- Chimera-users - RBVI Mailing Lists

MD trajectory play by commandline
by inhee park 14 Jan '14

14 Jan '14

Dear Chimera developers and users: I am using Chimera (production version 1.8 (build 38824) 2013-06-07 21:09:20 UTC). I wanted to process MD trajectories to extract their detailed H-bond information. To do so, I would like to process by script with Hbond.py file. $ chimera --script Hbond.py #---[Hbond.py] from chimera import runCommand # pr trajectory movie with open("metafile", 'w') as m: meta_input = """amber mypdb.prmtop pr_dry_netcdf.crd """ print >> m, meta_input # runCommand("open movie:metafile") runCommand("alias ^myhb hbond relax true savefile hbond.$1") runCommand("perframe myhb") runCommand("coordset #0 1,1000,10; wait 100") #----------------------- As I have many MD trajectories to be processed, I was looking for a commandline in lieu of actually clicking buttons in MD movie GUI to play. I thought that "coordset #0 1,10000,10; wait 100" may operate like automatically starting the MD movie to load frame 1 to 1000 at every 100 interval. But resulting saved H-bond files contain same information all about the first frame (because graphically displayed was the first frame without any update unless clicking the button in MD movie GUI). Is there a way to achieve an automatic play via commandline? Thank you, inhee park

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RMSD per residue NMR structure
by cantini＠cerm.unifi.it 14 Jan '14

14 Jan '14

Dear users Does anyone knows how to calculate through CHIMERA the backbone rmsd per residue of a NMR ensembles of protein structures ? thank a lot Francesca Cantini ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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batch writing of attributes
by Jay Eifler 13 Jan '14

13 Jan '14

I'm trying to automate saving the areaSAS for a bunch of models. I've got no problem loading the models, etc. The problem is simply how do I use command line arguments to save the areaSAS. I've tried writesel. This works all fine in Render/Select by attribute simply because it has a feature to save the areaSAS to a file. Thanks.

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Computing solvent accessible area without internal cavities
by Tom Goddard 13 Jan '14

13 Jan '14

Hi Numan, Chimera uses the MSMS program to compute solvent accessible surface area, and MSMS has an option to only compute for the outside surface component without internal cavities. So I think this is just what you want. Although you could script it in Chimera you might find it easier to write a script that uses the standalone program directly from Michel Sanner http://mgl.scripps.edu/people/sanner/html/msms_home.html The one trouble you may run into is the calculation failing on some molecules due to numerical instabilities. The older version of the MSMS library we use in Chimera often fails to compute the surfaces and areas for molecules larger than 10,000 atoms, and sometimes fails for much smaller molecules. The standalone program from Michel failed much less often in tests I did a few years ago, probably because it used some newer more reliable code. Tom On Jan 13, 2014, at 11:13 AM, "Oezguen, Numan" wrote: > Dear Tom, > > I am facing a problem that you have most probably already have solved and hoping you could help me out. I need to identify atoms that are solvent accessible. For this I used the program Getarea from Werner Braun’s group in Galveston Texas. It works fine, however it lists also internal cavity surface atoms as solvent exposed. Technically it is correct… but I am interested only in those surface areas that are not internal i.e. surface areas that are accessible to molecules approaching it from outside. > > Do you know of any commercial or free (preferably) program that can do this. Ideally it should be possible to call it from scripts (shell or Perl). > > Thank you very much for you time and help, > Numan > > > Numan Oezguen, Dr. rer. nat. > Instructor of Pathology & Immunology > Texas Children’s Microbiome Center > Feigin Center, Suite 830 > 1102 Bates Avenue > Houston, TX 77030

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Registration ?
by Jean-Paul Boissel 13 Jan '14

13 Jan '14

Just downloaded the new dally build. At opening got the message: Registration file "/Users/JPB/.chimera/registration" has expired. Do we have to register again for 2014 Thanks > > Dr. Jean-Paul Boissel, Team Leader > Solute Transport Through Biological Membranes/ Ellen I. Closs' group > Department of Pharmacology > University Medical Center of the Johannes Gutenberg-University > Obere Zahlbacher Strasse 67, D-55101 Mainz > Tel.: +49 6131-17 9189 > FAX: +49 6131-17 9329 > e-mail: boissel(a)uni-mainz.de > http://www.unimedizin-mainz.de/pharmakologie/research/solute-transport-thro… > -biological-membranes.html?L=1 > This e-mail contains confidential information and may also be legally > privileged. If you are not the intended recipient or received this mail by > mistake, please inform the sender immediately and delete the mail. Any > un-authorized use, copying, disclosure or forwarding of this mail and of > information contained therein is prohibited.

