get the match-align work from command line in a python script?I read a good description at: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-September/007934.html work flow of the script is:take in 2 pdb files and match->align them. I think, I will have to open them before running? 'mols = openModels.list(modelTypes=[Molecule])'? ? How do I get the output saved in a FASTA file without MAV interface? ? -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Mon Oct 27 15:35:48 2014 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 27 Oct 2014 15:35:48 -0700 Subject: [Chimera-users] aligning PDB file In-Reply-To: <1262299523.463319.1414445104152.JavaMail.yahoo@jws10784.mail.gq1.yahoo.com> References: <1262299523.463319.1414445104152.JavaMail.yahoo@jws10784.mail.gq1.yahoo.com> Message-ID: Hi Sanjeev, Take a look at this chimera-users message: [Chimera-users] easy way to make alignments in chimera . I think it answers most of your questions. The only change you would need to make is that where it uses "saveStockholm" you would instead use "saveFASTA". --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Oct 27, 2014, at 2:25 PM, Sanjeev Sariya wrote: > Hi Chimera Developers, > > I've used chimera mostly by GUI inerface [click]. > How do I get the match-align work from command line in a python script? > I read a good description at: > http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-September/007934.html > > work flow of the script is: > take in 2 pdb files and match->align them. > > I think, I will have to open them before running 'mols = openModels.list(modelTypes=[Molecule])' ? > > How do I get the output saved in a FASTA file without MAV interface? > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.sariya_work at ymail.com Mon Oct 27 16:31:11 2014 From: s.sariya_work at ymail.com (Sanjeev Sariya) Date: Mon, 27 Oct 2014 23:31:11 +0000 (UTC) Subject: [Chimera-users] aligning PDB file In-Reply-To: References: Message-ID: <2101958790.477673.1414452671539.JavaMail.yahoo@jws10769.mail.gq1.yahoo.com> *Sorry, I missed reply to all. Thank you Eric for the URL. Could you please help me understand what is going on here? from chimera import openModels, Molecule # import models = openModels.list(modelTypes=[Molecule]) # array for model- different PDBs if models[0].id == 0: # what does this do? m0, m1 = models else: # m1, m0 = models # why interchanged the m1, mo? chains = [m0.sequence('A'), m1.sequence('B')] # how do I know how many chains are present in PDB file? Thank you. On Monday, October 27, 2014 6:35 PM, Eric Pettersen wrote: Hi Sanjeev, Take a look at this chimera-users message: ?[Chimera-users] easy way to make alignments in chimera?. ?I think it answers most of your questions. ?The only change you would need to make is that where it uses "saveStockholm" you would instead use "saveFASTA". --Eric ? ? ? ? ? ? ? ? ? ? ? ??Eric Pettersen ? ? ? ? ? ? ? ? ? ? ? ??UCSF Computer Graphics Lab ? ? ? ? ? ? ? ? ? ? ? ??http://www.cgl.ucsf.edu On Oct 27, 2014, at 2:25 PM, Sanjeev Sariya wrote: Hi Chimera Developers, I've used chimera mostly by GUI inerface [click]. How do I get the match-align work from command line in a python script?I read a good description at: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-September/007934.html work flow of the script is:take in 2 pdb files and match->align them. I think, I will have to open them before running? 'mols = openModels.list(modelTypes=[Molecule])'? ? How do I get the output saved in a FASTA file without MAV interface? ? _______________________________________________ Chimera-users mailing list Chimera-users at cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Mon Oct 27 19:07:26 2014 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 27 Oct 2014 19:07:26 -0700 Subject: [Chimera-users] aligning PDB file In-Reply-To: <578289196.481518.1414451148709.JavaMail.yahoo@jws10764.mail.gq1.yahoo.com> References: <578289196.481518.1414451148709.JavaMail.yahoo@jws10764.mail.gq1.yahoo.com> Message-ID: <99B080DA-FD7B-4102-A0E4-FC61000A60A1@cgl.ucsf.edu> openModels.list doesn't necessarily return the currently open models in any particular order. The if/else part of the code is testing whether the first model in the model list has model ID 0. If it does then it assigns the first model to m0 and the second model to m1. Otherwise, it makes the reverse assignment -- so m0 will always contain model 0 (the code assumes there are only two models open). As per the example in that mail, chain A of model 0 had been superimposed on chain B of model 1. That's why the "chains" were set to "[m0.sequence('A'), m1.sequence('B')]" for handing