- Chimera-users - RBVI Mailing Lists

Powerpoint
by Beale, John 12 Nov '08

12 Nov '08

Can movies created in Chimera be played in a Powerpoint presentation? If so, how do I set it up? John Beale

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Running a job in chimera
by tuhin＠iitk.ac.in 11 Nov '08

11 Nov '08

Dear All, I have run several simulations. But, I need to analyse a selective number of structures from each simulation saved at a given time step "t". Thus, for a 20ns simulation, starting t=0 and incrementing it by 50ps, I'll have ~400 individual structures. Each structure is within a waterbox, which contains approx. 20,000 water molecules. Once I get the structures, I need to do the following using CHIMERA: 1. Open each structure and save water molecules within a cutoff distance of 5.0 Angstrom from the protein. Thus, I'll end-up having a shell (<=5.0A) of water molecules around the protein. The saved structure will be in .pdb format and include the protein with 5.0A water shell. I know how to do it in CHIMERA using the commandline option/pulldown menu, but, how to do it for 400 structures. Is there a way to run it in a "Batch Job" ? 2. I also need to superimpose Ca-Ca atoms of 400 structures. But, I feel there is a limit to the no. of structures that CHIMERA could handle, thus, at max. I would be superimposing 20-30 structures at a time. How could I automatize the same through a script sothat I could run it in batches? Thanks in advance. Any suggestion(s) is welcomed. Warm regards, Tuhin

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How to make bonds between two pdb files
by Ann Spevacek 06 Nov '08

06 Nov '08

Hello - I am trying to make a bond between a protein and a polysaccharide chain in Chimera and am not quite sure how to do it. I am also curious as to whether the program will take into account interactions such as sterics when it generates the bond. Any guidance will be greatly appreciated! Thanks, Ann Spevacek Millhauser Lab UCSC

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successive minimizations: can we use a unique protein setup?
by Jean Didier Pie Marechal 06 Nov '08

06 Nov '08

Hi everyone, I want to do the following: 1. minimize a region of a structure 2. change some part of the region by hand (like swap a residue) 3. minimize once more. and this 2 or three times. However, each time I want to minimize I have to pass through the all setup of the protein (add H, hist protonation, and so one). Couldn't we keep the information of the first setup and directly fo through the minimization? All the best, JD Dr. Jean-Didier Maréchal Lecturer Computational Bioorganic and Bioionorganic Chemistry @ Transmet 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, Novembre 5, 2008 2:00 am Assumpte: Chimera-users Digest, Vol 67, Issue 4 > 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. Using match (Omar Davulcu) > 2. Re: Using match (Eric Pettersen) > 3. Re: Models or chain (Eric Pettersen) > 4. removing side chains (Matthew Dougherty) > 5. Re: removing side chains (Eric Pettersen) > 6. Re: Using match (Elaine Meng) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Mon, 3 Nov 2008 14:53:19 -0800 > From: "Omar Davulcu" <davulcuo(a)ohsu.edu> > Subject: [Chimera-users] Using match > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <001301c93e06$f7394020$e5abc060$@edu> > Content-Type: text/plain; charset="us-ascii" > > Hi, > > > > I'm using the match command with a cutoff to align specific regions of > related enzymes. It appears to work fine and remove residue pairs > above the > cutoff, but is there a way to list those residue pairs which were > (or were > not) removed? > > > > Thanks for any help! > > Omar Davulcu > >

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Using match
by Omar Davulcu 04 Nov '08

04 Nov '08

Hi, I'm using the match command with a cutoff to align specific regions of related enzymes. It appears to work fine and remove residue pairs above the cutoff, but is there a way to list those residue pairs which were (or were not) removed? Thanks for any help! Omar Davulcu

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removing side chains
by Matthew Dougherty 04 Nov '08

04 Nov '08

I have a session that someone has given me. It consists of 24 monomers in two states, each monomer colored differently. In the model panel I see only two IDs. I need to do a morph showing just the ribbons. Because the overall number of atoms is quite large, I want to strip off the side chains in order to reduce the computation. Is there an easy way to do this? Or do I have to go back to individual monomers, strip off the side chains, recolor, and recombine them, before morphing? thanks, Matt

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Re: [Chimera-users] Models or chain
by Eric Pettersen 04 Nov '08

04 Nov '08

Hernando Sosa wrote: > Hi Elaine, > > The problem I have is actually not with chimera itself. I can > display all the models etc nicely within it. However, I want to make > now a PDB file of a multi-protein complex in a format that can be > deposited in the PDB database. Then I run into problems if the models > are separated by Model ENDMDL lines or have chains with the same > letter > identifier. I was hoping to be able to generate a multi-protein PDB > file from my chimera fitting without having to manually edit a lot of > lines in the multimodel PDB file. Any suggestions on how to best do > this > would be appreciated. > Hi Hernando, Elaine kind of mentioned this in passing in another posting, but you can now do what you wanted to do above with the new "combine" command (also available as the Combine button of the Model Panel). It's in the current daily build and upcoming release candidate/production release. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Coloring snapshots using time as attribute
by Ibrahim Moustafa 03 Nov '08

03 Nov '08

Dear Chimera team, I have several snapshots from simulation loaded as different models. I wonder if there is a way to color them coded according to time as an attribute, e.g. Red-white-blue for t0 -> t. Thanks in advance, Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

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Re: [Chimera-users] How to add change to multiple molecules
by CHIU,YEUNG 03 Nov '08

03 Nov '08

Hi Yang You mean adding "charge"? I think you can add charge to all of the models as long as you check the box referred to them at the bottom. If you want to add charge to some models only, you can ~disp all, then display one by one and add charge to them. I hope this would help. Good luck! On Sun Nov 02 20:32:46 EST 2008, zhouyang <zhouyang(a)mail.shcnc.ac.cn> wrote: > Hi > Recently I wanna add change to a series of molecules for DOCK6 > which are stored in a single .mol2 file. It seems that the > Chimera GUI can just add change for one molecules at one > operation. I wonder how to add change to all of them? > Alternatively I just suppose to use 'split' shell command to > seperate these molecules to single files and then add change to > them. Then the key point is whether Chimera can run in > command-line mode so that I can achieve by writing a shell > script? > Thanks in advance > Yang > zhouyang(a)mail.shcnc.ac.cn > > 2008-11-03 ?????? ZHOU Yang > Master Candidate > Drug Discovery and Design Center > Shanghai Institute of Meteria Medica > China Academy of Sciences > 555 Zu Chong Zhi Road , Zhang Jiang Hi-Tech Park, Shanghai, China > (Postcode: 201203) > > Mobile: 86-137-6430-7897 > MSN: zhouyang_pku(a)hotmail.com > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > Sincerely yours CHIU,YEUNG

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How to add change to multiple molecules
by zhouyang 02 Nov '08

02 Nov '08

Hi Recently I wanna add change to a series of molecules for DOCK6 which are stored in a single .mol2 file. It seems that the Chimera GUI can just add change for one molecules at one operation. I wonder how to add change to all of them? Alternatively I just suppose to use 'split' shell command to seperate these molecules to single files and then add change to them. Then the key point is whether Chimera can run in command-line mode so that I can achieve by writing a shell script? Thanks in advance Yang zhouyang(a)mail.shcnc.ac.cn 2008-11-03 周阳 ZHOU Yang Master Candidate Drug Discovery and Design Center Shanghai Institute of Meteria Medica China Academy of Sciences 555 Zu Chong Zhi Road , Zhang Jiang Hi-Tech Park, Shanghai, China (Postcode: 201203) Mobile: 86-137-6430-7897 MSN: zhouyang_pku(a)hotmail.com

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Fwd: Combining fragments for RESP charges
by Francesco Pietra 31 Oct '08

31 Oct '08

Sorry I used the wrong address for the message below. ---------- Forwarded message ---------- From: Francesco Pietra <chiendarret(a)gmail.com> Date: Fri, Oct 31, 2008 at 8:34 AM Subject: Combining fragments for RESP charges To: chimera-users-request(a)cgl.ucsf.edu I was reading Ross Walker's tutorial A1, in the suite of tutorials for Amber. When deriving RESP charges for an unusual molecule covalently bound to a protein, the unusual molecule is first detached from the protein and then further divided into fragments. RESP charges are derived for the fragments, then the fragments are recombined using Sirius visualization program. The recombined fragments are then attached to the protein, again using Sirius. Can these recombinations be carried out with Chimera? Thanks francesco pietra

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morph-coordinates and camera movements
by Matthew Dougherty 30 Oct '08

30 Oct '08

I was generating a morph of atoms and wanted to rotate the camera 242 degrees on the x axis. I am thinking there may be several ways to do this, such as per-frame script in the morph tool or through the movie recorder script. Is one way better than the other? What would the scripts look like? Thanks, Matt

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directory within Chimera ??
by Barry Lever 30 Oct '08

