- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] longer bonds in image
by Elaine Meng 03 Mar '08

03 Mar '08

Hi Bala, This is an expected behavior of Chimera: the ribbon is a smoothed path that does not go exactly through the atom positions. When ribbon is shown, the default is to simply draw the longer or shorter bonds where the ribbon is farther from or closer to the displayed atoms (ribose/base or amino acid side chain) than are the backbone atoms that the ribbon represents. However, there are ways to change the behavior: (A) use the command "ribbackbone" to allow display of both backbone atoms and ribbon. This will not make any bonds look longer or shorter, but it is usually ugly because the ribbon is not in the same place as the backbone atoms. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribbackbone.html (B) with Ribbon Style Editor, "Residue Class" section, you can set which atoms control the ribbon path and which are hidden automatically (by default, without using "ribbackbone") when ribbon is shown: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ ribbonstyle.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 P.S. you can send attachments such as images to chimera-users, but the message will not appear until the moderator has a chance to approve it... just be patient and it will be sent! On Mar 2, 2008, at 9:00 PM, bala wrote: > -----Original Message----- > From: bala > Sent: Fri 2/29/2008 12:13 PM > To: chimera-users(a)cgl.ucsf.edu > Subject: longer bonds in image > > 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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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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NOT ABLE TO VIEW SURFACE USING PHYRE MODEL DATA
by nyyount＠cox.net 25 Feb '08

25 Feb '08

Hi, I have not been able to view my Phyre pdb files using Chimera�s surface view. I get the error code -1073741785 and am immediately shut out of the program. I am not a computer person � yet. Are there any quick fixes that I can add to my Phyre generated PDB files to be able to view them in �surface� view? I�m very pleased with Chimera and have used it for all of the molecular graphics for our next publication. I would like to be able to view my Phyre models using the same software. Thank you! Nannette Y. Yount, Ph.D. Harbor-UCLA

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save manipulated electron density maps in spider
by Jan-Christian Schuette 25 Feb '08

25 Feb '08

Dear Chimera Developers, I quite often have to manipulate electron density maps in the spider format. When using chimeras volume eraser function, it doesn't allow me to save the new map back to spider or another easy-to-convert file format (such as brix or ccp4). I would be great if you could add such a feature in the next version of the software. Best regards, Jan-Christian Schuette

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Re: [Chimera-users] distance
by Elaine Meng 22 Feb '08

22 Feb '08

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.

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Driving matchAtoms from the IDLE
by Jean-Didier Maréchal 22 Feb '08

22 Feb '08

Hi Guys, I'd like to superpose two inorganic complexes using two differently "ordered" atom sets. My compound has quite similar substructures but I am sure at all what is the best "ordered" selection of atom pairs to align. Therefore, I'd like to make a "extensive" search (with an heuristic approach to define...) passing by the idle. I am unfortunately missing something before getting to this point! Lets say that I just want to align the nitrogen atoms of the my two structures. I have: import chimera import numpy from chimera import match from chimera import runCommand runCommand("select #1@N=") an1=chimera.selection.currentAtoms() runCommand("select #0@N=) an2=chimera.selection.currentAtoms() chimera.match.matchAtoms(an1,an2) And then it's when I am already stuck! the resulting prompt does not provide mistake an gives: chimera.match.matchAtoms(an1,an2) (<_chimera.Xform object at 0x9463ef8>, 0.034256915079603358) But how this results can be send to the graphical window? I guess I have to use the Xform object, but I can not clearly understand how to do this. Thanks for any help! JD On Thu, 2008-02-21 at 12:00 -0800, chimera-users-request(a)cgl.ucsf.edu wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: distance (Elaine Meng) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 21 Feb 2008 09:00:37 -0800 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] distance > To: "??" <lynnwuchao(a)gmail.com> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <0E85C396-8C7D-4182-A029-5C0155245C3A(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=UTF-8; delsp=yes; format=flowed > > Hi! > > 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. > > 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 20, 2008, at 11:38 PM, ?? wrote: > > > Hi, folks, > > I select two atoms and measured their distance using the command > > distance and can see the exact distance value in the graphic > > interface, but when I go the log file i can not find it. > > Can anybody give me a hand and tell me why can I find it? Thanks.. > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 58, Issue 24 > *********************************************

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placing a helium atom at a given position.
by Jean-Didier Maréchal 22 Feb '08

22 Feb '08

Hi again, that follows an e-mail exchange with Eric a while ago. I am trying to place a given atom (for the moment, helium is fine) to given x,y,z coordinates. You told me that the new BuildStructure module could do that, unfortunately after having imported the module import BuildStructure when I do BuildStructure.placeHelium(res,model=0,position=13.2909,75.4474,25.4248) I have SyntaxError: non-keyword arg after keyword arg I tried different argumentations of this but I can't have it working, if you can tell me how to do this, that would be perfect. All the best, JD some time ago Eric On Thu, 2008-02-21 at 12:00 -0800, chimera-users-request(a)cgl.ucsf.edu wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: distance (Elaine Meng) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 21 Feb 2008 09:00:37 -0800 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] distance > To: "??" <lynnwuchao(a)gmail.com> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <0E85C396-8C7D-4182-A029-5C0155245C3A(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=UTF-8; delsp=yes; format=flowed > > Hi! > > 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. > > 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 20, 2008, at 11:38 PM, ?? wrote: > > > Hi, folks, > > I select two atoms and measured their distance using the command > > distance and can see the exact distance value in the graphic > > interface, but when I go the log file i can not find it. > > Can anybody give me a hand and tell me why can I find it? Thanks.. > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 58, Issue 24 > *********************************************

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managing bond order
by Victor Kenyon 21 Feb '08

21 Feb '08

hi all, typically when i import a paired back active site of a protein, chimera wants to connect atoms that should not be connected. is there a way to select bonds that violate a certain bond length so i can remove them? or a possible work around? thanks for your help. victor Victor A. Kenyon kenyon(a)chemistry.ucsc.edu 831.252.7667.

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distance
by 吴超 21 Feb '08

21 Feb '08

Hi, folks, I select two atoms and measured their distance using the command distance and can see the exact distance value in the graphic interface, but when I go the log file i can not find it. Can anybody give me a hand and tell me why can I find it? Thanks..