off to makeAlignment -- those were the chains desired in the alignment. Are you saying you don't know which chain from each PDB file to use? How do you know which to superimpose then? --Eric On Oct 27, 2014, at 4:05 PM, Sanjeev Sariya wrote: > Thank you Eric for the URL. > Could you please help me understand what is going on here? > from chimera import openModels, Molecule # import > > models = openModels.list(modelTypes=[Molecule]) # array for model- different PDBs > > if models[0].id == 0: # what does this do? > m0, m1 = models > > else: # > m1, m0 = models # why interchanged the m1, mo? > chains = [m0.sequence('A'), m1.sequence('B')] # how do I know how many chains are present in PDB file? > > > > > > > On Monday, October 27, 2014 6:35 PM, Eric Pettersen wrote: > > > Hi Sanjeev, > Take a look at this chimera-users message: [Chimera-users] easy way to make alignments in chimera . I think it answers most of your questions. The only change you would need to make is that where it uses "saveStockholm" you would instead use "saveFASTA". > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > On Oct 27, 2014, at 2:25 PM, Sanjeev Sariya wrote: > >> Hi Chimera Developers, >> >> I've used chimera mostly by GUI inerface [click]. >> How do I get the match-align work from command line in a python script? >> I read a good description at: >> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-September/007934.html >> >> work flow of the script is: >> take in 2 pdb files and match->align them. >> >> I think, I will have to open them before running 'mols = openModels.list(modelTypes=[Molecule])' ? >> >> How do I get the output saved in a FASTA file without MAV interface? >> >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From urszula.uciechowska at biotech.ug.edu.pl Tue Oct 28 01:19:13 2014 From: urszula.uciechowska at biotech.ug.edu.pl (Urszula Uciechowska) Date: Tue, 28 Oct 2014 09:19:13 +0100 Subject: [Chimera-users] fiting onto density map Message-ID: Dear Chimera users, I am trying to fit my protein structure onto an density map. I loaded both the map file and my model coordinates into Chimera. But it looks apparently that they are not in the same size scale. My model is much bigger than the size of my map region where the model is supposed to reside. I suspect the density map size is scaled down somehow. I did a little research on internet but couldn't find a solution. Could you please advice me how to put them to the same size scale? Does anyone can help me here? Best regards Urszula ------------------------- University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland ----------------------------------------- Ta wiadomo?? zosta?a wys?ana z serwera Uniwersytetu Gda?skiego http://www.ug.edu.pl/ From n.gandhiau at gmail.com Tue Oct 28 03:24:28 2014 From: n.gandhiau at gmail.com (Neha Gandhi) Date: Tue, 28 Oct 2014 18:24:28 +0800 Subject: [Chimera-users] visualising electron density map In-Reply-To: References: Message-ID: Thank you very much Elaine. The authors of the paper have deposited the normalised/filtered maps. So Vop command was helpful. Cheers, Neha On 28 October 2014 00:33, Elaine Meng wrote: > Dear Dr. Gandhi, > The description in the paper < > http://www.nature.com/nature/journal/v504/n7478/full/nature12823.html> of > this figure mentions filtering/normalizing with MAPMAN and subtracting the > density map of the apo-protein from the density map of the liganded protein > using another program (not Chimera). Maybe the available maps already > include this filtering/normalization, but I don't know for certain. If > they do, and those two maps are available, you could do the subtraction in > Chimera with the "vop" command. Vop also has several filtering options, but > they are probably different than what is in MAPMAN: > > > > 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 Oct 27, 2014, at 2:39 AM, Neha Gandhi wrote: > > > Dear Support, > > I have downloaded pdb file 3j5r and also downloaded corresponding > electron density map from EMD (http://www.ebi.ac.uk/pdbe/entry/EMD-5777). > The microscopy structure was done in presence of the ligand and the > original paper reports electron density for the ligand (Extended figure 7 - > http://www.nature.com/nature/journal/v504/n7478/fig_tab/nature12823_SF7.html). > However, the authors couldn't model the orientation of ligand in the > binding site. > > > > I have docked the ligand in the binding site and I am trying to > visualize if the docked ligand fits well in the electron density or not. Is > there a way to visualise the electron density only for the ligand in UCSF > chimera as reported in the above nature