30 Oct '08

Elaine: I know you are busy .. but as a fairly new user....when I restore a previous session.. can I extract from Chimera, the names of the input data files that were used to create that molecule and subsequent manipulations- I am especially interested to know where I can locate the name of the input geometry file that set up the molecule. In future I will know to include that information in the overall session file name but for now..... Thanks so much Barry -- A. B. P. Lever Distinguished Research Professor Emeritus Chemistry, CB124, York University 4700 Keele St., Toronto, Ont., Canada M3J 1P3 Tel:416-736-2100 x22309 Fax: 416-736-5936 http://www.chem.yorku.ca/profs/lever

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multiple Chimera windows on Mac
by Elaine Meng 30 Oct '08

30 Oct '08

On Oct 30, 2008, at 8:07 AM, Chin-Hsien (Emily) Tai wrote: > > One quick question, is there any way to have several sessions of > Chimera running at the same time so that we can compare/rotate > different domain parsing results of the same structure at the same > time? > Hi Emily, I assume you are using a Mac... Yes, you can have multiple Chimera instances, as many as you want, if you start Chimera from the Terminal window. For example, I have Chimera version 1.2540 installed as /Applications/Chimera2540, so to start it from Terminal I would type: /Applications/Chimera2540.app/Contents/MacOS/chimera Actually I don't really type that because it is too troublesome, and instead have an alias in my home directory .tcshrc file (or .cshrc file). If you don't have either of these files you can just create a file by that name in your home directory and put the alias in it, in my case: alias chimera /Applications/Chimera2540.app/Contents/MacOS/chimera Then after you source that file or log in again, simply typing "chimera" (or whatever you used as the alias) starts Chimera. In a second Terminal window, you can enter "chimera" for a second running Chimera, etc. I have multiple different Chimera versions with different aliases, for example, a recent daily build is on my Desktop: alias chinew ~/Desktop/Chimera.app/Contents/MacOS/chimera Even if you have only one version, you can start it as many times as you want from different Terminal windows. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) 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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scripts in Chimera
by Ben Keshet 29 Oct '08

29 Oct '08

Hi, I am reviewing a large number of structures (docking results). I uses the ViewDock tool which is great and makes life much easier. Still, for every file I open with ViewDock, I repeat the same set of commands before actually reviewing the poses, that is (initially only the receptor structure is open, with only ribbon shown): 1. open the ligands mol2 file. 2. color by element 3. choose atoms within 6A from the ligands (by selecting the ligand, than select zone<6A). 4. show the selected atoms. This is to show only receptor atoms within 6A of the ligand. Is there a way I can "record" this sequence or write some simple script that I could run after opening the ligands mol2 file? Thanks! Ben

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volume planes display loop
by Benoit Zuber 28 Oct '08

28 Oct '08

Hi, I have got some questions regarding plane display of volumes: Is there a way to cycle through a limited range of planes? For example if the thickness of my volume is 300, is it possible to cycle from z = 100 to z = 120, instead of from z = 0 to z = 299? Is there a way to make the cycling through the planes start in the other direction than when it stopped last time? For example, I click stop while the display is cycling from low z value to high z value. If I then click start, the display is going to cycle again from low to high z value but I would like it to cycle from high to low z value. Is it possible to specify a starting plane and an end plane, and to have the display going from the starting plane to the end plane only once (without cycling)? Finally, can all of this be specified through the command line? Cheers, Ben Benoît Zuber MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH United Kingdom +44 1223 402209 bzuber(a)mrc-lmb.cam.ac.uk

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Flushing output during the script execution
by Lukas Palatinus 27 Oct '08

27 Oct '08

Hello all, I am using Chimera as a visualization tool for small-molecule electron densities obtained by ab initio structure solution. I want to create a small script that will make Chimera read and display the intermediate electron densities as they are produced during the iterative structure solution process. I am not skilled in Python, but I could make a simple Python script by copying and modifying scripts previously posted in this list. Here is the script: from chimera import runCommand as run from os.path import exists from time import sleep map_file= 'test.xplor' while exists(map_file): run('close all') run('open ' + map_file) sleep(1) I am sure this is not the most elegant way to achieve what I need, but it should do the job. What the script should in my opinion do is to read and display the file test.xplor, then wait one second, close the map and reopen it again, until the file test.xplor is deleted. The script does >>almost<< that, it opens the volume viewer, reads the map, but it does not display the map in the main Chimera window. Only after the file test.xplor is deleted, the last map is displayed. Can anybody give me a hint what am I doing wrong? I am using Chimera 1.2540 on Mac OS X 10.4. Thanks in advance for any help. Best regards Lukas Lukas Palatinus Laboratoire de Cristallographie EPFL Lausanne Tel.: +41 (0)21 693 0639 mailto: palat(a)fzu.cz

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forget previous error
by Jean Didier Pie Marechal 27 Oct '08

27 Oct '08

Sorry, I made a mistake and found my problem. All the best JD Dr. Jean-Didier Maréchal Lecturer Computational Bioorganic and Bioionorganic Chemistry @ Transmet 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: Divendres, Octubre 24, 2008 9:00 pm Assumpte: Chimera-users Digest, Vol 66, Issue 22 > 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. volume planes display loop (Benoit Zuber) > 2. Re: volume planes display loop (Tom Goddard) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Fri, 24 Oct 2008 16:36:42 +0100 > From: Benoit Zuber <bzuber(a)mrc-lmb.cam.ac.uk> > Subject: [Chimera-users] volume planes display loop > To: chimera users list <chimera-users(a)cgl.ucsf.edu> > Message-ID: <4901EB8A.9040102(a)mrc-lmb.cam.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi, > > I have got some questions regarding plane display of volumes: > Is there a way to cycle through a limited range of planes? For > example > if the thickness of my volume is 300, is it possible to cycle from > z = > 100 to z = 120, instead of from z = 0 to z = 299? > > Is there a way to make the cycling through the planes start in the > other > direction than when it stopped last time? For example, I click stop > while the display is cycling from low z value to high z value. If I > then > click start, the display is going to cycle again from low to high z > value but I would like it to cycle from high to low z value. > > Is it possible to specify a starting plane and an end plane, and to > have > the display going from the starting plane to the end plane only > once > (without cycling)? > > Finally, can all of this be specified through the command line? > > Cheers, > Ben > > > Beno?t Zuber > MRC Laboratory of Molecular Biology > Hills Road > Cambridge > CB2 0QH > United Kingdom > +44 1223 402209 > bzuber(a)mrc-lmb.cam.ac.uk > > > > ------------------------------ > > Message: 2 > Date: Fri, 24 Oct 2008 10:31:44 -0700 > From: Tom Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] volume planes display loop > To: Benoit Zuber <bzuber(a)mrc-lmb.cam.ac.uk> > Cc: chimera users list <chimera-users(a)cgl.ucsf.edu> > Message-ID: <49020680.2070802(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Ben, > > The current Chimera daily builds have a more flexible volume > plane > cycling interface. In the planes panel it now has a switch > > Cycle through [20] planes at speed [30] > > It lets you play through a specified number of planes centered on > the > currently shown plane. You start it by clicking a switch and stop > it > the same way. There is no control to stop after N planes, and the > initial direction of play is the same as when you last stopped > playback. > There is currently no Chimera command equivalent which would > obviously > be handy for making movies. I've attached a Python script which > can be > used with Chimera commands (example given in script) to control > exactly > which frames to show in a movie. Note that the frame rate is only > relevant for real-time cycling in Chimera. Movie recording > captures > every new frame no matter how slow they are rendered and plays in a > movie player at 25 frames per second (adjustable with a movie > encode > command option). Chimera movie recording capabilities are very > limited > now but it is an area we intend to improve. > > Tom > > > Benoit Zuber wrote: > > Hi, > > > > I have got some questions regarding plane display of volumes: > > Is there a way to cycle through a limited range of planes? For > example > > if the thickness of my volume is 300, is it possible to cycle > from z = > > 100 to z = 120, instead of from z = 0 to z = 299? > > > > Is there a way to make the cycling through the planes start in > the other > > direction than when it stopped last time? For example, I click > stop > > while the display is cycling from low z value to high z value. If > I then > > click start, the display is going to cycle again from low to high > z > > value but I would like it to cycle from high to low z value. > > > > Is it possible to specify a starting plane and an end plane, and > to have > > the display going from the starting plane to the end plane only > once > > (without cycling)? > > > > Finally, can all of this be specified through the command line? > > > > Cheers, > > Ben > > > > > > Beno?t Zuber > > MRC Laboratory of Molecular Biology > > Hills Road > > Cambridge > > CB2 0QH > > United Kingdom > > +44 1223 402209 > > bzuber(a)mrc-lmb.cam.ac.uk > > > > _______________________________________________ > > 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 66, Issue 22 > ********************************************* >

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Problem with sum?
by Jean Didier Pie Marechal 27 Oct '08

