- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Automatic struts for 3D printing?
by Hurt, Darrell (NIH/NIAID) [E] 23 Aug '13

23 Aug '13

Ask and it shall be given! Thanks for the explanation! -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. From: Tom Goddard <goddard(a)sonic.net<mailto:goddard@sonic.net>> Date: Friday, August 23, 2013 1:44 PM To: Darrell Hurt <darrellh(a)niaid.nih.gov<mailto:darrellh@niaid.nih.gov>> Cc: "chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>" <chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: Re: [Chimera-users] Automatic struts for 3D printing? Hi Darrell, You can get struts between a protein and ligand with the current command -- just include the ligand atoms in the argument to the struts command. For example, open 2ghb struts @CA|ligand&element.C This is just a fancier atom specification that says consider atoms named CA or ligand carbon atoms. Here's a picture of the result. [cid:E793C582-C88D-4680-B08B-DC92C52D671B@cgl.ucsf.edu] Another tip. Yesterday I added command "~struts" that removes all struts or "~struts ligand" that removes all struts involving ligand atoms. You can use any atom specifier and remove the struts to those atoms. Tom On Aug 23, 2013, at 10:27 AM, "Hurt, Darrell (NIH/NIAID) [E]" wrote: Hi Tom, I've been playing with the command and it works very well. I really like the "replace" feature for trying several strut options without having to delete the previous ones. Thanks Elaine! You've already given me much. Thank you! One additional feature that we've thought of would be automatically create these kinds of struts to small molecule ligands. The way I thought to do this would be to use the same algorithm you've already implemented, but extend it to check if a ligand is present. If so, then struts would be created from the designated macromolecular atoms (@CA or @P) to the "heavy" (non-hydrogen) atoms of the ligand(s). I think that your "loop" parameter would prevent too many struts from being created. This would make the algorithm even more automated! Thanks! Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. From: Tom Goddard <goddard(a)sonic.net<mailto:goddard@sonic.net><mailto:goddard@sonic.net>> Date: Thursday, August 22, 2013 3:46 PM To: Darrell Hurt <darrellh(a)niaid.nih.gov<mailto:darrellh@niaid.nih.gov><mailto:darrellh@niaid.nih.gov>> Cc: "chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu><mailto:chimera-users@cgl.ucsf.edu>" <chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu><mailto:chimera-users@cgl.ucsf.edu>> Subject: Re: [Chimera-users] Automatic struts for 3D printing? Hi Darrell, I improved the struts command today so it automatically replaces the previous struts if you run it a second time with the same set of atoms but different parameter values. This avoids having to delete the first set of struts with model panel -- much easier to use. Will be in tonight's daily build. Improvement suggested by Elaine Meng. If you really do want to keep multiple sets of struts for the same atoms use the struts command option "replace false". Tom On Aug 21, 2013, at 2:27 PM, "Hurt, Darrell (NIH/NIAID) [E]" wrote: Hi Tom, OMG! You're amazing! I'll certainly give this a try and let you know how it works. I really like the "loop" parameter. It seems more robust and will produce more evenly spaced struts than the second "distance" parameter I tried to explain. Thank you! Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. From: Tom Goddard Date: Wednesday, August 21, 2013 5:06 PM To: Darrell Hurt Cc: "chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu><mailto:chimera-users@cgl.ucsf.edu><mailto:chimera-users@cgl.ucsf.edu>" <chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu><mailto:chimera-users@cgl.ucsf.edu><mailto:chimera-users@cgl.ucsf.edu>> Subject: Re: [Chimera-users] Automatic struts for 3D printing? Hi Darrell, I added a "struts" command to Chimera -- in tonight's daily builds. I've attached your picture of hemagglutinin with struts and a similar picture made with the new struts command and also a picture of a tRNA (4tna) with a small number of struts made in Chimera. [cid:2AFCE3A1-824B-4430-8153-A5616DAE2C5E@cgl.ucsf.edu<mailto:A5616DAE2C5E@cgl.ucsf.edu><mailto:2AFCE3A1-824B-4430-8153-A5616DAE2C5E@cgl.ucsf.edu<mailto:A5616DAE2C5E@cgl.ucsf.edu>>][cid:54ACB2C8-EF27-4A47-A8B0-8718D93CAF28@cgl.ucsf.edu<mailto:EF27-4A47-A8B0-8718D93CAF28@cgl.ucsf.edu><mailto:54ACB2C8-EF27-4A47-A8B0-8718D93CAF28@cgl.ucsf.edu<mailto:EF27-4A47-A8B0-8718D93CAF28@cgl.ucsf.edu>>] [cid:7CBA5018-1ED2-48AD-BD7B-5D6F71E439C4@cgl.ucsf.edu<mailto:BD7B-5D6F71E439C4@cgl.ucsf.edu><mailto:7CBA5018-1ED2-48AD-BD7B-5D6F71E439C4@cgl.ucsf.edu<mailto:BD7B-5D6F71E439C4@cgl.ucsf.edu>>][cid:960E041D-8A30-4F42-8DB2-28758F7F411E@cgl.ucsf.edu<http://cgl.ucsf.edu><mailto:960E041D-8A30-4F42-8DB2-28758F7F411E@cgl.ucsf.edu<http://cgl.ucsf.edu>>] The Chimera command for the hemagglutinin model struts is struts @CA length 7 loop 30 I decided to try a different algorithm in Chimera for adding struts from the one in the Jmol code. The Chimera struts command uses two parameters. It finds all pairs of C-alpha atoms within a distance of 7 Angstroms of each other. Then it considers those from shortest to longest distances. It adds a strut if the two atoms the strut would join are more than 30 Angstroms away via bonded connections. Basically it adds struts up to a given maximum length so that C-alphas are connected via bonds and struts by no more than a maximum loop length. The maximum strut length (7 Angstroms) and maximum loop length (30 Angstroms) are the two parameters. For the tRNA model I used 15 and 80 and use P atoms instead of CA atoms (command "struts @P length 15 loop 80"). Here's roughly what the Jmol code does, that I decided not to copy 1) make struts short (less than 7 Angstroms), 2) make struts join residues at least 6 residues apart in polymer, 3) space out struts, ends of different struts no closer than 6 residues, 4) include as many struts as possible meeting spacing and length constraints, 5) put a strut within 3 residues of the end of each polymer. The exact details of how it does this would take a long explanation -- which is my