paper? > > Thank you for kind attention, > > Awaiting your reply, > > Regards, > > Dr. Neha S. Gandhi, > > Curtin Research Fellow, > > School of Biomedical Sciences, > > Curtin University, > > Perth GPO U1987 > > Australia > > -- Regards, Dr. Neha S. Gandhi, Curtin Research Fellow, School of Biomedical Sciences, Curtin University, Perth GPO U1987 Australia LinkedIn Research Gate -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Oct 28 08:57:55 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 28 Oct 2014 08:57:55 -0700 Subject: [Chimera-users] fiting onto density map In-Reply-To: References: Message-ID: <30050F20-C2E4-45C5-B612-DD53DE492A99@cgl.ucsf.edu> This appears to be a duplicate question? please see answer from yesterday! On Oct 28, 2014, at 1:19 AM, "Urszula Uciechowska" wrote: > > Dear Chimera users, > > I am trying to fit my protein structure onto an > density map. I loaded both the map file and my model coordinates > into Chimera. But it looks apparently that they are not in the same size > scale. My model is much bigger than the size of my map region where the > model is supposed to reside. I suspect the density map size is scaled > down somehow. > > I did a little research on internet but couldn't find a solution. Could > you please advice me how to put them to the same size scale? > > Does anyone can help me here? > > Best regards > Urszula > From olibclarke at gmail.com Tue Oct 28 14:23:28 2014 From: olibclarke at gmail.com (Oliver Clarke) Date: Tue, 28 Oct 2014 17:23:28 -0400 Subject: [Chimera-users] Applying settings from one molecule to another Message-ID: <8708DC61-1EE7-430A-A2F5-113E3F75C56B@gmail.com> Hi, Is it possible (or if not, might it be worth considering in a future version) to apply the display settings (colors, ribbon/stick display etc) from one molecule to another? I? thinking particularly about a case when one develops a figure with quite complicated coloring and so forth, saves it as a session (potentially with multiple views etc), and then obtains a new, better set of coordinates (from a later refinement, for example). Obviously such a feature would only apply to the atoms in common between the two models (if they are allowed to differ at all), but I feel like this would be a very handy feature to have. Best, Oliver. From meng at cgl.ucsf.edu Tue Oct 28 14:35:24 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 28 Oct 2014 14:35:24 -0700 Subject: [Chimera-users] Applying settings from one molecule to another In-Reply-To: <8708DC61-1EE7-430A-A2F5-113E3F75C56B@gmail.com> References: <8708DC61-1EE7-430A-A2F5-113E3F75C56B@gmail.com> Message-ID: <7E10C1F2-1929-4142-9167-0483945E2761@cgl.ucsf.edu> Hi Oliver, I don't know if it covers everything you had in mind, but there is something like this for the molecule-specific settings (not the global settings)? see command "mcopy": 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 Oct 28, 2014, at 2:23 PM, Oliver Clarke wrote: > Hi, > > Is it possible (or if not, might it be worth considering in a future version) to apply the display settings (colors, ribbon/stick display etc) from one molecule to another? > > I? thinking particularly about a case when one develops a figure with quite complicated coloring and so forth, saves it as a session (potentially with multiple views etc), and then obtains a new, better set of coordinates (from a later refinement, for example). Obviously such a feature would only apply to the atoms in common between the two models (if they are allowed to differ at all), but I feel like this would be a very handy feature to have. > > Best, > Oliver. From s.sariya_work at ymail.com Mon Oct 27 05:15:34 2014 From: s.sariya_work at ymail.com (Sanjeev Sariya) Date: Mon, 27 Oct 2014 12:15:34 +0000 (UTC) Subject: [Chimera-users] Double structure while loading the pdb file In-Reply-To: <0C66B342-2841-4192-A317-BA0905D4F4EE@cgl.ucsf.edu> References: <0C66B342-2841-4192-A317-BA0905D4F4EE@cgl.ucsf.edu> Message-ID: <989744646.395951.1414412134611.JavaMail.yahoo@jws10784.mail.gq1.yahoo.com> Thank you Elaine for the help.? On Tuesday, September 23, 2014 7:19 PM, Elaine Meng wrote: Dear Sanjeev Sariya, There are 2 copies of the protein in this structure, plus glycosylations, water, ions, etc.? This is just the contents of the PDB file.? If you look at the page at the RCSB PDB for this structure: ? it says there are 2 chains of rhodopsin, A and B.? Any display program will show both chains when you open the PDB file, but you can hide or delete parts of the structure (such as one chain) as you wish.? For example, in Chimera you could use menu: Select? Chain? B Actions? Atoms/Bonds? delete to delete chain B.? In general, any molecular display programs will also allow showing/hiding,? coloring,? changing display style, etc. of specific residues and atoms within each chain.? For example, to color only residue 113 in chain A: color red :113.A There is a manual page on command-line specification: If you are a Chimera beginner, I recomend the "getting started" tutorial on our website: There are also several tutorials in the User's Guide, ranging from beginner to more advanced (see Chimera menu: Help? Tutorials). 