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displaying electrostatic field
by Bala subramanian 10 Jan '14

10 Jan '14

Friends, Kindly see the following link (Fig 22, left panel). http://www.bioscience.org/2009/v14/af/3398/fulltext.php?bframe=figures.htm Has anyone tried making the display of electric field in Chimera. Is there any way i can make the same in chimera. Thanks, Bala -- C. Balasubramanian

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running wild with Chimera :-)
by Eric Pettersen 09 Jan '14

09 Jan '14

New Year Cards in 3D

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BioPython in a Chimera Python script; PDBio?
by Hurt, Darrell (NIH/NIAID) [E] 07 Jan '14

07 Jan '14

Hi Chimera friends, I've been trying to install BioPython into the Python interpreter embedded within Chimera. I've been following the guidelines posted a couple of years ago: http://www.cgl.ucsf.edu/pipermail/chimera-dev/2011/000807.html This works up to a point for me. I'm using Mac OS X 10.8.5 with MacPorts installed. I'm trying to install BioPython 1.63: http://biopython.org/wiki/Download#Installation_Instructions The "build" process starts to work, but gets hung up with the error "xcrun: Error: failed to exec real xcrun. (No such file or directory)". It seems to be referencing "/Developer/SDKs/MacOSX10.6.sdk", which does not exist in recent versions of Xcode. I've been able to install the 10.6 frameworks into both Xcode 4.6.2 and Xcode 5.x, but that still doesn't work. I manually installed the MacOSX10.6.sdk from Xcode 4.2 into the appropriate location, but still no luck. I'm using BioPython because I want to pull some information out of the PDB headers. I was able to use PDBio as described in this discussion: http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-February/001291.html But the "dictionary" entries "keyed by record type" need additional cleanup/parsing before I can use them (which is why I wanted to use BioPython). Is this just a case of Apple not building in enough backwards compatibility? Or is it something that Chimera needs to fix? Do you have any additional suggestions for me about "PDBio"? The fields I want are the DOI and title information. Finally, is there an analogous "EMDBio" for EMDB records? Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.…> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Updating coordinates without having to regenerate the depiction of an atomic model
by Mike Lawrence 07 Jan '14

07 Jan '14

Hi, Within Chimera is there any way in which the underlying coordinates of an atomic model can be updated in order to yield the same depiction but based on the new coordinates, or (equivalently) can the attributes of one model be transferred to another, assuming of course that they have the same underlying protein sequence, etc. thanks Mike Lawrence Walter + Eliza Hall Institute of Medical Research Parkville Australia ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________

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the old Mac OX 10.4 can not run Chimera
by Zhang, Yinghui 06 Jan '14

06 Jan '14

Dear Sir/Madam, This is Yinghui Zhang from Massachusetts General Hospital. I am a postdoc here and my project requires me to use the Chimera often. However, the desktop I used is some old and I can not update and use Chimera right now. The Chimera installed is 1.2 version but cannot be started. The specifics of computer is as follows: Apple PowerMac G5 chip, duo core and 3G memory. The OS is Mac OX 10.4.11. The operating system very probably cannot be updated because of chip version problem. Could you please give us some information if there is some alternative we can install executable Chimera on this computer? Thank you very much! Yinghui Zhang EDR 514, Dept. of Anesthesia MGH Boston, MA 02148 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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General question about Chimera
by Lili Peng 06 Jan '14

06 Jan '14

Hi, When I load a structure of a protein into Chimera, the structure is automatically rendered in ribbon mode, with select atoms being rendered in stick mode. I am curious as to why certain atoms are rendered as sticks, and other are not. What is the selection criteria? Thank you, Lili

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How to measure the radius of density map
by Jian Guan 03 Jan '14