main reason for not copying it. The algorithm of the Chimera struts command is easily and precisely described above and produced reasonable struts for the half dozen test cases I tried. But it may prove not as good as the Jmol approach -- experience will tell -- and I can change it if needed. Here is and example using all available strut command options struts @CA length 7 loop 30 radius 0.75 color blue name struts_7_30 fat true model #5 Any set of atoms can be specified as strut end points, radius is the strut cylinder radius, color is the strut color, name is the name of the pseudo-bond model created for the struts (struts can be hidden using Model Panel), fattenRibbon sets a fatter ribbon style better for printing (can adjust as desired with Ribbon Style Editor, menu Tools / Depiction), modelId is the model number you want for the strut pseudobonds. Struts can span multiple models, or be restricted to just a part (e.g. one chain) of a model. The command will get documented in the Chimera User's Guide. Tom On Aug 16, 2013, at 7:02 PM, "Hurt, Darrell (NIH/NIAID) [E]" wrote: Hi Tom, Thanks. This is some of our best stuff. For our material, the struts are vitally important or the whole thing crumbles. We use so many struts that a script is really important to doing this efficiently. I have no idea how it will work in a monochrome plastic printer. However, there are some plastic printers emerging on the market now that can print in two colors plus a support material. That might help with distinguishing between structure and strut. One idea is to print both the struts and the building supports in the same material and then dissolving all that, leaving just the protein. You're right about the struts being too short. They would be pointless along a helix. So I think there is a hard-coded minimum strut distance to prevent struts within the helix, but a user-settable parameter for the maximum strut distance. This is especially important in protein complexes. The pink and baby blue blobs are glycosylation on the surface of the proteins. These are modeled in using the glycoprotein builder: http://glycam.ccrc.uga.edu/ccrc/gp/index.jsp?tool=crystallography&option=ff 99:glycam06 If you think this is cool, you've got to check out what Kawakami Masaru is doing with 3D printed molecules: http://www.youtube.com/watch?v=NVtE_AS3jbI http://dx.doi.org/10.1063/1.4739961 Thanks! Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559Web: BCBB Home Page <http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb .aspx#niaid_inlineNav_Anchor> Twitter: @niaidbioit <https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. On 8/16/13 8:46 PM, "Tom Goddard" wrote: Hi Darrell, Your plastic models are super cool. I'm jealous -- we don't have a color printer. I had no idea you were adding so many struts. I'm afraid it would look less attractive in one color. I see that some models are ribbon only and some have the residues depicted as surface blobs -- none of your pictured models used spheres and cylinders for atoms and bonds. That helps avoid confusing the struts for molecular bonds. I'm a puzzled by your dozens of pink blobs in image 3 and 7 and cyan blobs in image 9 in each case connected by lots of sticks. They look like individual residues but are too far apart to be a polypeptide I think -- maybe many copies of a small ligand? The algorithm for placing struts sounds quite simple. Chimera has ribbon splines that go exactly through the C-alphas, and can also join side chains to a ribbon even when the C-alpha is not on the ribbon. So I think that won't be a problem. The Jmol strut code I looked at looked more complex than what you describe. If it simply chose short distance struts wouldn't you get a bunch of unneeded struts say within one alpha helix, and maybe lack some long range struts that are needed to hold everything together? In any case, if we come up with an algorithm, or just want to copy the Jmol code, it looks very easy to add to Chimera. I can probably do an implementation in half a day. The main thing is to figure out exactly what the algorithm should do. Maybe I can put something in next week. Tom On Aug 16, 2013, at 5:16 PM, "Hurt, Darrell (NIH/NIAID) [E]" wrote: Hi Tom, I've been printing ribbon/cartoon and surface representations of proteins and nucleic acids for many years using a Z Corp machine. I've also done some "ball-and-stick" and "VDW-sphere" kinds of prints. Often we print substrates in "stick" mode and connect the sticks to the ribbon using manually-placed struts. We will continue to use our Z Printer, but we are also buying a "desktop" 3D printer that more people can afford. It is an "FDM" printer similar to the uPrinter your webpages describe. The algorithm used by the George Phillips script is a little different (and perhaps simpler) than the one you describe. It has two parameters: (1) the maximum length of a strut and (2) the minimum closeness of any two struts. The second parameter is a little funky; I'll describe it below. The script first identifies all pairs of C-alphas (or pairs of initial phosphates on the backbone for nucleic acids). Then it creates "pseudobonds" (the struts) between all of those pairs which conform to the maximum length parameter. The next step is to cull the list of pseudobonds according to the minimum distance parameter so that you don't get struts everywhere. Here's where it gets kind of funky because I don't know how this distance is calculated. Either it is calculated from the starting end of a pseudobond (which is what I expect from what I can see of the results of the script) or it does it from center/centroid of the pseudobond. The script also adjusts some parameters to thicken the ribbons, sticks, etc. and increase the triangle count of the exported mesh. This usually works great, but there is one little problem because the struts are calculated to put the ends of the struts at the C-alpha positions. For helices, this usually isn't a problem because the helix ribbon/cartoon goes through the C-alpha position. But for strands which are drawn on a spline of the C-alphas, the struts sometimes either go through or do not reach the ribbon, making the struts