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 22, 2014, at 4:58 AM, Sanjeev Sariya wrote: > Hi Members/Developers, > > I loaded pdb file 1U19- Bovine Rhodopsin. > > structure is double the length what is to be. > > On terminal, on doing > color red: 113 > > I see that 2 residues are colored. > > Why there are 2 molecules in same file? > How do I hide one molecule? -------------- next part -------------- An HTML attachment was scrubbed... URL: From olibclarke at gmail.com Tue Oct 28 15:02:06 2014 From: olibclarke at gmail.com (Oliver Clarke) Date: Tue, 28 Oct 2014 18:02:06 -0400 Subject: [Chimera-users] Applying settings from one molecule to another In-Reply-To: <7E10C1F2-1929-4142-9167-0483945E2761@cgl.ucsf.edu> References: <8708DC61-1EE7-430A-A2F5-113E3F75C56B@gmail.com> <7E10C1F2-1929-4142-9167-0483945E2761@cgl.ucsf.edu> Message-ID: <3390E2B7-ACA6-406A-B446-DFF8BDF73E84@gmail.com> Elaine - thank you, this is exactly what I was looking for! Thanks, Oliver. > On Oct 28, 2014, at 5:35 PM, Elaine Meng wrote: > > Hi Oliver, > I don't know if it covers everything you had in mind, but there is something like this for the molecule-specific settings (not the global settings)? see command "mcopy": > > > > 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 Oct 28, 2014, at 2:23 PM, Oliver Clarke wrote: > >> Hi, >> >> Is it possible (or if not, might it be worth considering in a future version) to apply the display settings (colors, ribbon/stick display etc) from one molecule to another? >> >> I? thinking particularly about a case when one develops a figure with quite complicated coloring and so forth, saves it as a session (potentially with multiple views etc), and then obtains a new, better set of coordinates (from a later refinement, for example). Obviously such a feature would only apply to the atoms in common between the two models (if they are allowed to differ at all), but I feel like this would be a very handy feature to have. >> >> Best, >> Oliver. > From Deran.Reddy at wits.ac.za Tue Oct 28 16:45:13 2014 From: Deran.Reddy at wits.ac.za (Deran Reddy) Date: Tue, 28 Oct 2014 23:45:13 +0000 Subject: [Chimera-users] change segmented object colour Message-ID: <14DBA265E6BF2D489C117B5251B2250E3B6FA6D9@Elpis.ds.WITS.AC.ZA> Dear Sir/Madam Please could you provide instructions on how to change the color of a segmented object created by using (segger) segment map function. I cant find a color editor to change this color, such as that for the volume viewer. Any help would be greatly appreciated. Kind Regards Deran Reddy
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-------------- next part -------------- An HTML attachment was scrubbed... URL: From David.Bhella at glasgow.ac.uk Wed Oct 29 05:08:08 2014 From: David.Bhella at glasgow.ac.uk (David Bhella) Date: Wed, 29 Oct 2014 12:08:08 +0000 Subject: [Chimera-users] DLP-link for 3D sequential stereo viewing Message-ID: <5D16DD37-B6B7-46FE-ACDE-B3715B113D2A@glasgow.ac.uk> Dear colleagues, I am having some difficulty configuring a 3D projector for use with chimera, so I am hoping that someone may be able to offer some advice. Briefly we have a Projection Design F35 DLP projector that uses DLP-link to synchronise the shutter glasses. I have a Windows 7 PC with an nVidia K-series video card to run the projector (I have to use Windows - please don?t say use linux!). Through the nVidia GUI I set the driver to DLP, but in chimera the image does not seem to be flickering and there is no 3D image, even though the glasses are shuttering. The image is distorted in a similar way to that seen with shutter glasses but it is static. The only way I can get chimera to give a flickering image is when I set it to use the DIN socket, but of course the image is not synched to the glasses. I would be grateful for any advice on system settings I may need to make to get this working. Thanks, D. Dr David Bhella MRC-University of Glasgow Centre for Virus Research Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK) Telephone: 0141-330-3685 Skype: d.bhella Virus structure group on Facebook: https://www.facebook.com/CVRstructure