03 Jan '14

Hi all, I have density map of virus (mrc format) and want to measure the radius of it. I tried measure command, High-order structure-->Icosahedron surface. Both of them need me to measure it manually by eye. Are there any tools to measure the radius by chimera, so we can get more accurate result? Or does anybody know how to measure it accurately? Thank you so much. Sincerely yours, Happy New Year. Jian -----Original Message----- From: chimera-users-bounces(a)cgl.ucsf.edu [mailto:chimera-users-bounces@cgl.ucsf.edu] On Behalf Of chimera-users-request(a)cgl.ucsf.edu Sent: 2014年1月2日 15:00 To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 129, Issue 1 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.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. rate of a reaction (Haider Abbas) 2. Error in generating sqm for FAD (Isha) 3. Re: rate of a reaction (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Wed, 1 Jan 2014 10:51:05 +0530 From: Haider Abbas <haiderabbasphy(a)gmail.com> To: chimera-users(a)cgl.ucsf.edu Subject: [Chimera-users] rate of a reaction Message-ID: <CAO+nnti1fDSY+i59Fa4ioQzwVF+k77OPUDLC=jHJ5m_zt-4P_g(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Dear all user, Could you please let me know how to calculate reaction rate of a barrierless chemical reaction in gas phase by chimera. with regards Haider Abbas

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Error in generating sqm for FAD
by Isha 02 Jan '14

02 Jan '14

Dear Sir/Mam I used antechamber in chimera to add charges to ligand "FAD" using am-bcc, amber ffo3r.1 and +5 charge (as depicted by chimera). The procedure was Tools > structure editing > add H and then add charge. The error shown is : Charge model: AMBER ff03.r1 Assigning partial charges to residue FAD (net charge +1) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/Chimera 1.8.1/bin/amber12/binantechamber -ek qm_theory='AM1', -i c:usersamehtaappdatalocaltemptmpjjpoaqante.in.mol2 -fi mol2 -o c:usersamehtaappdatalocaltemptmpjjpoaqante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 (FAD) (FAD) Running: "C:/Program Files/Chimera 1.8.1/bin/amber12/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac (FAD) (FAD) Running: "C:/Program Files/Chimera 1.8.1/bin/amber12/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (FAD) Total number of electrons: 412; net charge: 1 (FAD) (FAD) Running: "C:/Program Files/Chimera 1.8.1/bin/amber12/bin/sqm" -O -i sqm.in -o sqm.out (FAD) Error: cannot run ""C:/Program Files/Chimera 1.8.1/bin/amber12/bin/sqm" -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit Failure running ANTECHAMBER for residue FAD Please help as it is very urgent. Hope for your reply. I have also attached the ligand. Please find the attachment. With Regards, Isha C/O Dr. Raman Parkesh Protein Science & Engg. Institute of Microbial Technology Sector 39A, Chandigarh 160036 Ext: 0172-6665489

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rate of a reaction
by Haider Abbas 02 Jan '14

02 Jan '14

Dear all user, Could you please let me know how to calculate reaction rate of a barrierless chemical reaction in gas phase by chimera. with regards Haider Abbas

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Set and rna commands
by pythonchemia Gazeta.pl 30 Dec '13

30 Dec '13

Hello ! I have winXP and Chimera version 1.8. I wanted to use the commands rna and set. Unfortunately, they do not work. Why? What is it? I tried to repeat the example of the User's Guide for rna command and failed. Please help me or give me examples on the set command and rna Sincerely, Janusz Grabowski

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Find pseudo 2-fold axes relating heavy and light chain
by Jian Guan 30 Dec '13

30 Dec '13

Dear all, I am trying to find pseudo 2-fold axes relating heavy and light chains in the constant domain and variable domain respectively in Fab. I tried Define Axes, it failed. And I made artificial double heavy chain, it failed again. I can only get axis which is horizontal passing through both light chain and heavy chain. It is not what I want. Can anyone help to give some clues? Thanks Jian

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Failure of energy miminization
by Ross KK Leung 30 Dec '13

30 Dec '13

In August there was a discussion entitled "Minimization and mystery nonstandard HIS atom name" and that's the exact problem supposed to have been solved last year. What I did is similar to Jason (http://www.cgl.ucsf.edu/pipermail/chimera-users/2013-August/009069.html) and unfortunately I'm unable to resolve the problem, giving that I'm using chimera 1.8.1 on a Win 7 32G RAM computer. I attach two files, one succeeded till completion while the other one failed early. What I did is simply "Structure editing", next, ok, next, .. Charges of 0.0 were assigned to the unknown atoms 1 model(s) had non-integral total charge Details in reply log No MMTK name for atom "HC1" in standard residue "ALA" Any suggestions to fix the problem is highly appreciated because Chimera is so impressive and I've been using it for many good analyses already. A pity to give up and switch to other programs at this very last stage.