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modifying presets
by glenn millhauser 20 Feb '08

20 Feb '08

Hi Folks, Is there a way to edit the Presets to include additional protein features? Specifically, I work with quite a few disulfide rich proteins and it would be great to select the Preset Interactive 1 and have it automatically draw Cys side chains with disulfide links. Many thanks, glenn Glenn L. Millhauser Department of Chemistry & Biochemistry UC Santa Cruz Santa Cruz, CA 95064 831 459 2176 voice 831 566 3337 cell 831 459 2935 fax http://chemistry.ucsc.edu/~glennm http://www.chemistry.ucsc.edu/faculty/millhauser.html

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Re: [Chimera-users] [chimera-dev] change hand ?
by Tom Goddard 20 Feb '08

20 Feb '08

Hi Stefan, You can flip the hand of the map by making the grid spacing negative along one axis. Chimera wasn't intended to do this so I'm not sure everything will work correctly. To make this change use the volume dialog Coordinates panel and change voxel size from (for example) 0.37 to 0.37 0.37 -0.37. The three numbers are grid plane spacing along the x, y, z axes. If they are all the same Chimera just shows one number. In Chimera 1.2470 the volume surface will become dark. To remedy this use the volume dialog Surface and Mesh options panel and turn off "two-sided surface lighting". A current Chimera daily build will not have that problem. Chimera won't correctly save the flipped map. So this is not an ideal way to proceed. I don't know of software that will write out the flipped map though it must exist. Tom Stefan Backstrom wrote: > Hi. > > Is it possible to flip the hand of a cryo-EM map in chimera ? > > Best wishes, > > Stefan Bäckström > Medical Biochemistry and Biophysics > Umeå University > Sweden > > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev >

2 2

volume rendering depth issue with multiple volumes (segmented layers)
by William Jeffrey Triffo 19 Feb '08

19 Feb '08

hello, I remember past posts mentioning depth issues when rendering multiple volumes. I have several layers (6) that I have segmented out individually. Last night, they appeared to render 'in order' (the layers are parallel, and up to 6 thus overlap if rotated into the correct view). this morning, though, I notice that 'volume 2' is rendering 'on top' of everything else. is there a way I can trick this to work, or is there something I may be missing / clicked wrong? thanks, -Jeff -- ------------------------------------------------------------- Jeff Triffo Auer Group, Donner Lab, Lawrence Berkeley National Laboratory Raphael Group, Bioengineering Department, Rice University Medical Scientist Training Program (MSTP), Baylor College of Medicine phone (Berkeley): 510-486-7940 fax (Berkeley): 510-486-6488

2 4

menssage error
by DRT/BA - Elias Silva dos Santos 19 Feb '08

19 Feb '08

Hi!! I am preparing a molecule for docking that he has two centers of iron sulphur [ 4FE-4S]+2 and one molecule of FAD. When trying to place loads I am recebeno error messages (DOCK Prep). As I must proceed to decide the problem Elias

2 1

Mac OSX install issue: SOLVED
by Greg Williams 19 Feb '08

19 Feb '08

Thanks for the help. An upgrade from X11 1.1.1 to 1.1.3 solved the problem. GW

1 0

Raytracing
by Bernard Heymann 19 Feb '08

19 Feb '08

Hi I'm trying to use povray directly from Chimera and everything works. However, the isosurface of my density comes out practically black, even though the clipping plane is rendered fine. I played a bit with lighting, but that does not seem to make a difference. Could you give me some guidance? I can send an output picture if needed. Bernard Heymann Rm 1515, 50 South Dr, NIH, Bethesda, 20892-8025 Tel 301-451-8241, Fax 301-480-7629

3 2

Mac OSX install issue
by Greg Williams 19 Feb '08

19 Feb '08

I am running OSX 10.4.10 on an iMac with a 2.16 GHz Intel Core 2 Duo, 1 GB 66h MHz DDR2 SDRAM. I have installed X11 1.1.1 XFree86 4.4.0. I have downloaded the current production release of Chimera for Mac X11. The application doesn't open, either on a double click from the desk top or from the dock. I have also tried the Snapshot release dated 2-11-8, with the same result. The application will not open. I have also tried the Mac OSX (Aqua) version of 6-21-7. This version does open, and it works well, in limited doses. However, it is very unstable and closes spontaneously after a few minutes of work. Any ideas what may be incompatible between the X11 versions and my Mac? Thanks, Greg Williams

3 2

surface color and coloring particular residues
by Michael DiMattia 19 Feb '08

19 Feb '08

hello, Is there a way to both color a surface-rendered protein by radius AND simultaneously color certain residues of the same chain with a distinct color? I have figured out how to do each one of these tasks, but can't seem to get both colorings to remain at the same time on the same protein. If I color by radius using "surface color" and then decide to highlight a particular residue, the particular residue is indeed colored, but at the expense of losing the color by radius to whatever color the protein was before that. thanks. mike

2 1

Viewing mode
by James Fethiere 19 Feb '08

19 Feb '08

Hi, I'm trying to save an image of an EM map with atomic models fitting in and can't get pov-ray to write-out the displayed image. Using the side view panel, I cut out part of the surface and models to get the view I want. When I save the image without pov-ray, I get what is displayed but when I try using the pov-ray option, I get the full map and models without the clipping I imposed using the side view mode. What would be the right procedure? Thanks James

2 1

color by radius and other color simultaneously
by Michael DiMattia 18 Feb '08

18 Feb '08

hello, Is there a way to both color a surface-rendered protein by radius AND simultaneously color certain residues of the same chain with a distinct color? I have figured out how to do each one of these tasks, but can't seem to get both colorings to remain at the same time on the same protein. If I color by radius using "surface color" and then decide to highlight a particular residue, the particular residue is indeed colored, but at the expense of losing the color by radius to whatever color the protein was before that. thanks. mike

1 0

selection of different part of the protein through the sequence prompt
by Jean Didier Pie Marechal 16 Feb '08