useless. Using some standard tools in PyMOL, I force the ribbon to go through the C-alpha positions everywhere there is a strut terminus. In this way, the ribbon and the ends of the struts correspond and the print is strengthened without sacrificing the aesthetics of the splined ribbon. I've attached the results of this script for both the mesh and the actual print (the "ribbon.jpg" and "ribbon.png" images). Of course, printing in monochrome plastic will be different, but that's what we're hoping to experiment with. I've also attached a few other pictures of our prints. George and I have discussed sharing his script with a wider audience or even publishing some kind of technical note about it. He seems willing to share it with certain limitations. Maybe we can all write something together if we build it into Chimera. We might be able to do it internally, but I would have to get my developers more familiar with the internals of Chimera first. I welcome any efforts you or others might make. Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559Web: BCBB Home Page <http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bc bb .aspx#niaid_inlineNav_Anchor> Twitter: @niaidbioit <https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. On 8/16/13 6:14 PM, "Tom Goddard" wrote: Hi Darrell, Here are some of the molecule models we have printed in plastic. http://www.cgl.ucsf.edu/Outreach/technotes/ModelGallery/index.html and a description of the printer we used http://www.cgl.ucsf.edu/Outreach/technotes/uprint.html Chimera does not currently have any tool to automatically add struts, although I've done this by hand in Chimera. For instance the heptatis B virus pentamer on the above web page had part of an icosahedral cage made from cylinders underneath it to hold the proteins on the virus surface together. One thing you'll see is that all our printed molecules came from surface depictions in Chimera (made with molmap command). I'm not sure if we successfully printed and ball and stick models via STL or VRML. We tried years ago and I recall them falling apart because where the spheres and cylinders intersected it put no plastic. Basically an atom sphere and bond cylinder are two surfaces and for points inside two surfaces (or any even number of surfaces I think) the printer places no plastic. So overlapped cylinders and spheres didn't hold together. This seems to be a printer driver issue -- how it takes a surface and makes a solid out of it. I don't know that we've tried with our newer printers at UCSF -- maybe it works now. Have you successfully printed ball and stick models exported from Chimera? What kind of printer? Now about automatically adding struts -- probably would not be hard. The struts code I saw online http://idp1.force.cs.is.nagoya-u.ac.jp/jmol/src/org/jmol/modelsetbio/Al ph aPolymer.java didn't have a clear description of the algorithm the use, but it would just take an hour to study it. I could see aiming to add struts that 1) are cylinders between atoms, 2) are short, 3) make the whole model one connected piece, 4) make every contiguous N (50) residues connected in at least 3 places (2 probably being continuations before and after and one being a crossbridge) to other residues for rigidity, 5) not put connections at the ends where they would be easily confused for real biological connections, 6) struts should not look like real bonds -- maybe make them fatter or better square cross-section. Actually that rigidity constraint is more complex -- probably don't want to have two large pieces connected to each other through only one bond. I recall printing some ribbon models in ABS plastic with ribbon cross-section pretty small -- half a centimeter. With 100 residues and no cross bridges the model is very flexible and easy to break. Could you provide a picture of a ball and stick model with struts to give a better idea of what you are shooting for? Tom On Aug 16, 2013, at 2:32 PM, "Hurt, Darrell (NIH/NIAID) [E]" wrote: Hi everyone, We are assembling an open data portal or "exchange" for producing "ready-to-3D-print" files for biological molecules, EM data, and other imaging data using some automated pipelines. A little bit more on our project can be found here: http://www.hhs.gov/open/initiatives/ignite/3d-printing-exchange.html A few years ago this came up on the "dev" discussion board: http://www.cgl.ucsf.edu/pipermail/chimera-dev/2011/000800.html In the email thread above, it mentions a script by George Phillips called "struts.py" that was modified for use in RasMol. I am familiar with his version of this script for PyMOL. It works very well and I have been using it for years. However, the VRML from PyMOL is sometimes buggy. I like the exports from Chimera much better, including the X3D2VRML and X3D2STL utilities. If I could get the same functionality of this "struts" script in Chimera, that would be one less thing I need to go to PyMOL for (the list is getting shorter and shorter!). We're looking at doing it here, but I would welcome any contribution from the Chimera community if something already exists. Do you have anything? Is this script something of interest? Anyone interested in contributing to our "exchange" database/web portal? I would love any feedback you might have. Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pa ge s/bcbb.aspx#niaid_inlineNav_Anchor> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu><mailto:Chimera-users@cgl.ucsf.edu><mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <ribbon.png><ribbon.jpg><3D-print-4317.jpg><3D-print-4075.jpg><3D-print-4 119.jpg><3D-print-4169.jpg><3D-print-4275.jpg><3D-print-4145.jpg><3D-prin t-4347.jpg>_______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu><mailto:Chimera-users@cgl.ucsf.edu><mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu><mailto:Chimera-users@cgl.ucsf.edu><mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <darrell_hemagglutinin.jpg><chimera_hemagglutinin.jpg><4tna_15_80_model.jpg><4tna_15_80_print.jpg>_______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu><mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Automatic struts for 3D printing?
by Hurt, Darrell (NIH/NIAID) [E] 23 Aug '13

