May 2019 - Chimera-users - RBVI Mailing Lists

Help in validation of Mutant Structure
by carlo cast 20 May '19

20 May '19

Good Morning to everyone, it’s my first time here writing at you, I hope I’m doing right. The point is that I’m working with a wild type enzyme from which I got mutant versions by using swap aa command. My goal is to look at the effects that mutations have on the structure by superimposing the mutant form with the wild type one. When I perform matchmaker command, RMSD is equal to 0 and the structures overlap perfectly; thus I thought to minimize structure before superimposing and in this way I see a little difference in RMSD but it could be due to the different steps of the minimize process (e.g. adding protons) than the actual effect of mutations. Moreover when I perform multiple sequence alignment, the amminoacids I swapped actually are not different from the Wild type ones. If I point the cursor on the swapped aa I see the difference in name and side chain but by doing multiple sequence alignment they do not appear. Any suggestions? Inviato da Posta<https://go.microsoft.com/fwlink/?LinkId=550986> per Windows 10

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Re: [Chimera-users] Contact area between 2 Proteins
by Elaine Meng 17 May '19

17 May '19

Dear Fer Villa, (better to send questions to chimera-users(a)cgl.ucsf.edu, CC’d here) It is not really a matter of right and wrong. Instead it depends on what you want… If you want to measure buried solvent-accessible and solvent-excluded surface areas of atomic structures, use “measure buriedArea”. The “measure contactArea” command is similar but if the goal is measurement (rather than coloring for a figure), it is generally used for other kinds of surfaces that are not necessarily associated with any atoms, like density map isosurfaces. In that case, the appropriate cutoff value really depends on the judgment of the user based on what kinds of surfaces these are and what the user is trying to do. The tutorial you mention is for making a figure where the interaction surfaces of two proteins are colored, which is a different purpose than getting a measurement value. It explains that different cutoffs could be used with “measure contactArea", but the example has 2.5 because it gave similar appearance to using the other (buriedArea) method. The tutorial shows both methods because if you are making a figure, you could use either one as you like. It actually discusses three methods. For the other people on the list, here is that tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html> … 3 methods of coloring the interface: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html#in…> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 10, 2019, at 12:17 AM, Fernando Villa <fer.vdl1928(a)gmail.com> wrote: > > Dear Chimera users, > I would like to know which is the correct method to know what is the surface area of contact between two proteins: > measure contactArea or measure buriedArea? > When I apply the command: measure contactArea # 0.1 # 0.2 2.5 color yellow offset 0 that comes in the tutorial, it says that the cutting distance is equal to 2.5 A2 > But, is it correct? > How can I know that? > this example states that if this cut-off distance (2.5 A) is applied compared with a cut distance for measure buriedArea: > Command: measure buriedArea # 0.1 # 0.2 > Command: color yellow #0.1@/buriedSESArea> 1 > Command: color hot pink #0.2@/buriedSESArea> 1 > measure buried Area # 0.1 & protein # 0.2 & protein > atoms with> 1.0 Å2 > How can I know which is the correct contact area (protein protein interaction) of two models or crystals? > What is the correct cutting area that I should apply? > Could it be the default cut area of 1A? > Which method of calculation is better, measure contactArea or measure buriedArea? > I would thank you in advance for a possible solution to my problem. > > Best regards. > > Fer Villa. > Enviar comentarios > Historial > Guardadas > Comunidad > > <image.png> > > Command:open 1avx > Command: ~longbond > Command: split > Command: preset apply int 2 > Command: repr stick > Command: delete solvent > Command: color sea green #0.1 > Command: color medium purple #0.2 > Command: surface > Command: measure contactArea #0.1 #0.2 2.5 color yellow offset 0 > Command: measure contactArea #0.2 #0.1 2.5 color hotpink offset 0 > > > or > > Command: measure buriedArea #0.1 #0.2 > Command: color yellow #0.1@/buriedSESArea>1 > Command: color hot pink #0.2@/buriedSESArea>1 > > Command: measure buriedArea #0.1&protein #0.2&protein > > ATTE > Fernando Villa Díaz >

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display bond lengths and angles
by Thomas Evangelidis 17 May '19

17 May '19

Hello, Is it possible to load a small molecule in Chimera and display all bond lengths and angle values, pretty much as you can do using labelopt option for the atom names? If not directly, could you please give me some hints about how to write a Python script to do it? I thank you in advance for your help. Thomas -- ====================================================================== Dr. Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/>, Brno, Czech Republic email: tevang3(a)gmail.com, Twitter: tevangelidis <https://twitter.com/tevangelidis>, LinkedIn: Thomas Evangelidis <https://www.linkedin.com/in/thomas-evangelidis-495b45125/> website: https://sites.google.com/site/thomasevangelidishomepage/