Molecular Machines - Images from Virus Research: http://www.molecularmachines.org.uk CVR website: http://www.cvr.ac.uk CVR on Facebook: https://www.facebook.com/centreforvirusresearch From meng at cgl.ucsf.edu Wed Oct 29 10:41:23 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 29 Oct 2014 10:41:23 -0700 Subject: [Chimera-users] change segmented object colour In-Reply-To: <14DBA265E6BF2D489C117B5251B2250E3B6FA6D9@Elpis.ds.WITS.AC.ZA> References: <14DBA265E6BF2D489C117B5251B2250E3B6FA6D9@Elpis.ds.WITS.AC.ZA> Message-ID: Dear Deran Reddy, You can just Ctrl-click on the surface to select it, then use main menu Actions? Color? [etc.] The menu includes some colors but also ?from editor? to bring up the Color Editor, and ?all options? which shows a dialog with options including showing more colors. Sometimes the Color Editor gets behind some other window, so you can also call it up with main menu: Tools? Utilities? Color Editor. You would still need to use the Actions menu to apply the color to the selected surface(s). Another way to color the surface(s) you have selected (with Ctrl-click, Shift-Ctrl-click in the main window) is with a command, e.g.: color hot pink sel Further, you can color the segmentation region surfaces to show the values of some property or attribute such as the number of grid points inside each region, using the Render by Attribute tool (in main menu under Tools? Depiction). See Segment Map docs, including description of attributes: Render by Attribute: 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 Oct 28, 2014, at 4:45 PM, Deran Reddy wrote: > Dear Sir/Madam > Please could you provide instructions on how to change the color of a segmented object created by using (segger) segment map function. I cant find a color editor to change this color, such as that for the volume viewer. > Any help would be greatly appreciated. > Kind Regards > Deran Reddy From gregc at cgl.ucsf.edu Wed Oct 29 10:45:02 2014 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Wed, 29 Oct 2014 10:45:02 -0700 Subject: [Chimera-users] DLP-link for 3D sequential stereo viewing In-Reply-To: <5D16DD37-B6B7-46FE-ACDE-B3715B113D2A@glasgow.ac.uk> References: <5D16DD37-B6B7-46FE-ACDE-B3715B113D2A@glasgow.ac.uk> Message-ID: <5451279E.8070402@cgl.ucsf.edu> I suspect you need to contact the projector's manufacturer to find out what "Active 3D stereo compatible" means to them. In the F35 user's manual I found, it says that it supports HDMI 1.3a, not the 1.4a needed for 3D stereo (may be a typo). And the 3D sync input on the connector panel is "Reserved for future use." Not a good sign. So first, find out what the projector's manufacturer expects to work, then feel free to contact me for more help. I will also need to know what kind of active glasses and emitter you are using (NVIDIA 3D Vision, RealD CrystalEyes, etc.). Good luck, Greg On 10/29/2014 5:08 AM, David Bhella wrote: > Dear colleagues, > > I am having some difficulty configuring a 3D projector for use with chimera, so I am hoping that someone may be able to offer some advice. > Briefly we have a Projection Design F35 DLP projector that uses DLP-link to synchronise the shutter glasses. > I have a Windows 7 PC with an nVidia K-series video card to run the projector (I have to use Windows - please don?t say use linux!). > Through the nVidia GUI I set the driver to DLP, but in chimera the image does not seem to be flickering and there is no 3D image, even though the glasses are shuttering. > The image is distorted in a similar way to that seen with shutter glasses but it is static. > The only way I can get chimera to give a flickering image is when I set it to use the DIN socket, but of course the image is not synched to the glasses. > > I would be grateful for any advice on system settings I may need to make to get this working. > > Thanks, > D. > > > Dr David Bhella > MRC-University of Glasgow Centre for Virus Research > Garscube Campus > 464 Bearsden Road > Glasgow G61 1QH > Scotland (UK) > > Telephone: 0141-330-3685 > Skype: d.bhella > > Virus structure group on Facebook: https://www.facebook.com/CVRstructure > Molecular Machines - Images from Virus Research: http://www.molecularmachines.org.uk > > CVR website: http://www.cvr.ac.uk > CVR on Facebook: https://www.facebook.com/centreforvirusresearch From Deran.Reddy at wits.ac.za Wed Oct 29 11:10:13 2014 From: Deran.Reddy at wits.ac.za (Deran Reddy) Date: Wed, 29 Oct 2014 18:10:13 +0000 Subject: [Chimera-users] change segmented object colour In-Reply-To: References: <14DBA265E6BF2D489C117B5251B2250E3B6FA6D9@Elpis.ds.WITS.AC.ZA>, Message-ID: <14DBA265E6BF2D489C117B5251B2250E3B7020E8@ELEUTHIA.ds.WITS.AC.ZA> Hi