16 Feb '08

Hi guys, I'd like to select two precise beta strands of my prot and I thought it would be easier to do so from the sequence editor. Unfortunately, I can't find a way to select different parts of the same protein in the sequence editor; I alwys select the full length between first and last selected residues whatever combo I use (shift, ctrl and so on). Is it possible to do this in the sequence editor? Cheers, JD Dr. Jean-Didier Maréchal Professor Lector Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Dimecres, Febrer 13, 2008 9:00 pm Assumpte: Chimera-users Digest, Vol 58, Issue 15 > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Split into models (Sadler, Evan) > 2. Re: Split into models (Elaine Meng) > 3. Opaque volume planes (Tom Goddard) > 4. Re: Opaque volume planes (William Jeffrey Triffo) > 5. Re: Opaque volume planes (Tom Goddard) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Tue, 12 Feb 2008 17:51:30 -0600 > From: "Sadler, Evan" <ESADLER(a)dom.wustl.edu> > Subject: [Chimera-users] Split into models > To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Message-ID: <C3D78D22.18B15%esadler(a)dom.wustl.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Recent email address change caused the first try to bounce, so I > resent it. > > I've loaded a file (2rjp.pdb) with 4 chains and want to split it > into 4 > models so I can align them. But "split" returns: > > unrecognized command: "split" > > What am I doing wrong? > > Evan > > -- > J. Evan Sadler, M.D., Ph.D. > Howard Hughes Medical Institute > Washington University > 660 S. Euclid Ave., Box 8022 > St. Louis, MO 63110 > Tel: 314-362-9067 > FAX: 314-454-3012 > email: esadler(a)im.wustl.edu > > > > > ------------------------------ > > Message: 2 > Date: Tue, 12 Feb 2008 16:09:22 -0800 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Split into models > To: "Sadler, Evan" <ESADLER(a)dom.wustl.edu> > Cc: chimera BB <chimera-users(a)cgl.ucsf.edu> > Message-ID: <84C5F9DD-BED6-4476-B29C-F39C322D4BEB(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > Hi Evan, > You must be using a version of Chimera older than the "split" > command. If you use the documentation that came with your download > > (opened from the Help menu) it should be fairly synchronized with > your software and you won't get confused by features you don't > have! > However, in this case, just get a newer version. > > The pages at our web site under http://www.cgl.ucsf.edu/chimera/ > docs/UsersGuide/ > > are "development documentation," which I am constantly changing as > Chimera changes. It will generally have newer things than your > downloaded software. > > The pages under http://www.cgl.ucsf.edu/chimera/current/docs/ > UsersGuide/ > > are documentation for the most recent production release (currently > > Nov 2007) and I see it also lists "split". So to use that feature > you can get that production release: > http://www.cgl.ucsf.edu/chimera/download.html#production > > There are also much newer "daily builds" although they are > essentially untested and exist mainly to provide access to the very > > latest developments. > http://www.cgl.ucsf.edu/chimera/download.html#production > > I just tried your structure in the production release and last > night's daily build; "split" worked in both, so you should be all set! > 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 12, 2008, at 3:51 PM, Sadler, Evan wrote: > > > Recent email address change caused the first try to bounce, so I > > resent it. > > > > I've loaded a file (2rjp.pdb) with 4 chains and want to split it > > into 4 > > models so I can align them. But "split" returns: > > > > unrecognized command: "split" > > > > What am I doing wrong? > > > > Evan > > > > -- > > J. Evan Sadler, M.D., Ph.D. > > Howard Hughes Medical Institute > > Washington University > > 660 S. Euclid Ave., Box 8022 > > St. Louis, MO 63110 > > Tel: 314-362-9067 > > FAX: 314-454-3012 > > email: esadler(a)im.wustl.edu > > > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > ------------------------------ > > Message: 3 > Date: Tue, 12 Feb 2008 17:41:06 -0800 > From: Tom Goddard <goddard(a)cgl.ucsf.edu> > Subject: [Chimera-users] Opaque volume planes > To: William Jeffrey Triffo <triffo(a)rice.edu>, "'Chimera BB'" > <chimera-users(a)cgl.ucsf.edu> > Message-ID: <47B24AB2.3060501(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Jeff, > > The trouble obtaining opaque volume planes is not related to > volume > plane display being built into the volume dialog. It is related to > a > change I made in how transparency is handled in solid mode back in > Aug 2007. > > Today I changed transparency in "solid" style volume rendering so > it > is easier to obtain completely opaque data planes. In tonight's > builds > (if they succeed, may not since we are switching to Python 2.5 > today) > you can obtain completely opaque volume planes by using the > "Brightness > and Transparency" panel of the volume dialog to set transparency to > 0. > This transparency value represents the fraction (0-1) of the depth > of > the volume required to produce opacity to the degree indicated by > the > height of the yellow curve on the histogram. In other words it > modulates the overall transparency. But until today it was > arbitrarily > deciding not to modulate the transparency if this depth was less > than > one grid spacing. This meaning of the transparency factor was > introduced in August 2007, and prior to that the transparency > factor > just scaled the opacity given by the yellow curve. > > Tom > > Jeff wrote: > > hi Tom, > > > > in the older (plug-in) volume planes tool, I was able to generate > > images that were opaque planes. I don't seem to be able to do > this > > anymore, even with transparency = 0. is there a way for me to do > this > > in the current Chimera? > > > > ------------------------------ > > Message: 4 > Date: Tue, 12 Feb 2008 17:47:37 -0800 > From: William Jeffrey Triffo <triffo(a)rice.edu> > Subject: Re: [Chimera-users] Opaque volume planes > To: "'Chimera BB'" <chimera-users(a)cgl.ucsf.edu> > Message-ID: <47B24C39.10306(a)rice.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > thanks, > > do you know when tonight's builds will go through, I will test it > at > that point to see if the functionality made it in > > -Jeff > > > Tom Goddard wrote: > > Hi Jeff, > > > > The trouble obtaining opaque volume planes is not related to > volume > > plane display being built into the volume dialog. It is related > to a > > change I made in how transparency is handled in solid mode back > in Aug > > 2007. > > > > Today I changed transparency in "solid" style volume rendering > so it > > is easier to obtain completely opaque data planes. In tonight's > > builds (if they succeed, may not since we are switching to Python > 2.5 > > today) you can obtain completely opaque volume planes by using > the > > "Brightness and Transparency" panel of the volume dialog to set > > transparency to 0. This transparency value represents the > fraction > > (0-1) of the depth of the volume required to produce opacity to > the > > degree indicated by the height of the yellow curve on the > histogram. > > In other words it modulates the overall transparency. But until > today > > it was arbitrarily deciding not to modulate the transparency if > this > > depth was less than one grid spacing. This meaning of the > > transparency factor was introduced in August 2007, and prior to > that > > the transparency factor just scaled the opacity given by the > yellow > > curve. > > > > Tom > > > > Jeff wrote: > >> hi Tom, > >> > >> in the older (plug-in) volume planes tool, I was able to > generate > >> images that were opaque planes. I don't seem to be able to do > this > >> anymore, even with transparency = 0. is there a way for me to do > this > >> in the current Chimera? > > > > > > -- > ------------------------------------------------------------- > Jeff Triffo > Auer Group, Donner Lab, Lawrence Berkeley National Laboratory > Raphael Group, Bioengineering Department, Rice University > Medical Scientist Training Program (MSTP), Baylor College of Medicine > phone (Berkeley): 510-486-7940 > fax (Berkeley): 510-486-6488 > > > > ------------------------------ > > Message: 5 > Date: Tue, 12 Feb 2008 18:10:01 -0800 > From: Tom Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Opaque volume planes > To: William Jeffrey Triffo <triffo(a)rice.edu> > Cc: 'Chimera BB' <chimera-users(a)cgl.ucsf.edu> > Message-ID: <47B25179.5050005(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > The Chimera nightly builds usually run around 9 pm pacific standard > time > (california). The nightly build download web page has the date for > each > build, and that will not be updated if code checked in during the > day > does not compile. Code changes checked in before about 8 pm makes > it > into that night's build. > > http://www.cgl.ucsf.edu/chimera/alpha-downloads.html > > Tom > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 58, Issue 15 > ********************************************* >