27 Oct '08

Hi guys, I got back to the script on inertia axis calculation and I had the following error when running it on the built of th 15/10/2008 on my linux box: Traceback (most recent call last): File "/home/jd/Desktop/scripts/chimera/inertia_model.py", line 73, in <module> axes, d2, center = inertia_ellipsoid(m) File "/home/jd/Desktop/scripts/chimera/inertia_model.py", line 13, in inertia_ellipsoid mass = sum(amass) TypeError: 'float' object is not callable then I just try in the python shell: i=[1,2,3] sum(i) and I have the same prob. sum(i) Traceback (most recent call last): File "<pyshell#38>", line 1, in <module> sum(i) TypeError: 'float' object is not callable Some input? all the best JD Dr. Jean-Didier Maréchal Lecturer Computational Bioorganic and Bioionorganic Chemistry @ Transmet 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, Març 19, 2008 8:43 pm Assumpte: Chimera-users Digest, Vol 59, Issue 19 > 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: Principal axis of inertia (Tom Goddard) > 2. problem with 17/03 build linux 64 (Jean-Didier Mar?chal) > 3. Un-tile (Jim Nettles) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Wed, 19 Mar 2008 12:00:33 -0700 > From: Tom Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Principal axis of inertia > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > Cc: 'Chimera BB' <chimera-users(a)cgl.ucsf.edu> > Message-ID: <47E162D1.5070108(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Eric, > > Just ignorance -- didn't know Chimera could tell me the atomic > mass. > Attached is the same script only using atomic mass instead of > atomic number. > > Tom > > Eric Pettersen wrote: > > Just wondering why you weighted by atomic number rather than mass > > > (a.element.mass)? > > > > --Eric > > > >

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Re: [Chimera-users] coloring seperate domains
by Elaine Meng 23 Oct '08

23 Oct '08

On Oct 22, 2008, at 1:52 PM, Chin-Hsien (Emily) Tai wrote: > > We would like to use Chimera as a visualizing/figure drawing tool to > compare different domain parsing schemes and we are wondering how to > automate the process as much as possible. The tasks are: > 1.fetch a PDB > 2.select Chain (for example B) > 3.Invert (all models) > 4.Atoms/Bonds delete > 5.chain trace only > 6.backbone only > 7.Ribbon show rounded > > I am wondering if there is a simple way to combine step 1 to 4 to > display only specified chain in PDB? > Then rotate the structure to minimize domain overlapped area. > > Then color each domain according to different parsing schemes, for > example: > scheme1 "color red #0:1-38.A 150-190.A; color green #0:39-149.A; > color blue #0:192-347" > scheme2 "color red #0:1-30.A 160-195.A; color green #0:31-159.A; > color blue #0:196-347" > > Can Chimera read a script and displays different domains in > different colors? > Thanks for your advice in advance! > Cheers, > Emily, Dear Emily, You can definitely do all those steps in a script, except I'm not sure how to automatically orient the structure to best show the domains. I'll discuss the other parts first. A Chimera command script is just a text file containing the same things you would enter at the command line. If you name the file something.com or something.cmd it will automatically execute when opened in Chimera (with File... Open or the command "open"). Chimera can also execute python scripts (something.py) in the same way. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile > There are many possibilities for either type of script, but here are some example Chimera commands: open 2mnr delete ~ :.a ribbon ribrep rounded ~disp color red :3-132 color dodger blue :133-359 copy png file 2mnr.png This set of commands fetches PDB structure 2mnr, deletes everything that is NOT chain A, displays ribbon, uses the rounded ribbon style, undisplays all atoms, colors the specified residue ranges, and saves an image in PNG format. You don't have to specify the chain in the coloring command since there is only one chain left. Each of these commands has a manual page if you want to see details (for example, there are other image formats such as TIFF). You can try the commands in the Command Line to see what works before putting them into a script. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecommand.html> For saving images, you might want to make the background white (set bg_color white) before using the script, or after opening each structure use the ribbons preset and then a publication preset (preset apply int 1; preset apply pub 1) instead of ribbon and ribrep rounded. <http://www.cgl.ucsf.edu/home/meng/docs/UsersGuide/print.html#tips> There are some fancier approaches that may facilitate processing a large number of structures. You can separate the structure-specific and general commands using aliases: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html> alias mypdb 2mnr alias mychain :.a alias dom1 :3-132 alias dom2 :133-359 ~alias dom3 ~alias dom4 alias output /Users/meng/Desktop/2mnr.png # # the following general commands could be put in a separate file # open mypdb delete ~ mychain preset apply int 1 preset apply pub 1 color red dom1 color dodger blue dom2 color yellow dom3 color magenta dom4 copy png file output close 0 This structure only has two domains, so I clear any previous dom3 and dom4 assignments from previous structures. There will be error messages when commands refer to nonexistent aliases, but they can be ignored. The reason you might want to separate the specific and general commands is that all of the general commands can then be put in a second command file (for example named "process.com" ) that is opened by the first script. The second script file could be in the same directory (folder) as the first, or you could specify its whole pathname. alias mypdb 2mnr alias mychain :.a alias dom1 :3-132 alias dom2 :133-359 ~alias dom3 ~alias dom4 alias output /Users/meng/Desktop/2mnr.png open /Users/meng/Desktop/process.com # # now go to next structure # alias mypdb 4enl alias mychain :.a alias dom1 :1-141 alias dom2 :142-436 ~alias dom3 ~alias dom4 alias output /Users/meng/Desktop/4enl.png open /Users/meng/Desktop/process.com [... etc.] Putting the general commands in a separate file minimizes the number of lines in the primary command file. However, it may still be tedious if you are processing a very large number of structures. Since I don't know python, I would probably write a script or program (in some other language) to make the long main Chimera command file. If you know python, another approach is to make the main script python instead of Chimera commands, and have it cycle through multiple structures. You could call the Chimera commands in my examples from inside the python script. Finally, now about orienting the structure to best show the domains. The only way I can think of with Chimera commands is to use "align" to put domains 1 and 2 front and back, then rotate 90 degrees, for example: align dom1 dom2 turn y 90 That worked pretty well in my tests. Those commands could be in the general script (process.com in my example), assuming all the structures have at least two domains, before the image-saving command. There are some other possibilities that require python; I'll get back to you if we come up with something good. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) 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] Chimera-users Digest, Vol 66, Issue 20
by Ibrahim Moustafa 22 Oct '08

22 Oct '08

Hi All, I figured it out. The problem turned to be the resolution of the files that did not play in the powerpoint. Editing the movie to have a lower resolution enabled the file to play fine in the powerpoint. I wonder if there can be an option to determine the resolution in the output file from Chimera to avoid such problems with powerpoint and also, this can be added to the tips on Chimera site for making the movie for use in powerpoint: "make sure of the produced file to match the projector and the computer. Usually, something like 800x600 should work" Thanks to Elaine for her help. Ibrahim On 10/22/08 3:00 PM, "chimera-users-request(a)cgl.ucsf.edu" <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. Question about movie in powerpoint (Ibrahim Moustafa) > 2. Re: Question about movie in powerpoint (Elaine Meng) > 3. Re: orthogonal views (Elaine Meng) > 4. Re: orthogonal views (Tom Goddard) > 5. Re: orthogonal views (Greg Couch) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 22 Oct 2008 13:05:51 -0400 > From: Ibrahim Moustafa <I.moustafa(a)psu.edu> > Subject: [Chimera-users] Question about movie in powerpoint > To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Message-ID: <C524D5AF.343C%I.moustafa(a)psu.edu> > Content-Type: text/plain; charset="us-ascii" > > Dear Chimera team who is always giving the best support, > > I have a question regarding movie playing in power point and hope you can > help. > > I'm setting a power point presentation and want to play some movie (.avi > MSMPEG-4v2), created in Chimera, in the presentation. The movie play fine; > however, if I'm in the presenter view mode it does not play and gives me a > black screen. > I tried to re-insert the movie, change the view size, put everything in the > same place...but none of these solved the problem. > > The funny thing is that other movies bigger in size can play fine in the > presenter view mode. These have the same format (avi MSMPEG-4v2) and created > using the same program. > > Do you have any idea how to resolve this issue? Any advice is more than > welcome. > > Also, I noticed that sometimes the movie, that is known to be working > fine, does not work for unknown reason. > Especially in the case of 2 movies in the same slide. Any tips to have two > movies in the same slide to work in a more robust way is really appreciated. > > Really appreciating your help, thanks; > Ibrahim

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orthogonal views
by Thomas C. Marlovits 22 Oct '08