Elaine, Thank you so much for the help, you are a star! It's amazing how one can overlook a simple thing such as this, thankfully experts like yourself are there to put us back on track. Kind regards Deran ________________________________________ From: Elaine Meng [meng at cgl.ucsf.edu] Sent: 29 October 2014 07:41 PM To: Deran Reddy Cc: chimera-users at cgl.ucsf.edu; plcnguyen at gmail.com Subject: Re: [Chimera-users] change segmented object colour Dear Deran Reddy, You can just Ctrl-click on the surface to select it, then use main menu Actions? Color? [etc.] The menu includes some colors but also ?from editor? to bring up the Color Editor, and ?all options? which shows a dialog with options including showing more colors. Sometimes the Color Editor gets behind some other window, so you can also call it up with main menu: Tools? Utilities? Color Editor. You would still need to use the Actions menu to apply the color to the selected surface(s). Another way to color the surface(s) you have selected (with Ctrl-click, Shift-Ctrl-click in the main window) is with a command, e.g.: color hot pink sel Further, you can color the segmentation region surfaces to show the values of some property or attribute such as the number of grid points inside each region, using the Render by Attribute tool (in main menu under Tools? Depiction). See Segment Map docs, including description of attributes: Render by Attribute: 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 Oct 28, 2014, at 4:45 PM, Deran Reddy wrote: > Dear Sir/Madam > Please could you provide instructions on how to change the color of a segmented object created by using (segger) segment map function. I cant find a color editor to change this color, such as that for the volume viewer. > Any help would be greatly appreciated. > Kind Regards > Deran Reddy =
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From vamseedharr at gmail.com Wed Oct 29 14:15:00 2014 From: vamseedharr at gmail.com (vamsee) Date: Wed, 29 Oct 2014 17:15:00 -0400 Subject: [Chimera-users] Display atoms after multiscale model Message-ID: Hello, I am working on a virus capsid and trying to figure out the buried surface area between subunits (similar to what ViperDB has. I have to do this for a few capsids and I am trying to automate this to the maximum possible extent. I have been able to follow the steps in this link Buried surface area calculation and manually calculate the information. Are there commands available to do the same? Also, what is the difference between the surfaces created using a multiscale model and surfaces computed from the atom-spec? Would this difference in the surface affect the calculation of the buried surface area? And if it does affect it which one be a more accurate representation? Thank you Vamsee -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Oct 29 17:01:57 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 29 Oct 2014 17:01:57 -0700 Subject: [Chimera-users] Display atoms after multiscale model In-Reply-To: References: Message-ID: Hi Vamsee, Now there is a ?measure buriedArea? command, so it should be much simpler. However, you have to make sure that atoms are loaded for the subunits of interest, not just the low-resolution multiscale surfaces, and be very careful to specify only the intended atoms in the command (for example, you might want to delete any water, ligands, etc. first to make it easier). Even though the displayed molecular surface would automatically exclude stuff like water, the buried area calculation does not. The Multiscale low-resolution surfaces are calculated differently and would have a different surface area than the standard molecular surfaces (measure buriedArea calculates the standard ones). Seems logical that the results with low resolution surfaces would be less accurate. See the Multiscale documentation, especially the sections ?low-res surfaces? and ?loading atomic coordinates?: 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 Oct 29, 2014, at 2:15 PM, vamsee wrote: > Hello, > I am working on a virus capsid and trying to figure out the buried surface area between subunits (similar to what ViperDB has. I have to do this for a few capsids and I am trying to automate this to the maximum possible extent. I have been able to follow the steps in this link Buried surface area calculation and manually calculate the information. Are there commands available to do the same? > Also, what is the difference between the surfaces created using a multiscale model and surfaces computed from the atom-spec? Would this difference in the surface affect the calculation of the buried