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ImportError: /lib/x86_64-linux-gnu/libfontconfig.so.1: undefined symbol: FT_Done_MM_Var
by Thomas Evangelidis 17 May '19

17 May '19

Greetings, I did a fresh installation of Chimera on Ubuntu 19.04 but although the installation finished successfully, I get this error message whenever I launch the executable: > > Traceback (most recent call last): > File "/home2/thomas/Programs/Chimera-1.13.1/share/__main__.py", line 73, > in <module> > value = chimeraInit.init(sys.argv) > File "/home2/thomas/Programs/Chimera-1.13.1/share/chimeraInit.py", line > 666, in init > import chimera > File "/home2/thomas/Programs/Chimera-1.13.1/share/chimera/__init__.py", > line 2777, in <module> > from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION > File > "/home2/thomas/Programs/Chimera-1.13.1/share/SimpleSession/__init__.py", > line 14, in <module> > from save import saveSession, sessionID, noAutoRestore, > autoRestorable, \ > File > "/home2/thomas/Programs/Chimera-1.13.1/share/SimpleSession/save.py", line > 13, in <module> > from chimera import replyobj, selection, SessionPDBio, version > File "/home2/thomas/Programs/Chimera-1.13.1/share/chimera/replyobj.py", > line 24, in <module> > import Tkinter > File > "/home2/thomas/Programs/Chimera-1.13.1/lib/python2.7/lib-tk/Tkinter.py", > line 39, in <module> > import _tkinter # If this fails your Python may not be configured for > Tk > ImportError: /lib/x86_64-linux-gnu/libfontconfig.so.1: undefined symbol: > FT_Done_MM_Var > What is strange is that the following works without error: /home2/thomas/Programs/Chimera-1.13.1/bin/python2.7 -c 'import _tkinter' > Any idea what might be wrong? Best, Thomas -- ====================================================================== Dr. Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/>, Brno, Czech Republic email: tevang3(a)gmail.com, Twitter: tevangelidis <https://twitter.com/tevangelidis>, LinkedIn: Thomas Evangelidis <https://www.linkedin.com/in/thomas-evangelidis-495b45125/> website: https://sites.google.com/site/thomasevangelidishomepage/

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Still won't work after libfreetype.so* and libz.so* removal
by Яцкевич Максим 14 May '19

14 May '19

Hi! I am running Fedora 29. Now I'm trying to install chimera-1.13.1-linux_x86_64.bin. After successful installation it failed to create a window in a desktop applecation menu. So I followed the instructions on the web-site (http://www.cgl.ucsf.edu/chimera/data/downloads/1.13.1/linux_x86_64.html) After running the command <dir_name>/bin/xdg-setup install it stumbled upon the same error that was discussed in this thread (https://www.cgl.ucsf.edu/pipermail/chimera-users/2018-November/015237.html) Traceback (most recent call last): File "/home/sec/.local/chimera/share/__main__.py", line 73, in <module> value = chimeraInit.init(sys.argv) File "/home/sec/.local/chimera/share/chimeraInit.py", line 666, in init import chimera File "/home/sec/.local/chimera/share/chimera/__init__.py", line 2777, in <module> from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION File "/home/sec/.local/chimera/share/SimpleSession/__init__.py", line 14, in <module> from save import saveSession, sessionID, noAutoRestore, autoRestorable, \ File "/home/sec/.local/chimera/share/SimpleSession/save.py", line 13, in <module> from chimera import replyobj, selection, SessionPDBio, version File "/home/sec/.local/chimera/share/chimera/replyobj.py", line 24, in <module> import Tkinter File "/home/sec/.local/chimera/lib/python2.7/lib-tk/Tkinter.py", line 39, in <module> import _tkinter # If this fails your Python may not be configured for Tk ImportError: /usr/lib64/libfontconfig.so.1: undefined symbol: FT_Done_MM_Var So I followed your advise and removed the corresponding files: > rm ~/.local/chimera/lib/libz.so* > rm ~/.local/chimera/lib/libfreetype.so* Unfortunately it didn't solve the problem. So after typing: > ~/.local/chimera/bin/xdg-setup install It complained that it cannot find the libz.so file! Traceback (most recent call last): File "/home/sec/.local/chimera/share/__main__.py", line 73, in <module> value = chimeraInit.init(sys.argv) File "/home/sec/.local/chimera/share/chimeraInit.py", line 659, in init initialize_ssl_cert_dir() File "/home/sec/.local/chimera/share/chimeraInit.py", line 309, in initialize_ssl_cert_dir import ssl File "/home/sec/.local/chimera/lib/python2.7/ssl.py", line 146, in <module> import base64 # for DER-to-PEM translation File "/home/sec/.local/chimera/lib/python2.7/base64.py", line 11, in <module> import binascii ImportError: libz.so: cannot open shared object file: No such file or directory I will be grateful for any help. Best regards, Maxim. PhD Student, Physical Faculty, Lomonosov Moscow State University