22 Oct '08

Hi Chimera's ... is there an easy way to create orthogonal views at the same time of a molecule ? The idea is to open a (pdb) file and visualize the molecule from orthogonal directions at the same time in one viewer. Rotation/ movemements of the molecule should be done then on all three views at the same time of course. Maybe you have already implemented such an option (similar to the stereo viewing ...) Tx, -T. ------------------------------------------------------------------------ ------- Thomas C. Marlovits, PhD, M.A.S. Research Group Leader IMP-IMBA Research Center - Research Institute of Molecular Pathology (IMP) - Institute of Molecular Biotechnology, Austrian Academy of Sciences (IMBA) Dr. Bohr-Gasse 3 Room IMBA/6.02 A-1030 Vienna Austria, Europe fone: (++43-1) 79044-4630 fax: (++43-1) 79044-4401 email: marlovits(a)imp.univie.ac.at

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Question about movie in powerpoint
by Ibrahim Moustafa 22 Oct '08

22 Oct '08

Dear Chimera team who is always giving the best support, I have a question regarding movie playing in power point and hope you can help. I'm setting a power point presentation and want to play some movie (.avi MSMPEG-4v2), created in Chimera, in the presentation. The movie play fine; however, if I'm in the presenter view mode it does not play and gives me a black screen. I tried to re-insert the movie, change the view size, put everything in the same place...but none of these solved the problem. The funny thing is that other movies bigger in size can play fine in the presenter view mode. These have the same format (avi MSMPEG-4v2) and created using the same program. Do you have any idea how to resolve this issue? Any advice is more than welcome. Also, I noticed that sometimes the movie, that is known to be working fine, does not work for unknown reason. Especially in the case of 2 movies in the same slide. Any tips to have two movies in the same slide to work in a more robust way is really appreciated. Really appreciating your help, thanks; Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

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About Amber residue number renumbering
by Francesco Pietra 22 Oct '08

22 Oct '08

Hi Elaine: At the end of a long journey of ACE/NME capping a fractionated model, I would not leave the impression that I like the way Amber treats the layout of pdb files. With Chimera I had all HETATM capping groups on one side and the ATOM of protein stretches on another side, conserving the residue number they had in the unabridged model. Straightforward to relate to the starting crystallographic work Now, after Amber forced (forced against me) manipulation, the ACE/NMR residues are intermingled with the standard amino acid, all ATOM, and take part to the overall sequential numbering. As the number of atoms in ACE differs from NME, and the stretches are many, headache in relating residue numbers imposed by Amber to residue numbers in the original crystallographic work from which I started. Regards francesco pietra

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Error when fetching pdb by ID
by Kenward Vaughan 21 Oct '08

21 Oct '08

Hmm... is this my system or outside it? I'm at home behind a firewall and have never seen such an error before. I'm not sure where I should look for an answer... Fetch by ID. The error log: Opening 1ai2 Error reading 1ai2: Error during PDB fetch: [Errno socket error] (-2, 'Name or service not known') Done opening 1ai2 It doesn't fail at work, so I'm suspicious of my home network. ??? Both my workstation and gateway/firewall are Debian/Sid boxes. What port is the call made on?? Thanks for any ideas! Kenward -- ."^~;,_ Dr. Kenward Vaughan `:,'~~~~~ Professor of Chemistry \;:/ Chair, Physical Science Department |,;| Bakersfield College / ', \ 1801 Panorama Drive / o O \ Bakersfield, CA 93305 (oOoOOoOo) http://www2.bc.cc.ca.us/kvaughan ---========--- ???$$MM$$???

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Fwd: Pruning pdb graphically
by Francesco Pietra 21 Oct '08

21 Oct '08

Hi Elaine: LEaP does not understand capping, with a pdb file that Chimera understands perfectly. I have asked for light at both the Amber and Dock sites. Even Dock uses LEaP for amber score. LEaP adds and exta H to the terminal/beginning and OXT to the terminal/last. Moreover, it tries to join the first ACE with last NME. I have not tried separating the capping residue with TER. francesco ---------- Forwarded message ---------- From: Francesco Pietra <chiendarret(a)gmail.com> Date: Tue, Oct 21, 2008 at 10:34 AM Subject: Re: [Chimera-users] Pruning pdb graphically To: Elaine Meng <meng(a)cgl.ucsf.edu> Hi Elaine: I had fully protonated histidine and left the chain amino group of lysine in basic form! No excuse for that. Now the charge is 5.0000 so that I expect that dockprep (avoiding add-h!) will work. In my (brief) experience, Chimera is an excellent tool also for capping, especially if Add-H is revised for the cases of capped residues. In some cases (12 residues capped in my case) that is important. Also because I want to run MD under various pH conditions, so that capping will change (constant pH MD is not possible with Amber under explicit medium conditions). That Amber has updated to PDB rules is good news. Perhaps I was so suspicious because a few days ago I found a bug with the latest version of ambpdb (Amber's tool to get a pdb file from inpcr/prmtop): the N-hydrogen names for LEU as first residue are written incorrectly. A revised ambpdb is forthcoming. Regards francesco On Tue, Oct 21, 2008 at 12:49 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > After looking at more parameter files, I now believe that Amber and PDB atom > names in standard residues, including hydrogens, are the same. My previous > information was old (I haven't run Amber for 10 years!), sorry about that. > You would still need to worry about correctly naming any atoms changed or > added with Build Structure, though. > > Besides the Amber *lib files mentioned before, you can also look up the > standard atom names in the links from this PDB page: > http://remediation.wwpdb.org/downloads.html > > Elaine > > > On Oct 20, 2008, at 2:39 PM, Elaine Meng wrote: > >> I forgot to mention that usually you don't need to worry about the atom >> names, as Add Charge knows which PDB names go with which Amber >> names/charges, and AddH uses the standard names. >> >> I think you only have to worry about the names of atoms that were changed >> or added "manually" in Build Structure, and if the nonhydrogen atoms have >> the standard names (PDB = Amber for nonhydrogen atoms in standard residues), >> AddH will use correct names for the hydrogens later added to those atoms. >> If you use hydrogens added by Build Structure, however, you have to fix >> their names. >> >> Elaine >> >> > >

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Residue Accessibility
by Luis Alberto Alvarez 21 Oct '08

21 Oct '08

Hello, I am trying to calculate the relative surface accessibility of residues (It will come to getting the solvent accessibility I guess) and the only information I found is from a post in the mailing list dating to 2005 ( http://www.cgl.ucsf.edu/pipermail/chimera-users/2005-October/000482.html)I am just wondering if there is anything new in this front or I should just follow the 2005 instructions. Thank you -- Luis Alvarez alvarez(a)lcp.u-psud.fr Laboratoire de Chimie Physique Université Paris-Sud à Orsay microscope: 01 69 15 30 31 (80% du temps) bureau: 01 69 15 56 15

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Presets and multiple structures
by James Nettles 16 Oct '08

16 Oct '08

Something that often comes up is that I have some number of aligned protein structures with nicely color coded secondary features and specific side chains. I then want to fit another molecule in this same space and apply a "preset" graphic mode to the new structure without undoing the previous molecular views. I expect this is possible, but I haven't gotten it to work yet. I've tried making only my molecule of interest "active" in the Model Panel, but the preset still effects everything. I'm using Alpha build 2557 2008/09/13 at the moment. Thanks, Jim ________________________________________________________ James Nettles, Ph. D. Assistant Professor Department of Pediatrics, Emory University School of Medicine Laboratory of Biochemical Pharmacology (LOBP) Computer Assisted Discovery Research Environment (CADRE) ________________________________________________________

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Building ACE, NME (peptide caps)
by Elaine Meng 16 Oct '08

16 Oct '08

On Oct 16, 2008, at 6:22 AM, Francesco Pietra wrote: > Hi Elaine: > Thanks. > Is it possible with Chimera to cap the the protein termini (once the > work below is carried out) with ACE and NMA residues? I have no > experience with such a procedure. > francesco Hi Francesco, I wouldn't recommend doing it in Chimera. If you are using AMBER anyway, do it with that program. In Chimera, you could do it by using Build Structure (under Tools... Structure Editing), Modify Atom section. It would take several cycles of atom modification, being careful to name the residues ACE and NME and to give the atoms the correct types and names as you build out. For the first atom in the new residue you would use "change modified residue's name to ACE" (or NME) and then for the rest of the atoms in the residue, leave the residue name unchanged. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht… > Then, because the names of hydrogens added while building aren't standard for those residues, either delete all the hydrogens and re- add them using AddH, or use Modify Atom to change the hydrogen names to what AMBER expects (shown below), or just write out the file and use a text-editor to change their names. It is easy to make mistakes in this long process. In addition, I just found a bug where addh still thinks the first amino acid has a free N-terminus even though it is capped by ACE, so if you use addh, you would then have to delete the two hydrogens on the first amino acid's nitrogen and then use Build Structure (Modify Atom) on that nitrogen to make it trigonal and get one hydrogen back, and then change the name of that hydrogen to H. THEN you would get correct charges from addcharge. The atom names that AMBER (and addcharge) expect: for ACE: C O CH3 HH31 HH32 HH33 for NME: N H CH3 HH31 HH32 HH33 If you are capping the residues to avoid terminal charges on residues that are not really the termini, there is no need to do this. AddH looks at the SEQRES information in the file to decide what is really a terminal residue. If it is not a real terminus (for example, the structure starts at residue 5 because 1-4 are disordered), the residue will still be treated as an internal residue starting with NH-CA- (etc.) not as NH3+-CA-(etc.). The C-terminus is handled similarly, (...)C(=O) if not a real terminus instead of (...)CO2 minus for the real C-terminus. Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) 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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imposing symmetry
by Anindito Sen 16 Oct '08

16 Oct '08

Hi I have a density map with symmetry C8. I have docked the monomer crystal structure. I was wondering if there is any way I can put crystal structures in rest of the 7 monomers without doing it manually. Thanks for your reply in advance. Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908

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error
by Linnemayr Charlotte 16 Oct '08

16 Oct '08

Hello, I have a problem opening a file, I got it from a friend, who also installed chimera recently. On her computer it works nicly. But I get an errormessage and a white window, with some of the files text. I see the model for about 2 seconds, before the window turns white. Do I need an extra plugin?