2 1

Chimera user, about 'turn' command
by Aguang Dai 15 Feb '08

15 Feb '08

Dear Mr./Ms. I'm a Chimera user in FSU. I would like to use Chimera to build some models. I used 'turn' command to rotate the model around the z axis. The command and option was: turn z 27.6923. The model is from a PDB file. But the result was that it should have be, not what I wanted. The atoms should be always in the circle centered in the Z axis, respectively. So my question is: When Chimera open a PDB file recording a protein structure, whether the coordinate axis is exactly the same as that in the PDB file? Thank you for your information in advance. Best, Daniel

3 2

zone tool in volume rendering
by William Jeffrey Triffo 14 Feb '08

14 Feb '08

I've been using the new mask tool to extract features along surfaces, which is useful in its own right for generating separate maps of segmented areas. but, if I wish to color a region around a surface (or between surfaces) without generating a new map, I am not sure how to do this - the 'zone' and 'color zone' tools in Volume viewer expect atoms or marker files. I had thought about loading multiple files of these surface regions after segmenting them out, each with their own color, but loading them together produces the ordering problem with the volume rendering. also, loading multiple volumes consumes a lot of memory and I run short of memory. is there currently a way to color arbitrary regions in a volume rendering? for example, rendering all data within 60 A of a surface with a different color than the rest of the volume, or coloring a region between two surfaces a different color, analogous to the 'sandwich' option of the mask tool. thanks, -Jeff

2 1

save volume histogram transfer function
by William Jeffrey Triffo 14 Feb '08

14 Feb '08

hello, is there a way for me to save the histogram transfer function that is displayed in Volume Viewer? I see that I can write down where the nodes are placed as these values appear in the "Level" dialog, but do not see a place to input magnitude (or write it down) of each node on the line. Ideally, I would just like to save it out, to apply the identical transform to multiple segmented areas of a volume. thanks, -jeff

2 1

Per-model clipping plane flickering
by Tom Goddard 14 Feb '08

14 Feb '08

Hi Jeff, I think you need to increase the "cap to clip plane distance" in the Surface Capping dialog from its default value of 0.001 to maybe 0.01 or 0.1. I guess you have surface capping turned on. Sometimes the clip plane partially clips the surface cap causing a fractured appearance of the cap. The OpenGL clip plane is offset from the cap by a small amount to prevent this but the needed displacement depends on the precision of the OpenGL depth buffer. Chimera should figure out the right value for this offset but currently it is specified by the user. Tom Jeff wrote: > hi Tom, > > I am getting odd output using the per-model clipping plane - I have a > volume loaded w/ precomputed subsamplings, and have generated a > surface depiction of the volume. when I enable the per-model clipping > plane, there is a lot of blinking in the model at the interface with > the per-model clipping plane. > > this volume is a membrane that I masked out using contours (as I > explained a couple of emails ago, where I have a bunch of contours > plotted along a surface, and then use the zone tool along those > contours). this means that there are a lot of zeros where the masked > volume ends; could that be part of the problem? > > I am using Chimera build 2492, MacBookPro 2GB (identical model to > yours), and Leopard with the latest X11 patch. > > best, > > -Jeff >

1 0

Opaque volume planes
by Tom Goddard 12 Feb '08

12 Feb '08

Hi Jeff, The trouble obtaining opaque volume planes is not related to volume plane display being built into the volume dialog. It is related to a change I made in how transparency is handled in solid mode back in Aug 2007. Today I changed transparency in "solid" style volume rendering so it is easier to obtain completely opaque data planes. In tonight's builds (if they succeed, may not since we are switching to Python 2.5 today) you can obtain completely opaque volume planes by using the "Brightness and Transparency" panel of the volume dialog to set transparency to 0. This transparency value represents the fraction (0-1) of the depth of the volume required to produce opacity to the degree indicated by the height of the yellow curve on the histogram. In other words it modulates the overall transparency. But until today it was arbitrarily deciding not to modulate the transparency if this depth was less than one grid spacing. This meaning of the transparency factor was introduced in August 2007, and prior to that the transparency factor just scaled the opacity given by the yellow curve. Tom Jeff wrote: > hi Tom, > > in the older (plug-in) volume planes tool, I was able to generate > images that were opaque planes. I don't seem to be able to do this > anymore, even with transparency = 0. is there a way for me to do this > in the current Chimera?