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Upload color scheme
by Cornelius Hunter 10 May '19

10 May '19

I am looking for a 3D protein viewer that allows me to visualize the protein tertiary structure using my own color assignments, for each residue (or alpha carbon). In other words I would upload a file, with a value for each residue, which would drive the color assignments. Thx

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Volume Step default
by Rebecca Swett 10 May '19

10 May '19

HI all, I was wondering if it was possible to set the Volume Viewer step to 1 as default instead of 4. Is this something I could add to my .chimera/preferences file? Cheers, Rebecca This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.

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to hide atoms using command lines
by C.J. 08 May '19

08 May '19

Dear specialist, I know how to use hide selected atoms (Menu: Actions => Atoms/Bonds => Hide), but I would like to use command lines instead. Anyone could help me with that? Thank you! Best regards! C.J.

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FW: Association info
by Hernando J Sosa 08 May '19

08 May '19

Thanks Eric, it works. To summarize: #---------------------------------------------------------------------- def findMAV(): from chimera.extension import manager from MultAlignViewer.MAViewer import MAViewer mavs = [inst for inst in manager.instances if isinstance(inst, MAViewer)] if not mavs: raise AssertionError("No MAV instances") return mavs[-1] #---------------------------------------------------------------------- mav = findMAV() mav.saveAssocInfo('myfile.asc') #---------------------------------------------------------------------- Best Hernando

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Re: [Chimera-users] Non-standard atom names
by Sid Majaha 08 May '19