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Contact mapping
by Beale, John 16 Oct '08

16 Oct '08

Is there a way in Chimera to generate interresidue contact maps for proteins from MD data? Thanks! John M. Beale, Ph,D, Associate Professor of Medicinal Chemistry and Pharmaceutics St. Louis College of Pharmacy 4588 Parkview Place St. Louis, Missouri 63110 (314)-446-8461 Cell: (314)-315-0409 FAX (314) 446-8460 jbeale(a)stlcop.edu

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automating ensemble clustering in chimera
by Katryna Cisek 15 Oct '08

15 Oct '08

Dear Chimera Users, How can I automate/import the Ensemble Cluster (Structure Comparison, MD/Ensemble Analysis; cluster members of a conformational ensemble, determine cluster representatives) module into a python script? Thanks, Katryna

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Regarding blender
by Dr. Jean-Didier Maréchal 15 Oct '08

15 Oct '08

Hi guys, I saw on the mailing list some information on exporting/importing 3D files. However, I can't really figure out what would be the best way to export chimera scene so that blender can import them. Is the x3d format the best? Which plug-in do you use? Is there another way better? Cheers, JD -----Mensaje original----- De: chimera-users-bounces(a)cgl.ucsf.edu [mailto:chimera-users-bounces@cgl.ucsf.edu] En nombre de chimera-users-request(a)cgl.ucsf.edu Enviado el: lunes, 13 de octubre de 2008 21:00 Para: chimera-users(a)cgl.ucsf.edu Asunto: Chimera-users Digest, Vol 66, Issue 12 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: Helix-Numbers (skmolugu(a)miners.utep.edu) 2. automating ensemble clustering in chimera (Katryna Cisek) 3. Re: Printing on white background (Elaine Meng) 4. Re: Helix-Numbers (Elaine Meng) 5. Re: save reply log from chimera python script (Katryna Cisek) 6. Re: Pruning pdb graphically (Elaine Meng) 7. Re: save reply log from chimera python script (Thomas Goddard) ---------------------------------------------------------------------- Message: 1 Date: Sun, 12 Oct 2008 13:21:53 -0600 From: <skmolugu(a)miners.utep.edu> Subject: Re: [Chimera-users] Helix-Numbers To: chimera users <chimera-users(a)cgl.ucsf.edu> Message-ID: <BLU105-W44550A870C50C9AE487BFD85370(a)phx.gbl> Content-Type: text/plain; charset="iso-8859-1" Hi, I was wondering if there is a way in chimera for numbering the helices in the map fitted with coordinates. I Basically wanted to explain the location of helix in the map by means of numbering it, so that it will be easy for me to explain in my paper. thank you very much for your time, sudheer. ------------------------------ Message: 2 Date: Sun, 12 Oct 2008 15:42:47 -0400 From: "Katryna Cisek" <cisek.2(a)osu.edu> Subject: [Chimera-users] automating ensemble clustering in chimera To: chimera-users <chimera-users(a)cgl.ucsf.edu> Message-ID: <1bd6604c0810121242j2c9b4d48kc030b8a225af66d9(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Dear Chimera Users, How can I automate/import the Ensemble Cluster (Structure Comparison, MD/Ensemble Analysis; cluster members of a conformational ensemble, determine cluster representatives) module into a python script? Thanks, Katryna ------------------------------ Message: 3 Date: Sun, 12 Oct 2008 13:09:33 -0700 From: Elaine Meng <meng(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Printing on white background To: Christian Schudoma <Schudoma(a)mpimp-golm.mpg.de>, Francesco Pietra <chiendarret(a)gmail.com> Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> Message-ID: <350D2312-C5FB-4B46-B6B5-023FE8BA7875(a)cgl.ucsf.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Thanks, Christian! Besides the ways you mentioned, there is also the "set" command, for example: set bg_color white <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/set.html> Francesco and others may also be interested in the "tips on preparing images" page, which covers background color and other issues: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/print.html#tips> 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 Oct 12, 2008, at 8:50 AM, Christian Schudoma wrote: > Hi Francesco, > you can change the background colour in Chimera: Actions->Color- > >background, then Actions->Color->[choose your colour like you would > for colouring atoms etc.]. > Then just save your image as usual and it should be on a white > background. > > Also, some of the Publication Options in the Presets menu > automatically set the background colour to white. > > Maybe there is a command line call for changing the background as > well? I don't know... > Cheers, > Christian > ________________________________________ > From: chimera-users-bounces(a)cgl.ucsf.edu [chimera-users-bounces(a)cgl.ucsf.edu > ] On Behalf Of Francesco Pietra [chiendarret(a)gmail.com] > Sent: 12 October 2008 12:44 > To: chimera > Subject: [Chimera-users] Printing on white background > > When mapping protein residues around a ligand I would like to have a > printout of the enlarged binding site area, so as to put remarks by > pencil on the printout. However, on a white background, in order to > save ink. Is that a problem of working out the image (I have Gimp > only, of which I never gained expertise), or can Chimera provide > directly? > > Thanks > francesco pietra ------------------------------ Message: 4 Date: Sun, 12 Oct 2008 13:26:20 -0700 From: Elaine Meng <meng(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Helix-Numbers To: <skmolugu(a)miners.utep.edu> Cc: chimera users <chimera-users(a)cgl.ucsf.edu> Message-ID: <F5081034-A931-431B-B612-2A930580D98F(a)cgl.ucsf.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Hi Sudheer, Sounds like you want 2D labels (Tools... Utilities... 2D Labels): <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels. html > Since these labels don't move when you rotate the structure, you would first find the position you want to show in your figure, and then add the labels. Alternatively, for labels in 3D that move with the structure, you could just label one atom in each helix and then manually change what is in the label (for example with "Actions... Label... other..."). However, for figures I think 2D labels are much better, since they allow more control over location and can include symbols such as Greek letters, and it is easier to change their sizes and colors. Some example images with 2D labels: <http://www.cgl.ucsf.edu/chimera/feature_highlights/2gbp-bfactor.png> <http://www.cgl.ucsf.edu/chimera/feature_highlights/2fma-density.png> <http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/cavities/cavities-larg e.png > Best, 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 Oct 12, 2008, at 12:21 PM, <skmolugu(a)miners.utep.edu> wrote: > Hi, > I was wondering if there is a way in chimera for numbering the > helices in the map fitted with coordinates. I Basically wanted to > explain the location of helix in the map by means of numbering it, > so that it will be easy for me to explain in my paper. > thank you very much for your time, > sudheer. ------------------------------ Message: 5 Date: Mon, 13 Oct 2008 12:22:59 -0400 From: "Katryna Cisek" <cisek.2(a)osu.edu> Subject: Re: [Chimera-users] save reply log from chimera python script To: "Tom Goddard" <goddard(a)cgl.ucsf.edu> Cc: chimera-users(a)cgl.ucsf.edu Message-ID: <1bd6604c0810130922m35b031c4sc4694d7e46f6ce81(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Chimera Users, Could someone please point out the syntax error in this code: def save_reply_log("/tmp/tmplog.txt"): <<--- error should be here based on error info from chimera import dialogs r = dialogs.find('reply') text = r.text.get('1.0', 'end') f = open('/tmp/tmplog.txt', 'w') f.write(text) f.close() ---------------------------chimera error info from reply log------------------------------- <type 'exceptions.SyntaxError'> Exception in Tk callback Function: <function command at 0x132d230> (type: <type 'function'>) Args: () Traceback (innermost last): File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ None File "CHIMERA/share/chimera/baseDialog.py", line 244, in command None File "CHIMERA/share/chimera/baseDialog.py", line 453, in OK None File "CHIMERA/share/OpenSave/__init__.py", line 161, in Apply None File "CHIMERA/share/SimpleSession/gui.py", line 41, in _openCB None File "CHIMERA/share/chimera/__init__.py", line 1344, in open None File "CHIMERA/share/chimera/__init__.py", line 787, in _openPython None <type 'exceptions.SyntaxError'>: invalid syntax (refalignrotatewholesymmetrysavelog.py, line 58) -------------- Thanks, Katryna On Wed, Oct 8, 2008 at 10:33 PM, Tom Goddard <goddard(a)cgl.ucsf.edu> wrote: > Hi Katryna, > > I don't think there is a command to save the text in the reply log. In the > Python function the variable path is the path to the file, for example > "/tmp/mylog.txt". > > Tom > > > Katryna Cisek wrote: >> >> Hi Chimera users, >> Is there a new way to save the reply log from a chimera python script, >> other than below (from Chimera Archive 2006)? >> >> def save_reply_log(path): >> from chimera import dialogs >> r = dialogs.find('reply') >> text = r.text.get('1.0', 'end') >> f = open(path, 'w') >> f.write(text) >> f.close() >> >> If not, what is the filename given to the reply log in this function? >> Is it possible to >> designate the name? >> Thanks, >> Katryna >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > ------------------------------ Message: 6 Date: Mon, 13 Oct 2008 10:02:10 -0700 From: Elaine Meng <meng(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] Pruning pdb graphically To: "Francesco Pietra" <chiendarret(a)gmail.com> Cc: chimera <chimera-users(a)cgl.ucsf.edu> Message-ID: <DD923F0C-8D7F-478E-991A-FD8E054B7E81(a)cgl.ucsf.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Hi Francesco, As usual in Chimera, there are several possible ways to do this, and what is "best" depends not only on what you plan to do with the result, but also your personal preferences and working style. I would probably start by using either zones or Find Clashes/Contacts with a conservative cutoff to select all the residues you want to keep, which would probably also include several extra residues. If you used Find Clashes/Contacts, one option selects the contacting atoms, and you would press the keyboard up arrow to promote the selection to whole residues. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#zones > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclas h.html > Next, invert the selection (for example with Select... Invert (all models)) to include the residues you do NOT want, then undisplay them (for example with Actions... Atoms/Bonds... hide). Then you can manually get rid of the few extra residues here and there: Ctrl-click to select one atom or bond in an unwanted residue, press keyboard up arrow to promote to whole residue, undisplay as before. Repeat as needed. I don't know if you meant you wanted to just undisplay atoms or actually delete them. If you wanted to delete them: you could save PDB(s) and choose the option to include only the atoms that are displayed. Alternatively, you could use the approach described above except instead of undisplaying atoms, deleting atoms (for example with Actions... Atoms/ Bonds... Delete) and then save PDB(s). <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht ml#deletion > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Oct 12, 2008, at 10:05 AM, Francesco Pietra wrote: > I would like to remove several parts from a complex protein, just > leaving the portion where a complex has been created with amberscore. > Which is the besr way in Chimera, while observing the pruning on the > screen? > Thanks > francesco pietra ------------------------------ Message: 7 Date: Mon, 13 Oct 2008 10:49:43 -0700 From: Thomas Goddard <goddard(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] save reply log from chimera python script To: Katryna Cisek <cisek.2(a)osu.edu> Cc: chimera-users(a)cgl.ucsf.edu Message-ID: <48F38A37.5080803(a)cgl.ucsf.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Katryna, The original code defines a function. You leave it unchanged and add a line at the end to call it as follows. Tom def save_reply_log(path): from chimera import dialogs r = dialogs.find('reply') text = r.text.get('1.0', 'end') f = open(path, 'w') f.write(text) f.close() save_reply_log("/tmp/tmplog.txt") Katryna Cisek wrote: > Hi Chimera Users, > Could someone please point out the syntax error in this code: > > def save_reply_log("/tmp/tmplog.txt"): <<--- error should be here > based on error info > from chimera import dialogs > r = dialogs.find('reply') > text = r.text.get('1.0', 'end') > f = open('/tmp/tmplog.txt', 'w') > f.write(text) > f.close() > > ---------------------------chimera error info from reply > log------------------------------- > > <type 'exceptions.SyntaxError'> Exception in Tk callback > Function: <function command at 0x132d230> (type: <type 'function'>) > Args: () > Traceback (innermost last): > File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", > line 1747, in __call__ > None > File "CHIMERA/share/chimera/baseDialog.py", line 244, in command > None > File "CHIMERA/share/chimera/baseDialog.py", line 453, in OK > None > File "CHIMERA/share/OpenSave/__init__.py", line 161, in Apply > None > File "CHIMERA/share/SimpleSession/gui.py", line 41, in _openCB > None > File "CHIMERA/share/chimera/__init__.py", line 1344, in open > None > File "CHIMERA/share/chimera/__init__.py", line 787, in _openPython > None > <type 'exceptions.SyntaxError'>: invalid syntax > (refalignrotatewholesymmetrysavelog.py, line 58) > > -------------- > > Thanks, > Katryna > > > On Wed, Oct 8, 2008 at 10:33 PM, Tom Goddard <goddard(a)cgl.ucsf.edu> wrote: >> Hi Katryna, >> >> I don't think there is a command to save the text in the reply log. In the >> Python function the variable path is the path to the file, for example >> "/tmp/mylog.txt". >> >> Tom >> >> >> Katryna Cisek wrote: >>> Hi Chimera users, >>> Is there a new way to save the reply log from a chimera python script, >>> other than below (from Chimera Archive 2006)? >>> >>> def save_reply_log(path): >>> from chimera import dialogs >>> r = dialogs.find('reply') >>> text = r.text.get('1.0', 'end') >>> f = open(path, 'w') >>> f.write(text) >>> f.close() >>> >>> If not, what is the filename given to the reply log in this function? >>> Is it possible to >>> designate the name? >>> Thanks, >>> Katryna >>> _______________________________________________ >>> 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 66, Issue 12 *********************************************

