- Chimera-users - RBVI Mailing Lists

surface "holes"
by Fabian Gmail 29 Feb '08

29 Feb '08

Hi all, I enjoy very much using chimera, I have a question regarding surfaces. When I am working on a multi chain protein complex, and I want to present only one chain as surface and the others as ribbon or sticks, oftenly the surface present "holes" on the contact points with the ribbon. I understand they represent contact points between the chains, but I don't like how the surface looks like. Is there a way to avoid this? (I do that but uploading another copy of the chain). Thanks a lot, Fabian -- Fabian Glaser, PhD Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology Haifa 32000, ISRAEL Web: http://bku.technion.ac.il Email: fglaser(a)tx.technion.ac.il Tel: +972-(0)4-8293701 Cel: +972-(0)54-4772396

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longer bonds in image
by bala 28 Feb '08

28 Feb '08

Hi all, Thank you for the suggestions for my previous query. When the ribbons are displayed for the backbone of a RNA molecule. Some of the bonds look longer than usual. Herewith i have attached the image of a RNA molecule in which residues colored in cyan have some bonds longer in appearance. Kindly help me to get this of this. Thanks, Bala

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Re: [Chimera-users] command line mode
by snoze pa 28 Feb '08

28 Feb '08

Hi Eric, Is there some API with examples of chimera available. I am trying to add hydrogen in previous script. I tried cmdAddH and simpleAddhydrogens but it is not working. I am trying to put hydrogen and then charge to each ligand in the database. May be later I will call mmtk minimization from chimera itself to minimize each ligand. thanks in advance s

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calculating interphosphate distance
by bala 28 Feb '08

28 Feb '08

Dear chimera users, i) Greetings. I have a trajectory of 1000 conformations of a RNA molecule. I want to see the distribution of interphosphate distance. say i want to see the P-P distance of the residue 3 paired with a residue 38 in the opposite strand. Is it possible in anyways. ii) Suppose when i source a file from command line option : source dist, chimera nicely takes the distance commands in the file and displays the distances in the GUI. Is it possible to send the output to a file rather than seeing in GUI. Thanks, Bala

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distance in log
by 吴超 28 Feb '08

28 Feb '08

Hope it helps... And thanks Elaine and Eric again! :) ---------- Forwarded message ---------- From: 吴超 <lynnwuchao(a)gmail.com> Date: 2008/2/23 Subject: [Chimera-users] distance To: Eric Pettersen <pett(a)cgl.ucsf.edu> Cc: Elaine Meng <meng(a)cgl.ucsf.edu>, Chimera BB <chimera-users(a)cgl.ucsf.edu> Thanks very much, Elaine and Eric! Both of methods worked very well... On Sat, Feb 23, 2008 at 4:00 AM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > In particular, if you have a script (name "dist.com" for instance) > that sets up your distance measurements, something like: > > dist :12@c :17@c > dist :14@c :19@c > > Then you could run chimera like this: > > chimera --nostatus --nogui pdb:1gcn dist.com printDist.py > > to produce: > > #0:12.A@C <-> #0:17.A@C 8.74043923381 > #0:14.A@C <-> #0:19.A@C 8.19707020831 > > on standard output. You could redirect the output into a file named > "dist.out" with: > > chimera --nostatus --nogui pdb:1gcn dist.com printDist.py > dist.out > > --Eric > > On Feb 22, 2008, at 11:40 AM, Elaine Meng wrote: > > > Hi! > > Eric has kindly provided a python script (attached at the bottom) > > that will write all the current distance measurements to the Reply > > Log. Just open the python file with Chimera and it will happen. > > > > Alternatively, depending on your situation, you could use > > "findclash," as discussed in these chimera-users messages a few > > months ago: > > > > http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-November/ > > 002061.html > > http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-November/ > > 002069.html > > http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-November/ > > 002070.html > > > > I hope this helps, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu > > UCSF Computer Graphics Lab and Babbitt Lab > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > http://www.cgl.ucsf.edu/home/meng/index.html > > > > On Feb 21, 2008, at 5:24 PM, 吴超 wrote: > > > >> Thanks, Elaine! > >> The problem is that I want to automatically calculate a number of > >> distances in non-gui interface, and sent the date to a file, just > >> like the logfile. > >> So is there a chance that I can achieve it using chimera? > >> > >> On Fri, Feb 22, 2008 at 1:00 AM, Elaine Meng <meng(a)cgl.ucsf.edu> > >> wrote: > >> > >> The distances are listed in a separate dialog - choose "Tools... > >> Structure Analysis... Distances" from the menu to open that dialog. > >> You can adjust the number of decimal places in the measurement, and > >> there is a "Save" button if you want to save distances or other > >> measurements to a text file. > > > > <printDist.py> > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > -- Chao Wu Currently: National Institute of Biological Sciences, Beijing Huang Niu's Lab http://www.nibs.ac.cn/ Tel: 80726688-8572 Address: Beijing ZhongGuanCun Life Science Park, NO.7 Science Park East Road, NIBS B427 Postcode: 102206 Life Science Honors Program, China Agricultural University PO.1055, NO.2 YuanMingYuan west road, Beingjing, 100094 P.R. China Tel: 86-10-62812484 E-mail: lynnwuchao(a)gmail.com -- Chao Wu Currently: National Institute of Biological Sciences, Beijing Huang Niu's Lab http://www.nibs.ac.cn/ Tel: 80726688-8572 Address: Beijing ZhongGuanCun Life Science Park, NO.7 Science Park East Road, NIBS B427 Postcode: 102206 Life Science Honors Program, China Agricultural University PO.1055, NO.2 YuanMingYuan west road, Beingjing, 100094 P.R. China Tel: 86-10-62812484 E-mail: lynnwuchao(a)gmail.com