2 2

Split into models
by Sadler, Evan 12 Feb '08

12 Feb '08

Recent email address change caused the first try to bounce, so I resent it. I've loaded a file (2rjp.pdb) with 4 chains and want to split it into 4 models so I can align them. But "split" returns: unrecognized command: "split" What am I doing wrong? Evan -- J. Evan Sadler, M.D., Ph.D. Howard Hughes Medical Institute Washington University 660 S. Euclid Ave., Box 8022 St. Louis, MO 63110 Tel: 314-362-9067 FAX: 314-454-3012 email: esadler(a)im.wustl.edu

2 1

selection shadow is fixed
by jean-francois menetret 11 Feb '08

11 Feb '08

Recompiling the driver for the graphical card took care of the "selection shadow" Jean-Fran�ois M�n�tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street On Mon, 11 Feb 2008, chimera-users-request(a)cgl.ucsf.edu wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. selection shadow (jean-francois menetret) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 11 Feb 2008 08:49:42 -0500 (EST) > From: jean-francois menetret <menetret(a)bu.edu> > Subject: [Chimera-users] selection shadow > To: chimera-users <chimera-users(a)cgl.ucsf.edu> > Message-ID: <Pine.A41.4.63.0802110846190.146120(a)acsrs3.bu.edu> > Content-Type: text/plain; charset="x-unknown" > > > I am using the latest nightly build installed on our linux machine. If I > select a PDB and move it around, the selection leaves a "shadow" behind > (see attached snapshot). > Thanks > > > > Jean-Fran?ois M?n?tret, PhD > Boston University School of Medicine > Physiology and Biophysics Department > 700 Albany Street W315 > Boston, MA 02118 > Email: menetret(a)bu.edu > Mailing address: 715 Albany Street >

2 1

Dual display Mac problem moving Chimera window
by Tom Goddard 11 Feb '08

11 Feb '08

Jeff reports that with 2 displays on Mac OS 10.5 the Chimera window gets stuck when being dragged from one display to the other. Fixed by updating X11. Jeff wrote: > hi Tom, > > I thought since you also have a MacBookPro you might know the answer > to this question - I just bought a 24" monitor to extend the display > on my MBP (running Leopard). for all my other applications, I am able > to drag the application window onto the adjacent desktop space that > now exists on the new monitor (am still using the screen on my laptop > as well). however, the chimera window "gets stuck" - after I launch > it, the window spawns on my laptop screen, and when I try to move it > onto the new monitor, it stops halfway and I can't drag it any further. > > is there a properties file or something that Chimera / X uses to set > the bounds on the desktop? I took a screenshot but it saved 2 separate > files (one for each screen); the new 24" screen is set up on the left > side of the MBP. > Jeff wrote: > hi Tom, > > I downloaded the latest X11 update from macosforge (xquartz project) > and this relieved the Chimera window location problem, am now able to > move the window onto my attached 24" screen. > > -Jeff >

1 0

selection shadow
by jean-francois menetret 11 Feb '08

11 Feb '08

I am using the latest nightly build installed on our linux machine. If I select a PDB and move it around, the selection leaves a "shadow" behind (see attached snapshot). Thanks Jean-Fran�ois M�n�tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street

1 0

split-map
by Gatsogiannis, Christos 08 Feb '08

08 Feb '08

Hello chimera team, is there any memory-limitation for the split-map tool? When i perform a segmentation of a density-map larger than ~100MB i always get a chimera-error. In order to perform the segmentation, i have to coarse the density-map with a factor of 2, as example in imagic, and then split-map works fine with the new map. The result is of course density maps with a lower resolution. My Linux-PC has 4GB of memory and my first thought was that this should be enough for the segmentation of the density map as example in 10 parts (10x100=1GB). Is there any way to circumvent this problem and perform the segmentation with the original map? Thanks Christos Gatsogiannis Christos Dipl.Biol. Cryo-EM Lab Institut for Zoology Johannes Gutenberg University 55128, Mainz Germany Tel: +49(0)6131-39-23091

2 1

regd. DMS
by Vinay Kumar 08 Feb '08

08 Feb '08

Hello all, I had installed DMS previously. And recently upgraded my OS to fedora 8. When i try to recompile dms this is the following error i get. I did not face this the previous time!! could anyone guide me?? Regards Vinay Following is the error ----- [hpws@localhost dms]$ make cd libpdb ; make OPT="-O" make[1]: Entering directory `/home/hpws/dms/libpdb' cc -O -c -o pdb_read.o pdb_read.c pdb_read.c:25:20: error: stdio.h: No such file or directory pdb_read.c:26:20: error: ctype.h: No such file or directory pdb_read.c:27:21: error: string.h: No such file or directory In file included from pdb_int.h:20, from pdb_read.c:28: pdb.h:516: error: expected ')' before '*' token pdb.h:518: error: expected ')' before '*' token In file included from pdb_read.c:37: read_format.i:19: error: 'NULL' undeclared here (not in a function) In file included from pdb_read.c:45: pdbrun6_read.i:45: error: initializer element is not constant pdbrun6_read.i:45: error: (near initialization for 'pdbrun6[26]') pdbrun6_read.i:46: error: initializer element is not constant pdbrun6_read.i:46: error: (near initialization for 'pdbrun6[27]') pdbrun6_read.i:47: error: initializer element is not constant pdbrun6_read.i:47: error: (near initialization for 'pdbrun6[28]') pdbrun6_read.i:48: error: initializer element is not constant pdbrun6_read.i:48: error: (near initialization for 'pdbrun6[29]') pdb_read.c:59: error: expected ')' before '*' token pdb_read.c: In function 'pdb_read_string': pdb_read.c:304: warning: incompatible implicit declaration of built-in function 'memset' pdb_read.c:556: warning: incompatible implicit declaration of built-in function 'strncpy' pdb_read.c:913: warning: incompatible implicit declaration of built-in function 'sscanf' pdb_read.c:978: warning: incompatible implicit declaration of built-in function 'sscanf' pdb_read.c:992: warning: incompatible implicit declaration of built-in function 'sscanf' pdb_read.c:1027: warning: incompatible implicit declaration of built-in function 'sscanf' pdb_read.c:1047: warning: incompatible implicit declaration of built-in function 'sscanf' pdb_read.c:1076: warning: incompatible implicit declaration of built-in function 'sscanf' pdb_read.c:1094: warning: incompatible implicit declaration of built-in function 'sscanf' make[1]: *** [pdb_read.o] Error 1 make[1]: Leaving directory `/home/hpws/dms/libpdb' make: *** [pdb] Error 2