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Re: [Chimera-users] Chimera-users Digest, Vol 66, Issue 13, 1. Regarding blender ( Dr. Jean-Didier Mar?chal )
by Jonathan Hilmer 14 Oct '08

14 Oct '08

> 1. Regarding blender ( Dr. Jean-Didier Mar?chal ) > ---------------------------------------------------------------------- > Message: 1 > Date: Tue, 14 Oct 2008 18:16:29 +0200 > From: " Dr. Jean-Didier Mar?chal " <jeandidier.marechal(a)uab.cat> > Subject: [Chimera-users] Regarding blender > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <004a01c92e18$37236890$a56a39b0$%marechal(a)uab.cat> > Content-Type: text/plain; charset=iso-8859-1 > > Hi guys, > > I saw on the mailing list some information on exporting/importing 3D files. > However, I can't really figure out what would be the best way to export > chimera scene so that blender can import them. > > Is the x3d format the best? Which plug-in do you use? Is there another way > better? > > Cheers, > JD Quite a while ago I wrote a VRML importer for Blender that was specifically designed for Chimera-generated surfaces. It worked acceptably, but the X3D importer mentioned previously (http://blenderartists.org/forum/showthread.php?t=107126) looks like a much better overall solution. If that importer isn't working for some particular aspect of a Chimera scene, I could probably help adapt it to get what you're looking for. The only other good solution I know of is to import your structures directly into Blender, and use Blender to generate the scene from the base primitives. That approach gets very complicated for representations such as helices, and I wouldn't recommend it unless you have very specific needs. Jonathan

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save reply log from chimera python script
by Katryna Cisek 13 Oct '08

13 Oct '08

Hi Chimera users, Is there a new way to save the reply log from a chimera python script, other than below (from Chimera Archive 2006)? def save_reply_log(path): from chimera import dialogs r = dialogs.find('reply') text = r.text.get('1.0', 'end') f = open(path, 'w') f.write(text) f.close() If not, what is the filename given to the reply log in this function? Is it possible to designate the name? Thanks, Katryna

3 3

Pruning pdb graphically
by Francesco Pietra 13 Oct '08

13 Oct '08

I would like to remove several parts from a complex protein, just leaving the portion where a complex has been created with amberscore. Which is the besr way in Chimera, while observing the pruning on the screen? Thanks francesco pietra

2 1

Re: [Chimera-users] Helix-Numbers
by skmolugu＠miners.utep.edu 12 Oct '08

12 Oct '08

Hi, I was wondering if there is a way in chimera for numbering the helices in the map fitted with coordinates. I Basically wanted to explain the location of helix in the map by means of numbering it, so that it will be easy for me to explain in my paper. thank you very much for your time, sudheer.