08 May '19

Hi Eric So I have been only using dock6 for docking and now want to venture in using dock3. I tried checking online for tutorials that I could look at but there are just a couple of them. On the UCSF website, there is a tutorial but requires the use of dock blaster. I just have a few questions; Is there another way of using dock3.6 without using dock blaster? Is there another simpler tutorial for dock3.6 that you could recommend me to use? Are the dock 3.6 steps similar to the steps of dock6? Sid Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 From: Eric Pettersen <pett(a)cgl.ucsf.edu> Sent: Tuesday, April 16, 2019 6:46:31 AM To: Sid Majaha Cc: Elaine Meng Subject: Re: [Chimera-users] Non-standard atom names You’re welcome. AM1-BCC does take considerably longer than Gasteiger, but in this case the great majority of the time is spent adding the missing side chains. —Eric > On Apr 15, 2019, at 1:18 AM, Sid Majaha <sidumomajaha(a)live.com <mailto:sidumomajaha@live.com>> wrote: > > Hi Eric > > Thank you so much for your help. I was able to see as well that my protein might have been too large for the calculations of the charges to take place efficiently because after following the procedure you gave me, it took a much longer time than using Gasteiger. Thank you so much for your help. > > Sid > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 > > From: Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> > Sent: Saturday, April 13, 2019 2:18:39 AM > To: Sid Majaha > Cc: chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> > Subject: Re: [Chimera-users] Non-standard atom names > > Hi Sid, > The 2BXF structure has many, many missing heavy side-chain atoms. I recommend using the Dock Prep tool (Tools→Structure Editing→Dock Prep), which will use a rotamer library to fill out missing/incomplete side chains before adding hydrogens and assigning charges. Use the dialog check boxes to turn off any Dock Prep steps you don’t want (e.g. Write Mol2 file). Applying a lot of rotamers takes a few minutes, so you might want to bring up the Reply Log first (Favorites→Reply Log) so you can keep an eye on the Dock Prep progress while you possibly do something else. > > ―Eric > > Eric Pettersen > UCSF Computer Graphics Lab > >> On Apr 11, 2019, at 8:26 PM, Sid Majaha <sidumomajaha(a)live.com <mailto:sidumomajaha@live.com>> wrote: >> >> >> Hi Eric >> >> Problems with atom names in adding charge to a receptor using Chimera v1.13.1 >> (ToolsàSurface Binding/AnalysisàAdd charge) >> I first added my H to prepare my receptor. And I am using the protein PDB ID 2BXF. >> Net Charge is +0 for the residue HIS using charge method AM1_BCC >> >> Chimera warning received >> Correct charges are unknown for 9 non-standard atom names in otherwise standard residues. >> Charges of 0.0 were assigned to the unknown atoms. >> 1 model(s) had non-intergral total charge. >> >> Reply log is as follows, >> >> Charge model: AMBER ff14SB >> Assigning partial charges to residue HIS (net charge +0) with am1-bcc method >> Running ANTECHAMBER command: C:/Program Files/Chimera 1.13.1/bin/amber16/bin\antechamber -ek qm_theory='AM1', -i c:\users\hp\appdata\local\temp\tmplj8p6o\ante.in.mol2 -fi mol2 -o c:\users\hp\appdata\local\temp\tmplj8p6o\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n >> (HIS) >> >> (HIS) Welcome to antechamber 17.3: molecular input file processor. >> >> (HIS) >> >> (HIS) Info: Finished reading file (c:\users\hp\appdata\local\temp\tmplj8p6o\ante.in.mol2). >> >> (HIS) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac >> >> (HIS) >> >> (HIS) >> >> (HIS) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff >> >> (HIS) Info: Total number of electrons: 78; net charge: 0 >> >> (HIS) >> >> (HIS) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/sqm" -O -i sqm.in -o sqm.out >> >> (HIS) >> >> (HIS) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/am1bcc" -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program Files/Chimera 1.13.1/bin/amber16/dat/antechamber/BCCPARM.DAT" -s 2 -j 1 >> >> (HIS) >> >> (HIS) Running: "C:/Program Files/Chimera 1.13.1/bin/amber16/bin/atomtype" -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC >> >> (HIS) >> >> Charges for residue HIS determined >> Non-standard