2 1

clipping: solids or interior surfaces
by Ian Yarbrough 07 Feb '08

07 Feb '08

Hello, Is there any way to color the interior face of a surface (when exposed by clipping) a different color or shade than the outside surface? Or a way to show the interior as a volume instead of a cavity? Essentially I'm looking for the same thing as this fellow describes in his post on the following date: *Andrew Jewett* aij at physics.ucsb.edu <chimera-users%40cgl.ucsf.edu?Subject=%5BChimera-users%5D%20clipping%20%28interior%20surfaces%20and%20solids%29&In-Reply-To=Pine.LNX.4.44.0502252312570.5796-100000%40localhost.localdomain> *Mon Feb 28 16:56:34 PST 2005* http://www.cgl.ucsf.edu/pipermail/chimera-users/2005-February/000287.html He describes it much more elegantly than I can. Was this feature was ever implemented? Thanks and cheers, Ian Yarbrough Texas A&M University Biochem/Biophysics Dept 832-858-9278

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locating models in maps by unit cell transformations
by Trevor Sewell 07 Feb '08

07 Feb '08

Hi, It often turns out that the atomic model you create in O needs to be transformed by a crystallographic symmetry operation in order to fit into the map created by refmac. In O this is no problem because the map automatically covers the bit of model you put in the center of your screen. However this does not seem to happen in Chimera. Is there an easy way to make the map cover the model (i.e. without working out what the transformation is and then creating a transformed pdb file)? Many thanks Trevor

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using IDLE
by Ben Keshet 07 Feb '08

07 Feb '08

Hi, I am interested in performing the same actions several times on several different structures. For example: open a file, select the histidines, delete them, save and close. Is IDLE the right tool for that? I opened the python shell (Tools-> General Controls-> IDLE) but could not open files or manipulate them using the shell. I have no knowledge in python. What is the best way to write scripts to execute commands repeatedly? If IDLE is the tool, how can use it to do that? Is there a written source for that? Do I need to master python first? Many thanks, Ben

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clipping related models identically
by Eric Pettersen 06 Feb '08

06 Feb '08

Raven Huang asks (paraphrased): > I have four related structures that I want to show in cutaway view, > with the cut being in the same place in all the structures. How > can I do that? The technique varies depending on whether you are clipping using the global clip planes (i.e. the ones shown in the Side View), or with per-model clip planes (from the Per-Model Clipping tool). Both techniques share the same setup step though: open all your models and get the parts you care about superimposed. If the starting coordinates are already "in the same reference frame" then you don't have to do anything but open the models. Otherwise you will have to superimpose them either with the MatchMaker tool or the "match" command. There is a discussion of using those here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/tutorials/ images.html#matching To view just one of the structures at a time, use the Model Panel (Favorites->Model Panel) and use the buttons in the Shown column (or the Show Only button in the button list) to show one structure/ surface. Now for adjusting the clip plane... Global clipping: open the Side View and adjust the near clip plane until it is cutting where you want it to. Per-model clipping: use the Per-Model Clipping tool to adjust the clip plane of the visible model until it is cutting where you want it to. Then choose one of the other models you want to cut from Per- Model Clipping's "Model:" menu. Enable clipping and click the "Align plane" button once you have chosen the original model in the menu next to the button. The model clip planes will now be aligned. Once the models are all clipped, you can either show then individually (the Model Panel again) and save separate images, or move them apart using the "move" command and save one combined image. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Planes feature in the Volume Viewer
by William Jeffrey Triffo 05 Feb '08

05 Feb '08

hi, when using the Planes tool in Volume Viewer, are the planes numbered from 0 or 1? I loaded a contour using the IMOD import, where I had drawn the contour on slice 12 of a volume; however, it appears that the plane that transects the contour in Chimera is '11' when using the Planes tool. I tried to test the enumeration by exceeding bounds (150 slices are in the volume, so was expecting an error for an entry of '150' if it was enumerated from zero), but it appears that slice indices outside the range of the loaded volume just default to the limit in either direction (typing in '200' just sets it to the highest-enumerated slice). -- ------------------------------------------------------------- Jeff Triffo Auer Group, Donner Lab, Lawrence Berkeley National Laboratory Raphael Group, Bioengineering Department, Rice University Medical Scientist Training Program (MSTP), Baylor College of Medicine phone (Berkeley): 510-486-7940 fax (Berkeley): 510-486-6488

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Contact/clash detection for HETATMs
by Jonathan Magasin 05 Feb '08

05 Feb '08

Hello, I'm trying to use the clashes/contacts tool to explore valid phi/psi angles for L- and D-Ala (as part of a homework assignment; developing a Ramachandran plot for each). The tool worked great for L-Ala but does not report any contacts for D-Ala. (For each, I've snipped just the relevant sections out of a larger PDB. I'm using default params for collision detection, with detection calculated for any movement.) The difference in the PDB's for L-Ala and D-Ala is that the latter are in HETATM records. I did include the CONNECT info (to explicitly tell Chimera how HETATMs bond) but that did not help. Perhaps there's something else I must include, or some modification I can make to the HETATMS (element labeling?) so that collision detection will work as with peptides? Or is this a known limitation? (Is there a list of known limitations? I'm a new user.) I'm not Note that the distance tool works for D-Ala. If I can get collision detection to work, it take much less time. Thanks in advance. -Jonathan

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Aligning two residues same name
by Elaine Meng 05 Feb '08