23 Aug '13

Hi everyone, We are assembling an open data portal or "exchange" for producing "ready-to-3D-print" files for biological molecules, EM data, and other imaging data using some automated pipelines. A little bit more on our project can be found here: http://www.hhs.gov/open/initiatives/ignite/3d-printing-exchange.html A few years ago this came up on the "dev" discussion board: http://www.cgl.ucsf.edu/pipermail/chimera-dev/2011/000800.html In the email thread above, it mentions a script by George Phillips called "struts.py" that was modified for use in RasMol. I am familiar with his version of this script for PyMOL. It works very well and I have been using it for years. However, the VRML from PyMOL is sometimes buggy. I like the exports from Chimera much better, including the X3D2VRML and X3D2STL utilities. If I could get the same functionality of this "struts" script in Chimera, that would be one less thing I need to go to PyMOL for (the list is getting shorter and shorter!). We're looking at doing it here, but I would welcome any contribution from the Chimera community if something already exists. Do you have anything? Is this script something of interest? Anyone interested in contributing to our "exchange" database/web portal? I would love any feedback you might have. Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Minimization and mystery nonstandard HIS atom name
by Jason L Burkhead 22 Aug '13

22 Aug '13

I am trying to minimize a protein structure and run into the following error: 'No MMTK name for atom "HND1" in standard residue "HIS"' My .pdb file specifies this atom as ND1, and if I change it to HND1 it still gives me the same error. Does anyone have any suggestions for a solution? The reply log is below: Thanks Jason No incomplete side chains No SEQRES records for COMMD1_C_terminus_c.2.0.pdb (#0) chain A; guessing terminii instead Chain-initial residues that are actual N terminii: GLY 1.A Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: ASN 73.A Chain-final residues that are not actual C terminii: 42 hydrogen bonds Hydrogens added Charge model: AMBER ff99SB Non-standard atom names: HIS HND1 (HIS 17.A HND1, HIS 22.A HND1) Total charge for #0: -4.000 Correct charges are unknown for 1 non-standard atom names in otherwise standard residues Charges of 0.0 were assigned to the unknown atoms Details in reply log No MMTK name for atom "HND1" in standard residue "HIS"

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Re: [Chimera-users] [chimera-dev] UCSF Chimera Help
by Elaine Meng 21 Aug '13