2 1

Printing on white background
by Francesco Pietra 12 Oct '08

12 Oct '08

When mapping protein residues around a ligand I would like to have a printout of the enlarged binding site area, so as to put remarks by pencil on the printout. However, on a white background, in order to save ink. Is that a problem of working out the image (I have Gimp only, of which I never gained expertise), or can Chimera provide directly? Thanks francesco pietra

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Re: [Chimera-users] problem of sleap for solvation
by Eric Pettersen 09 Oct '08

09 Oct '08

Hi JD, I am now able to reproduce your problem. It should be fixed in the next daily build. You can fix it in your build directly by copying C: \Archivos de programa\Chimera\inst\cygwin1.dll into C:\Archivos de programa\Chimera\bin\amber10\exe . --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Oct 9, 2008, at 12:32 AM, Dr. Jean-Didier Maréchal wrote: > Hi Eric, > > I followed your instructions. I cleaned my previous chimera, > installed 08/10/2008 build, fetch for 1gcn, went to > ToolsàAmberàsolvate. Asked from 4ang box, with TIP3PBOX. The > hydrogens have therefore been built but then it came with the same > message: > > Terminii for #0 determined from SEQRES records > Chain-initial residues that are actual N terminii: HIS 1.A > Chain-initial residues that are not actual N terminii: > Chain-final residues that are actual C terminii: THR 29.A > Chain-final residues that are not actual C terminii: > 15 hydrogen bonds > Hydrogens added > > tempDir: d:\docume~1\jean\config~1\temp\tmpesjllr > command: ['C:\\Archivos de programa\\Chimera\\bin\\amber10\\exe\ > \sleap', '-f', 'd:\\docume~1\\jean\\config~1\\temp\\tmpesjllr\ > \solvate.cmd'] > Running sleap command: C:\Archivos de programa\Chimera\bin > \amber10\exe\sleap -f d:\docume~1\jean\config~1\temp\tmpesjllr > \solvate.cmd > Failure running sleap > Check reply log for details > > Best, > JD > > De: Eric Pettersen [mailto:pett@cgl.ucsf.edu] > Enviado el: jueves, 09 de octubre de 2008 2:57 > Para: "Dr. Jean-Didier Maréchal" > CC: chimera-users(a)cgl.ucsf.edu > Asunto: Re: [Chimera-users] problem of sleap for solvation > > Hi JD, > I tested solvating 1gcn with the Windows daily build and > it worked fine. You shouldn't need to install all those things you > tried. You have to realize that when Chimera runs sleap that > various environment variables are set that will cause sleap to find > files that it won't find it you run it standalone without those > environment variables set. > Can you try installing a "clean" version of the daily > build and see if you can solvate 1gcn (4 angstrom box) without > error? If you get an error, save the contents of the reply log and > mail it to me. If you don't get an error then try your structure. > If that fails, you will have to send it to me if I'm going to have a > chance to debug the problem... > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > On Oct 8, 2008, at 7:12 AM, Dr. Jean-Didier Maréchal wrote: > > > > Dear all, > > I tried yesterday's build on windows and tested the solvation plugin. > I had a first crash that reply log message I give here: > > command: ['C:\\Archivos de > programa\\Chimera\\bin\\amber10\\exe\\sleap', '-f', > 'd:\\docume~1\\jean\\config~1\\temp\\tmp7wpvvm\\solvate.cmd'] > Running sleap command: C:\Archivos de > programa\Chimera\bin\amber10\exe\sleap -f > d:\docume~1\jean\config~1\temp\tmp7wpvvm\solvate.cmd > Failure running sleap > Check reply log for details > > Running C:\Archivos de programa\Chimera\bin\amber10\exe\sleap alone, > I saw > that cygwin1.dll was missing. So I installed it in the same directory. > > Then came a second crash: > > tempDir: d:\docume~1\jean\config~1\temp\tmp6m0sm0 > command: ['C:\\Archivos de > programa\\Chimera\\bin\\amber10\\exe\\sleap', '-f', > 'd:\\docume~1\\jean\\config~1\\temp\\tmp6m0sm0\\solvate.cmd'] > Running sleap command: C:\Archivos de > programa\Chimera\bin\amber10\exe\sleap -f > d:\docume~1\jean\config~1\temp\tmp6m0sm0\solvate.cmd > (solvate) [gtkleap]$ source leaprc.ff03 > (solvate) Error: can not find file leaprc.ff03 in all > the search > path. > Failure running sleap > Check reply log for details > > Though I located the leaprc.ff03 file in another directory and > copied it in > the running one, I can not pass over this problem. > > All the best! > > JD > > > *************************************************** > Dr. Jean-Didier Maréchal > Lecturer > Computational Bioorganic and Bioionorganic Chemistry @ Transmet > 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 > > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

1 0

export scene to maya, obj, iges, stl, dwg-dxp?
by Eli Kuslansky 08 Oct '08

08 Oct '08

Hi Greg, I'm trying to export proteins using Chimera to a Maya file for animations and presentation, but when I export to an .obj file it has no geometry. How can I assure there is geometry in the file? Best regards, Eli Kuslansky

3 2

problem of sleap for solvation
by Dr. Jean-Didier Maréchal 08 Oct '08

08 Oct '08

Dear all, I tried yesterday's build on windows and tested the solvation plugin. I had a first crash that reply log message I give here: command: ['C:\\Archivos de programa\\Chimera\\bin\\amber10\\exe\\sleap', '-f', 'd:\\docume~1\\jean\\config~1\\temp\\tmp7wpvvm\\solvate.cmd'] Running sleap command: C:\Archivos de programa\Chimera\bin\amber10\exe\sleap -f d:\docume~1\jean\config~1\temp\tmp7wpvvm\solvate.cmd Failure running sleap Check reply log for details Running C:\Archivos de programa\Chimera\bin\amber10\exe\sleap alone, I saw that cygwin1.dll was missing. So I installed it in the same directory. Then came a second crash: tempDir: d:\docume~1\jean\config~1\temp\tmp6m0sm0 command: ['C:\\Archivos de programa\\Chimera\\bin\\amber10\\exe\\sleap', '-f', 'd:\\docume~1\\jean\\config~1\\temp\\tmp6m0sm0\\solvate.cmd'] Running sleap command: C:\Archivos de programa\Chimera\bin\amber10\exe\sleap -f d:\docume~1\jean\config~1\temp\tmp6m0sm0\solvate.cmd (solvate) [gtkleap]$ source leaprc.ff03 (solvate) Error: can not find file leaprc.ff03 in all the search path. Failure running sleap Check reply log for details Though I located the leaprc.ff03 file in another directory and copied it in the running one, I can not pass over this problem. All the best! JD *************************************************** Dr. Jean-Didier Maréchal Lecturer Computational Bioorganic and Bioionorganic Chemistry @ Transmet 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

2 1

coloring seperate domains
by Anindito Sen 08 Oct '08

08 Oct '08

HI all I was wondering how to color the c and n terminals of the crystal structure docked in the density map different. Thanks Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908

3 2

"extended" Zone specifier
by Francesco Pietra 08 Oct '08

08 Oct '08

What I would like to do is a global search of which residues of model #0 are within a certain distance from which residues of model #1. Where "model" stands for a protein in both cases. That would save time in simulations of docking (not using DOCK) between proteins. I can locate with Chimera key residues, but their number is large. Thanks francesco pietra

2 2

incorporate chimera commands into a shell script
by shyamala 07 Oct '08

07 Oct '08

Hi, I am fairly new to Chimera. I am trying to calculate the RMSD of the heavy atoms across two different ligand (small molecule) coordinate files. I don't need a least square fit performed, hence using rmsd as opposed to match. I have to do this comparison for around 200 docked conformations against the native ligand conformation, hence I am thinking shell script that can call chimera to execute this command is the way to go. I am not sure how to first select the two small molecules and then use the rmsd command when I start chimera in nogui mode. Any help, examples, pointers will be very much appreciated. Thanks a lot, Shyamala

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Re: [Chimera-users] symmetric fitting
by Tom Goddard 07 Oct '08

