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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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Color surface by underlying atom
by Tom Zhang 06 Jul '16

06 Jul '16

Hello, I have a question about surface coloring. I've noticed that when I create surfaces in a session for the first time, the surface are colored based on the colors of the underlying atoms. However, after setting the surface colors manually, I couldn’t find a way to change the colors back. I have tried settings in surface attributes, but none of them work. So my question is, how do I change the surface color back so that it is based on the underlying atoms? Many thanks, Tom

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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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