21 Aug '13

Dear Neil, Chimera does not do docking except for fairly limited single-ligand calculations using an AutoDock Vina web service: you can only dock one ligand at a time and get up to 10 orientations back. You can't search a database of ligands, for example. The interface to the Vina web service is in the menu of Chimera version 1.7 (Jan 2013) and newer: Tools... Surface/Binding Analysis... AutoDock Vina. It is recommended you run other tools first to prepare the receptor before using this tool. See the manual page for details: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> However, Chimera does have a nice "ViewDock" interface for looking at the output from several docking programs that could be run outside of Chimera: DOCK, AutoDock, AutoDock Vina, Glide, GOLD, Mordor. If the fairly simple interface mentioned above does not suffice for what you want to do, you may want to try one or more of those other programs (several are free). The ViewDock man page includes links to their websites; see the "input" section: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.…> There is also a ViewDock tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html> I CC'd the chimera-users list because this is more of a user question than a developer (programming) issue. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Aug 21, 2013, at 1:23 AM, Neil Bugeja wrote: > Dear Sir/Madam > > I am a student at the University of Malta and I am currently using your software to carry out homology modelling for my thesis. > > I have a slight problem figuring out how to dock a ligand into a receptor on the program...Is this possible or do I need to install another software? > I tried looking through the available tutorials but cannot find any so far > > Thank you for your help > > Regards

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Re: [Chimera-users] RMSD for two ligands
by Pavithra 21 Aug '13

21 Aug '13

Dear Ma'am, Thank you so much. its working now. On Thu, Aug 22, 2013 at 2:25 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Dear Pavithra, > Chimera cannot guess which atoms to use when there are different numbers > of atoms in the two groups (#0 and #1). You would have to either > > (A) include all the names of the atoms, in the order you want them > matched, in the rmsd command. It would be something like: rmsd #0:15@c1,c2,c3 > #1:12@c10,c5,c2 (if you wanted to match residue 15 atom C1 with residue > 12 atom C10, residue 15 atom C2 with residue 12 atom C5, etc.). To see the > atom names, show labels, for example command: label #0:15#1:12 > > or > > (B) select all the atoms with the mouse (Shift-Ctrl-click) one by one, > first the atoms you want to match in the first molecule, then the atoms you > want to match in the second molecule in the corresponding order, and then > use "sel" to specify the atoms in the rmsd command > > The "rmsd" manual page can be viewed here (or by using command: help rmsd): > <http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/rmsd.html> > > ... and more about how to specify atoms in the command line: > < > http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/atom_spec.html#bas… > > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Aug 21, 2013, at 1:05 AM, Pavithra wrote: > > > Dear Users, > > I want to calculate the RMSD of two ligand molecules of different atom > counts but have a common scaffold. > > I tried rmsd #0 #1 > > but I'm getting the error: unusual numbers of atoms chosen for > evaluation. > > > > rmsd #0:15-17 #1:15-17 > > atleast one atom must be selected. > > > could somebody help me to find the RMSD between two ligands of different > atom counts. > > -- > > regards, > > Pavithra.K.B. > > -- regards, Pavithra.K.B.

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RMSD for two ligands
by Pavithra 21 Aug '13

21 Aug '13

Dear Users, I want to calculate the RMSD of two ligand molecules of different atom counts but have a common scaffold. I tried rmsd #0 #1 but I'm getting the error: unusual numbers of atoms chosen for evaluation. rmsd #0:15-17 #1:15-17 atleast one atom must be selected. could somebody help me to find the RMSD between two ligands of different atom counts. -- regards, Pavithra.K.B.

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save colored blobs in session
by Zoltan Metlagel 20 Aug '13

20 Aug '13

Hi everyone, I've been trying to color blobs of different sizes in a tomogram by un-hiding them in order of size using the "hide dust" tool and coloring as they become visible. This has been working well and given me some insight into the structure I'm looking for, but I'm unable to restore the session to it's previous state using the "save session"/"restore session" features. The maps open fine, but all the coloring is lost. I've tried this in Chimera 1.7 and 1.8, with the same results. Am I missing something? According to the online manual, colors should be saved in a session. I apologize if this has been asked before, but I haven't been able to find the solution in the archives either. I'm otherwise very happy with Chimera, thanks for all your efforts. Thanks in advance, Zoltan Metlagel, LBNL

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transparencies within transparencies
by Elizabeth Montabana 17 Aug '13

17 Aug '13

Hi All I have a difference map that I'd like to have set to 50% transparent overlaid with the original data map set to 70% transparent. If I do this, I cease to see any off the difference map. Is there anyway to accomplish this in Chimera? thanks Liz Montabana Graduate Student Agard Lab, UCSF

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Hide all ribbons not in specific chain
by Thomas Hrabe 16 Aug '13

16 Aug '13

Hi everyone, I want to display one chain from a structure, only. However, I do not understand how to achieve that. After my PDB file opens, I can do select :*.A #select all residues in chain A that I want to have select invert #select everything else not in chain A ~ribbon hides everything. How can I tell ~ribbon to hide everything not in chain A. Or, how can I select everything not in chain A? I am calling chimera through the socket and do not want to parse out every chain. Thanks in advance, Thomas