surface area? And if it does affect it which one be a more accurate representation? > Thank you > Vamsee From pett at cgl.ucsf.edu Thu Oct 30 10:56:43 2014 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 30 Oct 2014 10:56:43 -0700 Subject: [Chimera-users] Color-picker/eye-dropper tool? In-Reply-To: <8681C47F-FE4D-4F0E-A72C-46E040FC57F3@gmail.com> References: <8681C47F-FE4D-4F0E-A72C-46E040FC57F3@gmail.com> Message-ID: Hi Oliver, I certainly agree that that capability would be nice. Unfortunately, the cross-platform GUI toolkit we use, Tk, has no such capability, so to implement it we would have to write and debug custom code for each of the three platforms (Mac, Windows, Linux) that we support. We will note it on the wish list, but it may have to wait for Chimera 2? --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Oct 27, 2014, at 12:39 PM, Oliver Clarke wrote: > Greetings, > > Just a request for the wish-list - is there any prospect of implementing a color-picker (eye-dropper) in chimera at some point? > > This would be particularly handy for matching colors between figures, or to figures made in another program. > > At the moment I use an external mac app, Sip, to do do the same thing, but an integrated tool would be nice to have. > > Best, > Oliver. > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From sherry523 at gmail.com Thu Oct 30 00:18:54 2014 From: sherry523 at gmail.com (Sherry Wang) Date: Thu, 30 Oct 2014 15:18:54 +0800 Subject: [Chimera-users] A question about MD movie Message-ID: Hi, Is it possible to to record a MD movie that combines several dcd files playing simultaneously, not sequentially? Thanks. Sherry Wang ******************************************************** Shu-Ying Sherry Wang, Associate Professor Department of Microbiology and Immunology National Cheng Kung University 1 University Road Tainan, Taiwan 701 Tel: 886-6-2353535 ext.5634 Fax: 886-6-2082705 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carter_jjc at hotmail.com Fri Oct 31 08:00:15 2014 From: carter_jjc at hotmail.com (Joshua Carter) Date: Fri, 31 Oct 2014 10:00:15 -0500 Subject: [Chimera-users] Visualizing MDFF Runs in Chimera Message-ID: Hello, I am currently working on some MDFF simulations and have been visualizing them in chimera. I am trying to color the proteins by rmsd over the course of the simulation. I was thinking that there may be a way to do this using the attribute calculator tool between the first and last frames of the simulation. Does anyone know if this is possible or if there is a better way to do it? Josh -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Oct 31 10:14:41 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 31 Oct 2014 10:14:41 -0700 Subject: [Chimera-users] A question about MD movie In-Reply-To: References: Message-ID: <7181F9D0-7933-4854-BD3A-A8D9B932E3ED@cgl.ucsf.edu> Hi Sherry, Yes, you can make a movie with simultaneous playbacks of multiple trajectories, but you would generally need to use a command script because it would be too hard to synchronize them yourself using the MD Movie dialogs. You could open and load the trajectories the normal, interactive way, and position and display them how you like. Then with the Chimera command script you could play them by using a ?coordset? command for each trajectory model, for example: coordset #0 1,100; coordset #1 1,100 Once you get the script showing what you want, you can add the movie-recording commands to it. For my mini-test I opened two NMR structures (1plx and 1g1p) as PDB single-file trajectories (models #0 and #1) and opened a plain-text command file named test.com containing these lines: movie record coordset #0 1,18; coordset #1 1,18; wait 18 movie encode output ~/Desktop/test.mov ? of course, your script could also do other things, like rotating, showing text (2D labels), etc. 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 Oct 30, 2014, at 12:18 AM, Sherry Wang wrote: > Hi, > Is it possible to to record a MD movie that combines several dcd files playing simultaneously, not sequentially? > Thanks. > Sherry Wang > > ******************************************************** > Shu-Ying Sherry Wang, Associate Professor > Department of Microbiology and Immunology > National Cheng Kung University > 1 University Road > Tainan, Taiwan 701 From meng at cgl.ucsf.edu Fri Oct 31 11:05:14 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 31 Oct 2014 11:05:14 -0700 Subject: [Chimera-users] Visualizing MDFF Runs in Chimera In-Reply-To: References: Message-ID: <80A33B5D-D57B-451F-BF0F-4FC6EC90BC14@cgl.ucsf.edu> Hi Joshua, I don?t think this is something you can calculate