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Reset surface programatically from python
by Thomas Hrabe 30 Dec '13

30 Dec '13

Hi everyone, I have this line of code where I want to load a density and export a negative surface of it: import chimera as ch mod = ch.openModels.open(‘./density.em')[0] mod.surface_levels = [-1,0] mod.display = True ch.exports.doExportCommand('WebGL', 'tmp.html’) However, the surface of the density is rendered for positive values. How can I refresh the display after I specify the surface_levels? Thanks, Thomas

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Re: [Chimera-users] [chimera-dev] writing in b-factor field
by Elaine Meng 30 Dec '13

30 Dec '13

On Dec 29, 2013, at 8:43 AM, MARIA VITTORIA CUBELLIS <cubellis(a)unina.it> wrote: > Dear sir/madam, > I have a file that associates to each amino acid of a protein A a given value v. > I would like to transfer this value to the b-factor field of the protein A the value v. I have a single value for each aminoacid N1,N2... I would like to transfer the value to each atom > > let say > > N1 C v1 > N1 CO v1 > N1 N v1 > .... > .... > N2 C v2 > N2 CO v2 > N2 N v2 > > and so on > > is it possible to this withe chimera? > thank you > > mvcubellis Dear M V Cubellis, Yes, you can do it, but another question is why do you want to do it? I'm guessing you want to color by those values. In Chimera you can assign the values to the atoms or residues directly as "attributes" and then do coloring to show those values. The B-factor from an input file is one atom attribute named bfactor, but you can create additional attributes with whatever names you wish, and color by any of them. The main work for you is to create an "attribute assignment file" which is mostly tab-separated columns with the atom (or residue) specifiers and values. The necessary format is described here, and there are also some example files: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defi…> Probably the trickiest part is how to specify the residues in the file, e.g. could be something like :12.a for residue 12 in chain A. See instructions on atom/residue specification: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#basic> Once you have created that text file, you can read it in with Define Attribute (in menu under Tools… Structure Analysis) or command defattr. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defi…> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/defattr.html> Then Render by Attribute (which may automatically appear when you create the attribute, but also is in menu under Tools… Structure Analysis) can be used to show the values with colors and/or radii: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.htm…> If you really wanted to write a PDB file with values in the B-factor column, you would still need to create an attribute assignment file as described above, but more specifically to assign an atom attribute named bfactor. Then when you use the File menu or write command to output a PDB file, your values will be in the B-factor column. See also the Attributes tutorial for examples of coloring by attribute value. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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keyboard shortcuts
by Dougherty, Matthew T 30 Dec '13

30 Dec '13

I am writing a bunch of USB-HID keyboard shortcuts for some extensions I am writing. Usually one shortcut per def. Since my decoding of HID is integrally tied to the extension, I would like to simplify all my shortcuts coming from one device to one def. As of now if I have 100 button commands I have to 1) register 100 shortcuts, 2) create 100 defs, 3) do corresponding stuff in my extension. I would prefer to call one def that passes the actual keyboard string to my extension, thereby simplifying my user accelerators to just registration. How do I get the string within my keyboard shortcuts python file? thanks, Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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display of improper peptide bond
by Tatiana Domitrovic 30 Dec '13

30 Dec '13

Hi, I am trying to get rid of an improper bond that chimera is displaying between two nearby segments that are actually cleaved. The bond is distorted, creating long CACB bonds if B-spline mode is active. I tried to turn off the auto-chaining, but didn’t work. Because PYmol can properly display these segments as independent polypetides, I was wondering if there is other adjustment that I can try before manually deleting the bond. The PDB is 1ohf and the bond is between residue 570 and 571. Cheers,

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Failure of energy miminization
by Ross KK Leung 29 Dec '13

29 Dec '13

In August there was a discussion entitled "Minimization and mystery nonstandard HIS atom name" and that's the exact problem supposed to have been solved last year. What I did is similar to Jason (http://www.cgl.ucsf.edu/pipermail/chimera-users/2013-August/009069.html) and unfortunately I'm unable to resolve the problem, giving that I'm using chimera 1.8.1 on a Win 7 32G RAM computer. I attach two files, one succeeded till completion while the other one failed early. What I did is simply "Structure editing", next, ok, next, .. Charges of 0.0 were assigned to the unknown atoms 1 model(s) had non-integral total charge Details in reply log No MMTK name for atom "HC1" in standard residue "ALA" Any suggestions to fix the problem is highly appreciated because Chimera is so impressive and I've been using it for many good analyses already. A pity to give up and switch to other programs at this very last stage.