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File Operations *veery* slow on Win 7
by Markus Heller 12 Aug '13

12 Aug '13

Hi, I'm running the latest release of Chimera (1.8 build 38824), but I've observed this with the 2 previous releases as well. Computer is a core i7 with 32 GB RAM and an Nvidia Quadro FX 1700 with 512 MB DDR2 memory and latest driver. OS is Windoze 7 64 bit. Pretty much every time I click File --> Save mol2 or Save pdb or Save Session As, I get the blue spinning wheel of death and (not responding) in the window title bar. It's not a deal breaker, but it's pretty annoying. Anybody else seeing this? Also, when I start Chimera, the screen goes black for a second and all window title bars change to standard blue. When I exit Chimera, the process reverses. Are these observations related? And how can I provide more information in addition to my vague description? Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F: (604) 827-1299 | E: mheller(a)cdrd.ca<mailto:mheller@cdrd.ca> | www.cdrd.ca [cid:image007.png@01CE950C.D960A9A0] Follow us: [Description: cid:image003.jpg@01CD86A6.39B41A10] <https://twitter.com/C_D_R_D> [Description: cid:image005.jpg@01CD86AE.B197F5D0] <http://www.linkedin.com/groups/CDRD-3186016/about?report%2Esuccess=3NcE4iZo…> [Description: cid:image009.png@01CD86AE.B197F5D0] <https://www.facebook.com/pages/The-Centre-for-Drug-Research-and-Development…> [Description: cid:image010.png@01CD86AE.B197F5D0] <http://www.youtube.com/user/CDRDCVI?view_as=public> This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email.

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Show backbone chain-trace by default
by Thomas Hrabe 09 Aug '13

09 Aug '13

Hi everyone, I was looking for the setting to tell Chimera to open a PDB file in backbone chain-trace mode rather than looking at the ribbon. Is that possible? Thanks in advance, Thomas

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About selection of atom
by Chung Fan LAM 09 Aug '13

09 Aug '13

Hi, I cannot select atoms by using Ctrl+left button/double click left button by using my home PC, but I can do so by using my notebook. I guess the difference between my two computers is the input device. My home PC is using mouse while my notebook is using touch pad. I would like to know if there is any setting I can change, so that I can use the mouse to select atoms. Thanks. Best wishes, Frankie

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Surface calculation failed problem
by Hunter Brown 09 Aug '13

09 Aug '13

Hello, I know this has been a somewhat common problem. When trying to display the molecular surface on a protein (I want to color by hydrophobicity and surface charge) I get the error "Surface calculation failed, mscalc returned code 5." I have tried increasing the VDW radius by 0.5, and lowering probe radius, and turning off 'display disjoint surfaces.' So far I have not been able to display the surface. I have a colleague that has displayed the molecular surface for a viral capsid, so I would think that I should be able to do it for a protein. Is there anything else I can do? It would be really nice to create some hydrophobicity and surface charge images. Thanks in advance! -Hunter Hunter Brown Bassoonist, Contrabassoonist, Composer, Chemical Engineering Major University of New Mexico

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Help with RMSD
by Chee Wezen, Xavier 09 Aug '13

09 Aug '13

Hello, may i know how to i use Chimera to calculate RMSD ? I opened the command line and typed "rmsd #0 #1" but the rmsd that i received from the two molecules above is way too high for something this superimposed. Can someone please suggest what should i do ? Meanwhile, i've also received error warnings for other molecules that i am testing (along the lines of "different number of atoms" found). this should not be the case as the molecules are identical to one another. Any help regarding this is much appreciated ! Thanks !

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ask for help about surface and Label color
by Jian Guan 08 Aug '13

08 Aug '13

Hi, I am Jian, working in Hershey Medical Center, PSU. I am a Chimera User. I have two questions. 1: When I fit protein molecule structure into the density map of Virus particle. Showing the protein molecule in Surface is not allowed by Chimera. An error window popped out said: "surface calculation failed, mscalc returned code 2". I wonder to know how to solve this problem. I want to modify the molecule structure after fitting. 2: When I label the selected residues, they are always with the same color with residues, can I set them separately? Can I edit the label font? Thank you so much. Hope to hear from you soon. Jian

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show middle slice of vol by using command line
by Dieter Blaas 07 Aug '13

07 Aug '13

Hi, I have been trying hard to do the following by using the command line but so far with no avail: select volume #0 and show just the middle slice as solid. Following the way the commands are usually structured I tried something like "vol #0 style solid planes one" but I do get the error "volume invalid planes argument "one" : Value must be x, y ,z, got 'one'''. But when I try ""vol #0 style solid planes x" I get "volume: invalid planes argument 'x'. So what? Thanks a lor for hints, Dieter -- ---------------------------------------------------------------------- Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Constrained movements
by Damien Larivière 07 Aug '13