05 Feb '08

> Changing residue name works. Deleted membrane, saved pdb without > membrane. > Loaded the two models. Command line: match :XXX :YYY Hi Francesco, You can still use the name without changing it, for example open 4hhb open 4cpp preset apply interactive 1 match #1:hem #0:hem.a ~ribbon This matches the single heme residue of 4cpp (#1) to the chain A heme of 4hbb (#0 - it has four heme residues, in chains A-D). The protein parts are totally different but I just used this as an example because they both have heme. It takes a little time, but I recommend learning about the command- line specification language because it is used in so many commands, and can be very powerful yet flexible. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ frameatom_spec.html Or, for some quick hints see the examples on the second page of the "Quick Reference": http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/quickref.pdf 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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Re: [Chimera-users] [Dock-fans] How to get the charged mol for the ligand
by cpsosa＠comcast.net 04 Feb '08

04 Feb '08

Thanks. We tried that but after the hydrogens were added. We saved it and "vi" the mol2 file. I'll try this. -- Carlos P. Sosa -------------- Original message ---------------------- From: Eric Pettersen <pett(a)cgl.ucsf.edu> > I forgot, there's actually a fourth thing you can do: change the > atom type directly. Select the oxygen atom and open the command line > (Favorites->Command Line) and type: > > setattr a idatmType O3 sel > > which will set the selected atom's "idatmType" attribute to sp3 > oxygen ("O3"). > > Do this before hydrogens are added. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > On Feb 3, 2008, at 1:27 PM, Eric Pettersen wrote: > > > Hi Carlos, > > There are basically three things you can do: > > > > 1) Download the latest daily build and try that. I have been > > working hard on atom typing for ring systems recently (and am still > > working on it) and there's a pretty good chance that it will type > > (and therefore protonate) the phenyl oxygen correctly now. You > > get a daily build by going to the Chimera home page > > (www.cgl.ucsf.edu/chimera) and following the "Daily Builds" link. > > > > 2) Directly edit the structure (after adding hydrogens but before > > adding charges). Control-double-click the oxygen and select > > "Modify Atom" from the pop-up menu. In the resulting dialog change > > the element type to O, the geometry to tetrahedral, and the number > > of bonds to 2. You should also probably change the atom name field > > to be the same as what the atom's name is. Then click the Change > > button and the hydrogen will be added. > > > > 3) Before doing any processing, change the bond length. Control > > double-click on the C-O bond and choose "Set Bond Length" from the > > pop-up menu. Type in a bond length appropriate for a C-O single > > bond and then run the rest of your processing. > > > > --Eric > > > > Eric Pettersen > > UCSF Computer Graphics Lab > > > > On Feb 2, 2008, at 5:19 PM, cpsosa(a)comcast.net wrote: > > > >> > >> Hello, > >> > >> We have the opposite problem, our PDB has one oxygen that is part > >> of a phenyl group and after using addH in Chimera, hydrogen does > >> not get added to that oxygen. Is there a way to add hydrogen to a > >> single atom? using Chimera. For Chimera to add a hydrogen to > >> that O... perhaps making the C-O bond larger. > >> > >> Any suggestions? > >> > >> Thanks, > >> > >> -- > >> Carlos P. Sosa > >> > >> -------------- Original message ---------------------- > >> From: Eric Pettersen <pett(a)cgl.ucsf.edu> > >>> I assume this is IMZ from 1rv1? Chimera is adding a proton to > >>> the N3 > >>> nitrogen that it shouldn't. After adding hydrogens and before > >>> saying > >>> OK to the charge calculation, type this command to Chimera's command > >>> line to delete the extra hydrogen: > >>> > >>> del :IMZ@h3 > >>> > >>> --Eric > >>> > >>> Eric Pettersen > >>> UCSF Computer Graphics Lab > >>> http://www.cgl.ucsf.edu > >>> > >>> > >>>> I could not get the charges for my molecule (ligand in x-crystal > >>>> structure). how to do that? > >>>> I am getting the following error message. > >>>> I am using chimera to do these funtions. > >>>> > >>>> Running ANTECHAMBER command: C:\Program Files\Chimera\bin > >>>> \antechamber\exe\antechamber -i c:\docume~1\thomas\locals~1\temp > >>>> \tmpkzw4il\ante.in.mol2 -fi mol2 -o c:\docume~1\thomas\locals~1 > >>>> \temp > >>>> \tmpkzw4il\ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 > >>>> (IMZ) > >>>> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe > >>>> \bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o > >>>> ANTECHAMBER_BOND_TYPE.AC - > >>>> f ac -j part > >>>> (IMZ) > >>>> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe > >>>> \atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff > >>>> (IMZ) Total number of electrons: 351; net charge: 1 > >>>> (IMZ) INFO: Number of electrons is odd: 351 > >>>> (IMZ) Please check the total charge (-nc flag) and spin > >>>> multiplicity (-m flag) > >>>> Failure running ANTECHAMBER for residue IMZ > >>>> > >>>> > >>>> Thomas > >>> > >>> > >> > >> > >> > >> From: Eric Pettersen <pett(a)cgl.ucsf.edu> > >> Date: January 31, 2008 12:54:24 PM PST > >> To: dock-fans(a)docking.org > >> Subject: Re: [Dock-fans] How to get the charged mol for the ligand > >> > >> > >> I assume this is IMZ from 1rv1? Chimera is adding a proton to the > >> N3 nitrogen that it shouldn't. After adding hydrogens and before > >> saying OK to the charge calculation, type this command to > >> Chimera's command line to delete the extra hydrogen: > >> > >> del :IMZ@h3 > >> > >> --Eric > >> > >> Eric Pettersen > >> UCSF Computer Graphics Lab > >> http://www.cgl.ucsf.edu > >> > >> > >>> I could not get the charges for my molecule (ligand in x-crystal > >>> structure). how to do that? > >>> I am getting the following error message. > >>> I am using chimera to do these funtions. > >>> > >>> Running ANTECHAMBER command: C:\Program Files\Chimera\bin > >>> \antechamber\exe\antechamber -i c:\docume~1\thomas\locals~1\temp > >>> \tmpkzw4il\ante.in.mol2 -fi mol2 -o c:\docume~1\thomas\locals~1 > >>> \temp\tmpkzw4il\ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 > >>> (IMZ) > >>> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe > >>> \bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o > >>> ANTECHAMBER_BOND_TYPE.AC -f ac -j part > >>> (IMZ) > >>> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe > >>> \atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff > >>> (IMZ) Total number of electrons: 351; net charge: 1 > >>> (IMZ) INFO: Number of electrons is odd: 351 > >>> (IMZ) Please check the total charge (-nc flag) and spin > >>> multiplicity (-m flag) > >>> Failure running ANTECHAMBER for residue IMZ > >>> > >>> > >>> Thomas > >> > >> > >> _______________________________________________ > >> Dock-fans mailing list > >> Dock-fans(a)docking.org > >> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans > >> > >> > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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Fwd: Loading prmtop/mdcrd with partial workout
by Francesco Pietra 04 Feb '08