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Sir, i donot want to recieve antomately letter from chimera, can you remove my email adress from your email list..
by 一波 28 Dec '13

28 Dec '13

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How to get central cross section which pass through two asigned cross axis
by Jian Guan 27 Dec '13

27 Dec '13

Dear all, I have a density map of virus-Fab complex. I want to make a central cross section which pass through the Fab pseudo-symmetry 2-fold axis. I have measure the angle of Fab relative to the capsid. Hope someone can help me. Thank you so much. Sincerely yours, Jian -----Original Message----- From: chimera-users-bounces(a)cgl.ucsf.edu [mailto:chimera-users-bounces@cgl.ucsf.edu] On Behalf Of chimera-users-request(a)cgl.ucsf.edu Sent: 2013年12月24日 15:00 To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 128, Issue 25 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://plato.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: saving coords from script (Eric Pettersen) ---------------------------------------------------------------------- Message: 1 Date: Mon, 23 Dec 2013 15:59:16 -0800 From: Eric Pettersen <pett(a)cgl.ucsf.edu> To: Tetsuro Fujisawa <fujisawa(a)gifu-u.ac.jp> Cc: "chimera-users(a)cgl.ucsf.edu Mailing List" <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] saving coords from script Message-ID: <04B15E0C-844B-4594-8AE6-760588744D85(a)cgl.ucsf.edu> Content-Type: text/plain; charset="windows-1252" On Dec 20, 2013, at 1:58 AM, Tetsuro Fujisawa wrote: > Hi, > > I found some strange behavior in saving pdb file by script file. > I tried to modify the orientation of pdb file ?tst.pdb? (#1) in reference to axis coordinate (#0), then save the atomic coordinates in pdb file. > When I typed in the commands through either command line window or IDLE, transformed coordinates were saved. It worked fine. However, the exact identical commands (inside the brancket) or lines (rc(?..?)) were run by script file shown in below, the untransformed coordinates were saved. This is also the case for ?Midas.write method?. > I wondered this might be a bug. > > Regards, > Tetsuro > > Sample.py: > ---------------------------------------------- > from chimera import runCommand as rc > > rc('open axis.bild') > rc('open tst.pdb') > rc('rock y 60 1 center #1 coord #0 models #1') # orientation of > tst.pdb was modified > rc('focus') > rc('write relative #0 #1 tstA.pdb') > # write current coordinates to tstA.pdb rc('open tstA.pdb') # opened > tstA has original untransformed orientation > ----------------------------------------------- Hi Tetsuro, The issue is that unlike using the command line or IDLE or running a chimera-command script, no frames get drawn during the execution of a Python script unless explicitly requested and therefore the "rock" command in your script doesn't actually do anything until after the entire script runs, and by that time your coordinate file has already been written. To get the rock command to complete before proceeding with the rest of the script you need to append "; wait" or "; wait 1" (since you are rocking for 1 frame) to the end of your rock command. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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saving coords from script
by Tetsuro Fujisawa 23 Dec '13

23 Dec '13

The following bug report has been submitted: Platform: windows Chimera Version: 1.8.1 Description Hi, I found some strange behavior in saving pdb file by script file. I tried to modify the orientation of pdb file ‘tst.pdb’ (#1) in reference to axis coordinate (#0), then save the atomic coordinates in pdb file. When I typed in the commands through either command line window or IDLE, transformed coordinates were saved. It worked fine. However, the exact identical commands (inside the brancket) or lines (rc(’..’)) were run by script file shown in below, the untransformed coordinates were saved. This is also the case for “Midas.write method”. I wondered this might be a bug. Regards, Tetsuro Sample.py: ---------------------------------------------- from chimera import runCommand as rc rc('open axis.bild') rc('open tst.pdb') rc('rock y 60 1 center #1 coord #0 models #1') # orientation of tst.pdb was modified rc('focus') rc('write relative #0 #1 tstA.pdb') # write current coordinates to tstA.pdb rc('open tstA.pdb') # opened tstA has original untransformed orientation -----------------------------------------------

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