07 Aug '13

Dear all, The image below shows 2 chains opened separately from 2 PDB files. I would like to move only the cyan chain. For that, I just have to deactivate the white chain. BUT I would also like to keep fixed a specific atom of the cyan chain, for instance the cyan atom in the red circle. This way this atom serves as a pivot point. I know that I can use "Constrained Move". If I understand well, the "origin" is either 0,0,0 or the center of a model bounding box, not a selected atom. Is it possible to manage this? Many thanks for your help Damien

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Shape complementarity
by Hernando J Sosa 07 Aug '13

07 Aug '13

Dear Chimera, Is there a way to evaluate protein-protein interfaces (e.g. using a program like CCP4 Sc) within chimera?. Thanks Hernando

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Re: [Chimera-users] some questions about Chimera
by Elaine Meng 05 Aug '13

05 Aug '13

> From: "Graham Johnson (qb3@UCSF)" <graham(a)grahamj.com> > Subject: Re: [Chimera-users] some questions about Chimera > Date: August 5, 2013 11:59:03 AM PDT > To: Ruijie Chen <spider32123(a)gmail.com> > > Hi Ruijie, > The "missing" colors are in the .dae or .wrl file, however, programs like Maya do not know how to read them (i.e., they only read and display the geometry, not the color-per-vertex colors). For doing this type of work, I recommend installing ePMV to directly manipulate your models in Maya. There are many things that ePMV cannot do where a Chimera–>universalFile–>Maya protocol is still useful, but ePMV will handle most of your goals. > http://epmv.scripps.edu > > Regards, > Graham > > Graham Johnson PhD > qb3@UCSF Fellow > UCSF Lab: http://mesoscope.org > Medical Illustration: http://grahamj.com > > On Aug 5, 2013, at 10:59 AM, Conrad Huang <conrad(a)cgl.ucsf.edu> wrote: >>> Dear Sir / Madam: >>> >>> I am a 3D animation student who recently started to making medical animation videos, and I found Chimera is a very usefull tool for building molecules and proteins. >>> >>> However, there are few things that I don't understand: >>> >>> 1. After I import a .dae file which exported from hemoglobin (PDB: 2hhb), I found that the color I have set for each ribbon is gone, the one I have got inside maya is a hemoglobin molecule with one color. And when I want to select each alpha or beta-globin, I failed to do so because there sometimes have some polygons from other alpha or beta-globin. Is there a way to solve these problems? >>> >>> 2. I have tried to export the scene to a .wrl file and convert it to maya file via wrl2ma, but when I open the finish converted maya file it always give me lots of error messages like this : >>> "Error: file: C:/Users/**/hemo_ribbon.ma line 116: setAttr: Too much data was provided. The last 173 elements were not used. // " >>> and this :"// Error: file: C:/Users/**/hemo_ribbon.ma line 13078: setAttr: Too much data was provided. The last 1193 elements were not used. // " >>> Is this a problem which happen during the export process of Chimera or some other reasons? >>> >>> Looking forward for your reply >>> Thank you >>> -- >>> With kind regards >>> Ruijie Chen

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some questions about Chimera
by Ruijie Chen 02 Aug '13

02 Aug '13

Dear Sir / Madam: I am a 3D animation student who recently started to making medical animation videos, and I found Chimera is a very usefull tool for building molecules and proteins. However, there are few things that I don't understand: 1. After I import a .dae file which exported from hemoglobin (PDB: 2hhb), I found that the color I have set for each ribbon is gone, the one I have got inside maya is a hemoglobin molecule with one color. And when I want to select each alpha or beta-globin, I failed to do so because there sometimes have some polygons from other alpha or beta-globin. Is there a way to solve these problems? 2. I have tried to export the scene to a .wrl file and convert it to mayafile via wrl2ma, but when I open the finish converted maya file it always give me lots of error messages like this : "Error: file: C:/Users/**/hemo_ribbon.ma line 116: setAttr: Too much data was provided. The last 173 elements were not used. // " and this :"// Error: file: C:/Users/**/hemo_ribbon.ma line 13078: setAttr: Too much data was provided. The last 1193 elements were not used. // " Is this a problem which happen during the export process of Chimera or some other reasons? Looking forward for your reply Thank you -- With kind regards Ruijie Chen

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Re: [Chimera-users] Using Surfnet tool in a per-frame python script
by Elaine Meng 01 Aug '13