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Re: [Chimera-users] minimize command
by snoze pa 27 Feb '08

27 Feb '08

Elaine, I guess i can use either 'minimize' or "addh and addcharge" otherwise it will run the antechamber twice. *minimize is working fine but i can not save the result in mol2 format using COMMAND option. I try wrtiemol2 but it is not accepting it as a command. save is also not saving in mol2 format. *Any help, thanks in advance. s * * On Wed, Feb 27, 2008 at 5:48 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Conrad, > From looking at the documentation, sounds like you can't use the > minimize command with any nondefault settings of Dock Prep, addh, and > add charge. Is that correct? > > It would be nice if it could tell that you already added hydrogens > and charges to your liking and skip those steps. However, since this > is all done via Dock Prep, that may or may not be possible. > Elaine > ----- > Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu > UCSF Computer Graphics Lab and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > > > >

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POV-Ray Export
by Greg Williams 27 Feb '08

27 Feb '08

I would like to render my files externally in POV-Ray, but I get error messages. As a test, I set the leucine zipper in wire mode and exported the file. I opened POV-Ray, turned on antialiasing and rendered at 640x480. I immediately get the following: Possible Parse Error: Could not find file 'transforms.inc' File zipper.pov line 6 Parse Warning: Check that the file is in a directory specifed with a +L switch or 'Library_Path=' .INI item. Standard include files are in the include directory or folder. Please read your documentation carefully. File zipper.pov line 6 I cut the line ³#include ³transforms.inc² and rendered again, and I get a new set of parsing errors, which include a couple errant bracket symbols that I managed to fix, at which point I get: Parse Error: Expected 'object or directive', undeclared identifier 'Axis_Rotate_Trans' found instead File zipper.pov line 1322 So I cut the ending lines of the file: Axis_Rotate_Trans(<0.000000, 0.000000, 1.000000>, 0.000000) translate <0.000000, 0.000000, 0.000000> } } Now the render works. I guess I should be happy with that, but I¹m wondering what it was I cut from the file. Any help here? Thanks, Greg

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command line mode
by snoze pa 26 Feb '08

26 Feb '08

Dear Chimera Users, How can I use chimera in --nogui mode to screen 1000 compunds from ZINC database and save them in to mol2 format. Is there any script so that I can convert preselected 1000 compound from ZINC database and convert them t o mol2 format so that I can use them in DOCK program. thanks in advance

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Making an omnimax POVray movie
by Kristina Furse 26 Feb '08