04 Feb '08

What I asked below has no sense. Deleting residues does not freed memory. Of course, because those residues can be resumed. francesco --- Francesco Pietra <chiendarret(a)yahoo.com> wrote: > Date: Fri, 1 Feb 2008 12:49:22 -0800 (PST) > From: Francesco Pietra <chiendarret(a)yahoo.com> > Subject: Loading prmtop/mdcrd with partial workout > To: chimera <chimera-users(a)cgl.ucsf.edu> > > I am experiencing difficulties with Amber ptraj in removing solvent/lipid/box > (i.e., unexpected problems of prmtop fitting after that, though I used a > prmtop > before creating solvent/lipid/box). > > Otherwise, I have memory problems with Chimera in loading such an extensive > MD > (many ns, in various coordinate files) with all the burden of > solvent/lipid/box. > > My question: is that feasible with Chimera to load a coordinate file, remove > solvent and lipid, load a second coordinate file, remove solvent and lipid, > and > so on for all coordinate files? > > Thanks > > francesco pietra > > > > ____________________________________________________________________________________ > Be a better friend, newshound, and > know-it-all with Yahoo! Mobile. Try it now. > http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ > > ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

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Re: [Chimera-users] [Dock-fans] How to get the charged mol for the ligand
by Eric Pettersen 04 Feb '08

04 Feb '08

Hi Carlos, There are basically three things you can do: 1) Download the latest daily build and try that. I have been working hard on atom typing for ring systems recently (and am still working on it) and there's a pretty good chance that it will type (and therefore protonate) the phenyl oxygen correctly now. You get a daily build by going to the Chimera home page (www.cgl.ucsf.edu/ chimera) and following the "Daily Builds" link. 2) Directly edit the structure (after adding hydrogens but before adding charges). Control-double-click the oxygen and select "Modify Atom" from the pop-up menu. In the resulting dialog change the element type to O, the geometry to tetrahedral, and the number of bonds to 2. You should also probably change the atom name field to be the same as what the atom's name is. Then click the Change button and the hydrogen will be added. 3) Before doing any processing, change the bond length. Control double-click on the C-O bond and choose "Set Bond Length" from the pop-up menu. Type in a bond length appropriate for a C-O single bond and then run the rest of your processing. --Eric Eric Pettersen UCSF Computer Graphics Lab On Feb 2, 2008, at 5:19 PM, cpsosa(a)comcast.net wrote: > > Hello, > > We have the opposite problem, our PDB has one oxygen that is part > of a phenyl group and after using addH in Chimera, hydrogen does > not get added to that oxygen. Is there a way to add hydrogen to a > single atom? using Chimera. For Chimera to add a hydrogen to that > O... perhaps making the C-O bond larger. > > Any suggestions? > > Thanks, > > -- > Carlos P. Sosa > > -------------- Original message ---------------------- > From: Eric Pettersen <pett(a)cgl.ucsf.edu> >> I assume this is IMZ from 1rv1? Chimera is adding a proton to the N3 >> nitrogen that it shouldn't. After adding hydrogens and before saying >> OK to the charge calculation, type this command to Chimera's command >> line to delete the extra hydrogen: >> >> del :IMZ@h3 >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> http://www.cgl.ucsf.edu >> >> >>> I could not get the charges for my molecule (ligand in x-crystal >>> structure). how to do that? >>> I am getting the following error message. >>> I am using chimera to do these funtions. >>> >>> Running ANTECHAMBER command: C:\Program Files\Chimera\bin >>> \antechamber\exe\antechamber -i c:\docume~1\thomas\locals~1\temp >>> \tmpkzw4il\ante.in.mol2 -fi mol2 -o c:\docume~1\thomas\locals~1\temp >>> \tmpkzw4il\ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 >>> (IMZ) >>> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe >>> \bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC - >>> f ac -j part >>> (IMZ) >>> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe >>> \atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff >>> (IMZ) Total number of electrons: 351; net charge: 1 >>> (IMZ) INFO: Number of electrons is odd: 351 >>> (IMZ) Please check the total charge (-nc flag) and spin >>> multiplicity (-m flag) >>> Failure running ANTECHAMBER for residue IMZ >>> >>> >>> Thomas >> >> > > > > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Date: January 31, 2008 12:54:24 PM PST > To: dock-fans(a)docking.org > Subject: Re: [Dock-fans] How to get the charged mol for the ligand > > > I assume this is IMZ from 1rv1? Chimera is adding a proton to the > N3 nitrogen that it shouldn't. After adding hydrogens and before > saying OK to the charge calculation, type this command to Chimera's > command line to delete the extra hydrogen: > > del :IMZ@h3 > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > >> I could not get the charges for my molecule (ligand in x-crystal >> structure). how to do that? >> I am getting the following error message. >> I am using chimera to do these funtions. >> >> Running ANTECHAMBER command: C:\Program Files\Chimera\bin >> \antechamber\exe\antechamber -i c:\docume~1\thomas\locals~1\temp >> \tmpkzw4il\ante.in.mol2 -fi mol2 -o c:\docume~1\thomas\locals~1 >> \temp\tmpkzw4il\ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 >> (IMZ) >> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe >> \bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC >> -f ac -j part >> (IMZ) >> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe >> \atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff >> (IMZ) Total number of electrons: 351; net charge: 1 >> (IMZ) INFO: Number of electrons is odd: 351 >> (IMZ) Please check the total charge (-nc flag) and spin >> multiplicity (-m flag) >> Failure running ANTECHAMBER for residue IMZ >> >> >> Thomas > > > _______________________________________________ > Dock-fans mailing list > Dock-fans(a)docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans > >

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