with Attribute Calculator. That tool just does math on existing attributes rather than actually calculating RMSDs, which can be done in various other ways in Chimera. (A) If you mean overall RMSD (one value per frame) vs. a reference frame: See MD Movie (the trajectory playback tool) menu: Analysis? Plot for calculating and plotting various quantities vs. trajectory frame number, including RMSD of specified atoms relative to a reference frame. There is a Dump Values button at the bottom to write out the values. Unfortunately I?m somewhat at a loss as to what you would do next. My understanding is that Chimera doesn?t store separate attributes for different frames in a trajectory, so it wouldn?t be that simple. In a per-frame script in MD Movie, maybe you could use ?setattr? to assign the value as an attribute and then ?rangecolor? to map it to color, thus avoiding calculating the colormapping yourself. However, it is still ugly in that you have to get the right value assigned to the right frame. (B) If you mean per-residue structural variability (one RMSD value per residue but considering all frames at once): (However, I somewhat doubt this is what you meant, since it generally wouldn?t be shown during playback, but instead with coloring or worms on a single structure.) This would be done by opening the whole ensemble at once (saving trajectory frames as a single multi-model PDB and then opening that the regular way instead of as a trajectory), superimposing the structures if they weren?t already, associating all of them with a single sequence, showing the sequence RMSD header, and then using Render by Attribute to show the per-residue RMSD values as coloring or worms on a single structure. More details on that approach in these previous posts: Sorry I couldn?t give a more definitive answer. Maybe this will get you closer, or others will have better ideas. 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 Oct 31, 2014, at 8:00 AM, Joshua Carter wrote: > Hello, > I am currently working on some MDFF simulations and have been visualizing them in chimera. I am trying to color the proteins by rmsd over the course of the simulation. I was thinking that there may be a way to do this using the attribute calculator tool between the first and last frames of the simulation. Does anyone know if this is possible or if there is a better way to do it? > Josh From khwest16 at wabash.edu Fri Oct 31 11:56:41 2014 From: khwest16 at wabash.edu (Korbin West) Date: Fri, 31 Oct 2014 18:56:41 +0000 Subject: [Chimera-users] Selection Mode via command line? Message-ID: <6501577732512740A4A42BF68972BEC314BC62D6@Ex2010Mailstore.wabash.main> Hi, I was wondering if there was a way to switch selection modes via the command line. I've been looking through the select command page on the user guide and can't figure a way to change the mode this way. Can anyone give me a tip? Thanks so much, Korbin West -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Oct 31 12:42:55 2014 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 31 Oct 2014 12:42:55 -0700 Subject: [Chimera-users] Selection Mode via command line? In-Reply-To: <6501577732512740A4A42BF68972BEC314BC62D6@Ex2010Mailstore.wabash.main> References: <6501577732512740A4A42BF68972BEC314BC62D6@Ex2010Mailstore.wabash.main> Message-ID: <39BA154D-791B-4D36-980D-9AD2801B896B@cgl.ucsf.edu> Hi Korbin, Actually there isn?t a way to change the mode with a command. Generally you can still select what you want without changing the mode, because in command-line atomspecs, ?&? (ampersand) is for intersection and ?|? (vertical bar) is for union. I can see that it might be less convenient if you have lots of sets of atoms to combine, however. Example: select ligand | :25-28 ? would select both ligand and residues 25-28. Often in commands you don?t bother going through selection because you can specify the target atoms directly, for example: color red,a ligand | :25-28 I don?t know if this would help, but you can show an icon for easy mode-switching using menu: Select? Selection Mode? Show mode icon. This icon appears next to the lightning-bolt icon for Rapid Access, and it both shows which mode you are in and allows toggling amongst the modes. 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 Oct 31, 2014, at 11:56 AM, Korbin West wrote: > Hi, > I was wondering if there was a way to switch selection modes via the command line. I've been looking through the select command page on the user guide and can't figure a way to change the mode this way. Can anyone give me a tip? > Thanks so much, > Korbin West > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users