07 Oct '08

Hi Sudheer, This means your GroEL map does not have the cylinder axis along z. When you press the Orient button in the volume dialog you can see the orientation, the screen horizontal axis is x, the screen vertical axis is y, and in/out of the screen is z. I've attached a Python script that can produce the symmetry matrices for different cylinder axes. You run it by opening it in Chimera and the output is seen in the Reply Log (Favorites menu). You'll need to edit the script to use the correct axis. Tom skmolugu(a)miners.utep.edu wrote: > Hi Tom, > I have used the matrix file you have gave me and could succesfully generate the coordinates file. After saving the pdb file with the new coordinates, I reopened the saved pdb file that has 14 subunits and it is turns out to be perpendicular to map that has been used. How can I avoid this problem? > thank you very much for your time, > sincerely, > sudheer. > ---------------------------------------- > >> Date: Mon, 6 Oct 2008 12:06:32 -0700 >> From: goddard(a)cgl.ucsf.edu >> To: skmolugu(a)miners.utep.edu >> CC: chimera-users(a)cgl.ucsf.edu >> Subject: Re: [Chimera-users] symmetric fitting >> >> Hi Sudheer, >> >> Figuring out the symmetry matrices for using the symmetric fitting >> capability >> >> http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#symcop… >> >> requires some work. First note that the symmetry matrices you want are >> those that transform (rotate and shift) the volume data to an identical >> configuration. >> >> Your case is 2 stacked 7-mer rings. Assuming the z axis is the >> symmetry axis of the map (need to set origin so the center of the >> cylinder is at xyz = 0,0,0 in the volume dialog Coordinates panel) you >> could just compute the needed rotation matrices >> >> cos(a), sin(a), 0 >> -sin(a), cos(a), 0 >> 0, 0, 1 >> >> Could write a script (python script attached) or use a calculator. Also >> you want to flip around x axis by 180 degrees to get 7 more rotations >> with the two 7-member rings exchanged. With that approach I get the >> following lines to add to the PDB file: >> >> REMARK 350 BIOMT1 0 1.000000 0.000000 0.000000 0.000000 >> REMARK 350 BIOMT2 0 -0.000000 1.000000 0.000000 0.000000 >> REMARK 350 BIOMT3 0 0.000000 0.000000 1.000000 0.000000 >> REMARK 350 BIOMT1 1 0.623490 0.781831 0.000000 0.000000 >> REMARK 350 BIOMT2 1 -0.781831 0.623490 0.000000 0.000000 >> REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.000000 >> REMARK 350 BIOMT1 2 -0.222521 0.974928 0.000000 0.000000 >> REMARK 350 BIOMT2 2 -0.974928 -0.222521 0.000000 0.000000 >> REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.000000 >> REMARK 350 BIOMT1 3 -0.900969 0.433884 0.000000 0.000000 >> REMARK 350 BIOMT2 3 -0.433884 -0.900969 0.000000 0.000000 >> REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.000000 >> REMARK 350 BIOMT1 4 -0.900969 -0.433884 0.000000 0.000000 >> REMARK 350 BIOMT2 4 0.433884 -0.900969 0.000000 0.000000 >> REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.000000 >> REMARK 350 BIOMT1 5 -0.222521 -0.974928 0.000000 0.000000 >> REMARK 350 BIOMT2 5 0.974928 -0.222521 0.000000 0.000000 >> REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.000000 >> REMARK 350 BIOMT1 6 0.623490 -0.781831 0.000000 0.000000 >> REMARK 350 BIOMT2 6 0.781831 0.623490 0.000000 0.000000 >> REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.000000 >> REMARK 350 BIOMT1 7 1.000000 -0.000000 0.000000 0.000000 >> REMARK 350 BIOMT2 7 -0.000000 -1.000000 0.000000 0.000000 >> REMARK 350 BIOMT3 7 0.000000 0.000000 -1.000000 0.000000 >> REMARK 350 BIOMT1 8 0.623490 -0.781831 0.000000 0.000000 >> REMARK 350 BIOMT2 8 -0.781831 -0.623490 0.000000 0.000000 >> REMARK 350 BIOMT3 8 0.000000 0.000000 -1.000000 0.000000 >> REMARK 350 BIOMT1 9 -0.222521 -0.974928 0.000000 0.000000 >> REMARK 350 BIOMT2 9 -0.974928 0.222521 0.000000 0.000000 >> REMARK 350 BIOMT3 9 0.000000 0.000000 -1.000000 0.000000 >> REMARK 350 BIOMT1 10 -0.900969 -0.433884 0.000000 0.000000 >> REMARK 350 BIOMT2 10 -0.433884 0.900969 0.000000 0.000000 >> REMARK 350 BIOMT3 10 0.000000 0.000000 -1.000000 0.000000 >> REMARK 350 BIOMT1 11 -0.900969 0.433884 0.000000 0.000000 >> REMARK 350 BIOMT2 11 0.433884 0.900969 0.000000 0.000000 >> REMARK 350 BIOMT3 11 0.000000 0.000000 -1.000000 0.000000 >> REMARK 350 BIOMT1 12 -0.222521 0.974928 0.000000 0.000000 >> REMARK 350 BIOMT2 12 0.974928 0.222521 0.000000 0.000000 >> REMARK 350 BIOMT3 12 0.000000 0.000000 -1.000000 0.000000 >> REMARK 350 BIOMT1 13 0.623490 0.781831 0.000000 0.000000 >> REMARK 350 BIOMT2 13 0.781831 -0.623490 0.000000 0.000000 >> REMARK 350 BIOMT3 13 0.000000 0.000000 -1.000000 0.000000 >> >> If your map origin is not the center of symmetry or an x-axis flip is >> not a symmetry then these matrices won't work. You can try to set the >> correct origin -- the right value can be found with some tricky use of >> the output of the Fit in Map tool, fitting one copy of the map into >> another copy. Or you could fit one copy of the map to another and use >> the matrixget command to output that symmetry matrix to a file, then do >> that for all symmetries to create the needed matrix text. >> >> As you see this process has not yet been made easy. >> >> Tom >> >> >> >> >> >> skmolugu(a)miners.utep.edu wrote: >> >>> HI, >>> In the symmetric fitting model session that explains about the symmetry generation, i did not understand the method to generate the matrix. I am working on a chaperonin protein called GroEL. It has 14 subunits with seven fold symmetry. can you please explain me how to update the pdb and the matrix values that i need to put in the pdb file. >>> thankyou, >>> sudheer >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> # Chimera script to print symmetry matrices for GroEL 14-mer. format = '''REMARK 350 BIOMT1 %3d %10.6f %10.6f %10.6f %10.6f REMARK 350 BIOMT2 %3d %10.6f %10.6f %10.6f %10.6f REMARK 350 BIOMT3 %3d %10.6f %10.6f %10.6f %10.6f''' axis = (0,0,1) import Matrix as m flip = m.rotation_from_axis_angle((1,0,0), 180) # 180 degree rotation about x. flip = [r + (0,) for r in flip] # Zero translation. for i in range(14): a = 360.0*i/7.0 t = m.rotation_from_axis_angle(axis, a) # Rotation by i/7 turn about z. t = [r + (0,) for r in t] # Zero translation. if i >= 7: t = m.multiply_matrices(flip, t) # Exchange top and bottom ring. print format % ((i,) + t[0] + (i,) + t[1] + (i,) + t[2])

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obtaining rotation angles
by Jaap Brink 06 Oct '08

06 Oct '08

Hi, I'm trying to figure out how I can obtain angles from chimera. I have a 3D object that I have to rotate in order to see certain features. I'd like to know those angles. Is there is a way to get this info? Thanks in advance, Jaap Brink

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Re: [Chimera-users] symmetric fitting
by skmolugu＠miners.utep.edu 06 Oct '08

06 Oct '08

HI, In the symmetric fitting model session that explains about the symmetry generation, i did not understand the method to generate the matrix. I am working on a chaperonin protein called GroEL. It has 14 subunits with seven fold symmetry. can you please explain me how to update the pdb and the matrix values that i need to put in the pdb file. thankyou, sudheer

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Failure of Surface Display
by Charles Letner, Ph.D. 04 Oct '08

04 Oct '08

Hello, I am trying to display a surface using the Actions > Surface>Show menu. The surface is not displaying and the following error is in the reply: C:\Program Files (x86)\Chimera\bin\mscalc.exe 1.400000 2.000000 1 Calculation of some surface components failed (code 5). Falling back to single-component calculation. C:\Program Files (x86)\Chimera\bin\mscalc.exe 1.400000 2.000000 0 Surface calculation failed, mscalc returned code 5 I am using Chimera version: production version 1 build 2540 2008/07/09 Platform is Windows Vista 64 bit. The file I am working with contains 2 subunits. If I split the two subunits into separate files and open individually in the same session, the surfaces display without any issue. I am trying to show the surface of the two subunits associated, not the surface of each individual subunit. Any help will be appreciated. Cheers, Chuck

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Re: [Chimera-users] Failure of Surface Display - Additional Info
by Charles Letner, Ph.D. 04 Oct '08

04 Oct '08

I just installed the latest daily build (1.2562) and get the same error. ----- Original Message ----- From: Charles Letner, Ph.D. To: chimera-users(a)cgl.ucsf.edu Sent: Saturday, October 04, 2008 11:59 AM Subject: Failure of Surface Display Hello, I am trying to display a surface using the Actions > Surface>Show menu. The surface is not displaying and the following error is in the reply: C:\Program Files (x86)\Chimera\bin\mscalc.exe 1.400000 2.000000 1 Calculation of some surface components failed (code 5). Falling back to single-component calculation. C:\Program Files (x86)\Chimera\bin\mscalc.exe 1.400000 2.000000 0 Surface calculation failed, mscalc returned code 5 I am using Chimera version: production version 1 build 2540 2008/07/09 Platform is Windows Vista 64 bit. The file I am working with contains 2 subunits. If I split the two subunits into separate files and open individually in the same session, the surfaces display without any issue. I am trying to show the surface of the two subunits associated, not the surface of each individual subunit. Any help will be appreciated. Cheers, Chuck

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