26 Feb '08

Hi- We're interested in using Chimera to prepare POVray files for a movie to be shown on a hemispherical dome. The first part of the movie will be a 360 degree rotation of a DNA/drug complex showing water occupancy around the drug, and the second half will come from an AMBER MD trajectory. We've figured out the content and rendering. The two remaining issues are that the camera must be changed from "perspective" to "omnimax" (fisheye), and the extensive rendering time that will be required for the large system at very high resolution (4096x4096). Here is our plan: 1. Use a command-line script to rotate the system and export the scene to x3d files. 2. Use per-frame scripting in MD movie to export each trajectory frame to x3d files. 3. Use x3d2pov to translate into *.pov files. 4. Change the camera from perspective to omnimax in each .pov file. 5. Render the individual images in parallel on our cluster using povray (different version than the one that ships with Chimera). 6. Compress to jpeg. 7. Assemble movie as .mov (format compatible with projection system in the dome). Does anyone have a better idea? I'm assuming that I can't change the camera to omnimax from within Chimera? Thanks for any suggestions! Kristina -- Kristina Furse Postdoctoral Research Associate 262 Stepan Chemistry Hall Notre Dame, IN 46556 (574)631-3904

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[chimera-users] --nogui
by 吴超 25 Feb '08

25 Feb '08

Hi, folks! I came across with a problem when using chimera --nogui file.cmd > data.log the file.cmd is as follows: open /home/lynn/project/hivrt_pdb/holo_without_mutation/1C1C.pdb findclash :.het@C1 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C2 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C3 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C4 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C5 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C6 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@S overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C7 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C12 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@CF overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@CH overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@CI overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C11 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@O11 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@N8 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@C9 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@O9 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@N10 overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@CA overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@OB overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@CC overlap -1 hbond 0 ignoreIntraRes true log true findclash :.het@CD overlap -1 hbond 0 ignoreIntraRes true log true If i use the graphic version and read the cmd file, it worked quite well and I can find all I need in the reply log. But when it came to the nogui version, the data file only contains the result of the first two lines of the cmd file. That is open /home/lynn/project/hivrt_pdb/holo_without_mutation/1C1C.pdb findclash :.het@C1 overlap -1 hbond 0 ignoreIntraRes true log true Results are: Opening 1C1C.pdb... 1 model opened Opened 1C1C.pdb containing 1 model, 7997 atoms, and 1096 residues Allowed overlap: -1 H-bond overlap reduction: 0 Ignore overlap between atoms separated by 4 bonds or less Ignore intra-residue overlaps 5 overlaps atom1 atom2 overlap distance #0:999.het@C1 #0:100.A@CD1 -0.352 4.112 #0:999.het@C1 #0:100.A@CD2 -0.643 4.403 #0:999.het@C1 #0:188.A@CD2 -0.723 4.363 #0:999.het@C1 #0:188.A@CB -0.883 4.643 #0:999.het@C1 #0:188.A@CG -0.989 4.479 Error in the shell is as follows: $ /usr/local/chimera/bin/chimera --nogui /home/lynn/cmd/1C1C.cmd > /home/lynn/project/data/distance/1C1C.dist Traceback (most recent call last): File "/usr/local/chimera/share/__main__.py", line 65, in ? value = chimeraInit.init(sys.argv) File "/usr/local/chimera/share/chimeraInit.py", line 358, in init replyobj.reportException( File "CHIMERA/share/chimera/replyobj.py", line 610, in reportException File "CHIMERA/share/chimera/replyobj.py", line 438, in nogui_message ValueError: I/O operation on closed file $ Could anyone give me hand? I am really frustrated! Thanks in advance... -- Chao Wu Currently: National Institute of Biological Sciences, Beijing Huang Niu's Lab http://www.nibs.ac.cn/ Tel: 80726688-8572 Address: Beijing ZhongGuanCun Life Science Park, NO.7 Science Park East Road, NIBS B427 Postcode: 102206 Life Science Honors Program, China Agricultural University PO.1055, NO.2 YuanMingYuan west road, Beingjing, 100094 P.R. China Tel: 86-10-62812484 E-mail: lynnwuchao(a)gmail.com

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