01 Aug '13

Hi William, Thanks for your kind words! I'd like to suggest an alternative approach: accumulate occupancy for the ligand over the whole trajectory and then show an isosurface for that occupancy map. You'd have to contour at a low level (e.g. 1 for everywhere the ligand has been during at least 1 frame), but in my mind at least, this produces a nice blob showing everywhere the ligand has been. I don't know how successful it would be on this specific data, but it should be relatively easy to try (no scripting involved). It may depend on how flexible everything is and how much it moves around… you can hold steady based on some set of atoms, but there may still be residual "motion blur." See the "Occupancy Analysis" section of the MD Movie man page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#…> You would have to first indicate atoms to "hold steady" (if an appropriate set exists, or maybe your trajectory is already pre-processed to keep the structure in the same place and orientation as possible), select the ligand, and then in the occupancy calculation dialog choose appropriate settings. Sounds like you would turn off (set to false) "limit data collection to within cutoff…" and "collect data separately…", maybe decrease "volume grid spacing" to get a less chunky final result, and adjust anything else as you see fit. As for pruning, you can hide disconnected bits of surface using Hide Dust and/or erase parts of a volume dataset using Volume Eraser (both in menu under Tools… Volume Data). <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/hide…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleras…> Just an idea, but maybe worth a try… Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco > First, thank you all for such a wonderful program! Also, thanks to the > users' list for such quick, thorough, and always-helpful answers! > > Second, a little background: I have a gromacs MD simulation (well several, > actually) of a small ligand diffusing through a protein. Because the ligand > requires the entire simulation to traverse the protein cavity, I was > thinking of using the Surfnet tool to accumulate or "build-up" the cavity > interface between the ligand and protein using a per-frame python script a > la Eric's suggestion in the Dec 2009 [Chimera-users] Surfnet command line > thread on this mailing list. I was thinking I could then "prune" the > accumulated SurfaceModel using the surfvol.py script available on the > http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts download page.

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Using Surfnet tool in a per-frame python script
by William McDonald 31 Jul '13

31 Jul '13

Dear Chimera Developers, First, thank you all for such a wonderful program! Also, thanks to the users' list for such quick, thorough, and always-helpful answers! Second, a little background: I have a gromacs MD simulation (well several, actually) of a small ligand diffusing through a protein. Because the ligand requires the entire simulation to traverse the protein cavity, I was thinking of using the Surfnet tool to accumulate or "build-up" the cavity interface between the ligand and protein using a per-frame python script a la Eric's suggestion in the Dec 2009 [Chimera-users] Surfnet command line thread on this mailing list. I was thinking I could then "prune" the accumulated SurfaceModel using the surfvol.py script available on the http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts download page. Now, I can generate a Surfnet surface easily (as Eric points out) for each MD frame using the python commands from Surfnet import interface_surfnet interface_surfnet("LigandAtoms","ProteinAtoms") But how, if possible, can I combine all the individual SurfaceModels into one surface? Also, and not secondarily, does this seem like a reasonable approach to obtain the ligand-protein cavity surface? Thanks again for all your generous support. -- William J. McDonald Postdoctoral Scholar Department of Chemistry and Biochemistry University of California, Santa Cruz

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Hello
by A Amiri 30 Jul '13

30 Jul '13

Hello. I have a problem with chimera! I want to combine two different pdb file by chimera , which will be merge into a single model. I used the "join models" section from chimera but the "apply" button was inactive and i don't know how i can activate it! please help me. thank you for your useful software.

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Amino acid scanning
by Alper Yilmaz 30 Jul '13

30 Jul '13

Hi, We are conducting a study to figure out the best amino acid mutation for increased affinity for a particular metal ion. I'm pretty novice in this field so I wanted to get suggestions as to my approach makes sense or not. I'll write a demo script (more probably python script) to substitute certain amino acids with all standard amino acids and then minimize the structure. As far as I know, Chimera can not calculate free energy, so I will save the PDB files and then use another program to calculate the free energy. My first question is, whether the commands below are appropriate for my purpose or not? The sample below is a snippet from an exhaustive list. I preferred to save the information regarding clashes before the minimization just to keep record. swapaa ala :22.a findclash :22.a log true saveFile clash_report_22ala minimize nogui true write #0 test_22ala swapaa val :22.a findclash :22.a log true saveFile clash_report_22val minimize nogui true write #0 test_22val swapaa ile :22.a findclash :22.a log true saveFile clash_report_22ile minimize nogui true write #0 test_22ile ... My second question is, when I have many PDB files, which software is suitable for calculating the free energy for each. Thanks, Assist.Prof.Dr. Alper YILMAZ Department of Bioengineering Faculty of Chemical and Metallurgical Engineering Yildiz Technical University Esenler, Istanbul/TURKEY 34210 Phone: +90.212.383-4657 (office) Fax: +90.212.383-4625

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Using Chimera in a non-graphics environment
by Devan Bicher 24 Jul '13

24 Jul '13

To Whom it may concern, Hi, my name is Devan Bicher and I am a researcher at Lehigh University. I am working on computational studies of proteins and Chimera's findHBond function is extremely useful! I have been using chimera a lot recently, however since I am working with a number of different protein/substrate combinations it would be great for me to use findHbond in a batch sort of way in which I can supply numerous inputs and allow chimera to run on all of them. Does chimera have any sort of built in batch processing option like this? -- -Devan Bicher Bioengineer, Computer Science minor Lehigh University

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