atom names: >> VAL HB1 (VAL 551.A HB1) >> VAL HB2 (VAL 551.A HB2) >> ILE HB3 (ILE 509.A HB3, ILE 1087.B HB3) >> VAL HB3 (VAL 551.A HB3) >> ILE HB2 (ILE 509.A HB2, ILE 1087.B HB2) >> THR HB1 (THR 79.A HB1, THR 621.B HB1, THR 657.B HB1) >> ILE HB1 (ILE 509.A HB1, ILE 1087.B HB1) >> THR HB3 (THR 79.A HB3, THR 621.B HB3, THR 657.B HB3) >> THR HB2 (THR 79.A HB2, THR 621.B HB2, THR 657.B HB2) >> Total charge for #0: -66.402 >> The following residues had non-integral charges: >> LYS 16.A 0.0867 >> LEU 27.A -0.0471 >> GLN 29.A 0.0392 >> LYS 37.A 0.0867 >> LYS 47.A 0.0733 >> ASP 52.A -0.2088 >> GLU 53.A -0.2103 >> GLU 56.A -0.1137 >> LYS 69.A 0.0867 >> ARG 77.A 0.0612 >> GLU 78.A -0.1137 >> THR 79.A 0.3128 >> TYR 80.A 0.0451 >> GLU 82.A -0.1137 >> GLN 90.A 0.0152 >> GLU 91.A -0.1137 >> GLU 93.A -0.1137 >> ARG 94.A 0.0612 >> PHE 98.A 0.0352 >> GLN 100.A 0.0392 >> ASN 107.A 0.0397 >> ARG 110.A 0.0612 >> LYS 132.A 0.0867 >> LYS 133.A 0.2148 >> LYS 155.A 0.0867 >> LYS 158.A 0.0733 >> GLN 166.A 0.0152 >> LYS 170.A 0.0733 >> LEU 174.A -0.0471 >> LYS 186.A 0.0867 >> GLN 200.A 0.0152 >> LYS 201.A 0.0733 >> ARG 205.A 0.153 >> LYS 221.A 0.0867 >> LYS 229.A 0.0733 >> LYS 236.A 0.0733 >> LEU 247.A -0.0471 >> LYS 272.A 0.0733 >> GLU 273.A -0.1137 >> GLU 276.A -0.1137 >> LYS 277.A 0.0733 >> GLU 281.A -0.1137 >> LYS 282.A 0.0733 >> GLU 293.A -0.1137 >> LEU 298.A -0.0471 >> LYS 309.A 0.0733 >> LYS 319.A 0.0867 >> ASP 320.A -0.2088 >> LYS 355.A 0.0867 >> ASP 361.A -0.2088 >> LYS 368.A 0.0867 >> LYS 374.A 0.0733 >> GLU 378.A -0.1137 >> GLU 392.A -0.1137 >> GLN 393.A 0.0152 >> LYS 398.A 0.0733 >> LEU 404.A -0.0471 >> LYS 428.A 0.0867 >> LYS 432.A 0.0867 >> LYS 462.A 0.0733 >> LYS 496.A 0.0867 >> GLU 497.A -0.2103 >> ASN 499.A 0.0397 >> ILE 509.A 0.0431 >> LYS 515.A 0.0733 >> GLU 516.A -0.1137 >> LYS 520.A 0.0733 >> LEU 528.A -0.0471 >> LYS 532.A 0.0733 >> LYS 534.A 0.0733 >> LYS 537.A 0.0733 >> LYS 541.A 0.0733 >> PHE 547.A 0.0352 >> VAL 551.A 0.1935 >> LYS 553.A 0.2148 >> LYS 556.A 0.0733 >> ASP 558.A -0.2088 >> LYS 560.A 0.0733 >> GLU 561.A -0.1137 >> GLU 566.A -0.2103 >> LYS 569.A 0.0733 >> LYS 570.A 0.0733 >> GLN 576.A 0.0152 >> LYS 586.B 0.0733 >> LEU 605.B -0.0471 >> GLN 606.B 0.0152 >> THR 621.B 0.3128 >> LYS 625.B 0.0733 >> ASP 630.B -0.2088 >> GLU 634.B -0.1137 >> ASN 635.B 0.0397 >> LYS 638.B 0.0867 >> GLU 656.B -0.1137 >> THR 657.B 0.3128 >> TYR 658.B 0.0451 >> GLU 660.B -0.1137 >> MET 661.B 0.0564 >> LYS 667.B 0.0733 >> GLN 668.B 0.0152 >> GLU 671.B -0.1137 >> ARG 672.B 0.0612 >> PHE 676.B 0.0352 >> GLN 678.B 0.0152 >> ARG 688.B 0.0612 >> LEU 689.B -0.0471 >> LYS 733.B 0.0733 >> GLN 744.B 0.0152 >> LYS 748.B 0.0733 >> LEU 752.B -0.0471 >> LYS 755.B 0.0733 >> ARG 760.B 0.0612 >> GLU 762.B -0.1137 >> LYS 764.B 0.2148 >> GLN 778.B 0.0152 >> LYS 779.B 0.0867 >> ARG 783.B 0.3792 >> LYS 799.B 0.0867 >> LYS 807.B 0.0733 >> LYS 814.B 0.0733 >> LEU 849.B -0.0471 >> LYS 850.B 0.0733 >> GLU 851.B -0.1137 >> GLU 854.B -0.1137 >> LYS 855.B 0.0867 >> LYS 860.B 0.0733 >> GLU 871.B -0.1137 >> ASP 875.B -0.2088 >> LYS 887.B 0.0733 >> LYS 891.B 0.0733 >> GLU 895.B -0.1137 >> LYS 897.B 0.0867 >> LYS 933.B 0.2148 >> GLU 942.B -0.1137 >> LYS 952.B 0.0867 >> GLU 956.B -0.1137 >> LYS 963.B 0.2148 >> LYS 976.B 0.0867 >> ARG 984.B 0.3792 >> LYS 1010.B 0.0867 >> LYS 1018.B 0.2148 >> LYS 1040.B 0.0733 >> GLU 1075.B -0.1137 >> ASP 1086.B -0.2088 >> ILE 1087.B 0.0431 >> LYS 1093.B 0.0733 >> GLU 1094.B -0.1137 >> GLN 1096.B 0.0152 >> LYS 1098.B 0.0867 >> LYS 1099.B 0.0867 >> LYS 1110.B 0.0733 >> LYS 1115.B 0.0733 >> LYS 1119.B 0.2148 >> ASP 1124.B -0.2088 >> PHE 1128.B 0.0352 >> LYS 1131.B 0.0733 >> ASP 1136.B -0.2088 >> LYS 1138.B 0.0733 >> GLU 1139.B -0.1137 >> GLU 1144.B -0.1137 >> LYS 1147.B 0.0733 >> LYS 1148.B 0.0733 >> LEU 1149.B -0.0471 >> GLN 1154.B 0.0152 >> Correct charges are unknown for 9 non-standard atom names in otherwise standard residues >> >> Charges of 0.0 were assigned to the unknown atoms >> >> 1 model(s) had non-integral total charge >> Details in reply log. >> >> How do I work around this? >> >> Sid >> >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <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> > Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>

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