- Chimera-users - RBVI Mailing Lists

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

06 Jul '16

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

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

05 Jul '16

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

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

05 Jul '16

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

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

05 Jul '16

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

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

01 Jul '16

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

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

30 Jun '16

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

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

30 Jun '16

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

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

30 Jun '16

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

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

30 Jun '16

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

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

29 Jun '16

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

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