- Chimera-users - RBVI Mailing Lists

DockPrep sometimes fails with altPos
by Visvaldas Kairys 24 Jun '17

24 Jun '17

Dear Chimera users and developers, I’d like to point out I often have a minor inconvenience when dealing with high resolution Xray structures when trying to add hydrogens via DockPrep. If two consecutive residues have both alternative postions A and B, Chimera in the process of hydrogen addition often gets confused and puts “TER” between the residues, also reporting non-integer charges in the log. I think what is happening, the program picks “A” variant for one residue and “B” for the consecutive residue, and apparently this causes bond detection algorithm to ignore the bond between the residues (due to length I guess). I resolve this by manually editing out one of the AltPos (say, “B”) out of the PDB file for the offending residues, but I guess the program should be able to do it automatically. A PDB example where this happens is 2r3i (or 2r3r). Best regards, Vis

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strand inside and edge color
by Kyle Morris 23 Jun '17

23 Jun '17

Dear Chimera dev, Sorry if I missed this in the documentation and online… Is it possible to make the inside and side edges of strands a color independent of the models coloring? Akin to using ribinsidecolor white to color the inside of helices white, I would like to color the inside and side edges of strands white. Thanks for your help as always! Best wishes, Kyle

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suggestion: data mode
by Dougherty, Matthew T 23 Jun '17

23 Jun '17

would be helpful to display data mode (byte, float, etc) on the volume viewer panel, approximately in the same location as origin index, voxel size, etc. For mrc files I can dump the header and pick thru it, for other formats the method is not so clear. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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Measuring Distances in the Reciprocal Space Transform
by Martin Lawrence 23 Jun '17

23 Jun '17

Dear Chimera Users, I would like to measure the reciprocal space distance between features in the fourier transform of my map. Can anyone give me a hint as to the easiest way to do this? Thanks, Martin Martin Lawrence Department of Chemistry and Biochemistry Montana State University Bozeman, MT 59717 USA

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Please Help Me: Vina Tool Error in Chimera:
by Sarah Qassem Azzam 22 Jun '17

22 Jun '17

Dear Chimera help desk, Hope this email finds you well. I am facing a problem with Vina Tool in Chimera, while running molecular docking. I got the following error message: "\Program Files\The Scripps Research Institute\vina.exe"' is not recognized as an internal or external command, operable program or batch file. ---- Application stdout ----- [no output] I did install Vina, and I am trying to run it in Chimera using 'Local' option for executable location. Can you please advise on how to solve this issue? Your time is highly appreciated. Kind regards, Sarah Azzam

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Selecting only protein surfaces programmatically
by Ashton Omdahl 20 Jun '17

20 Jun '17

Chimera friends- I am creating a python script to take the sum of the distance from every atom in a given zone around selected residues to the surface of the protein. As part of this, I would also like to calculate the minimum distance to the surface of any given atom (based on the current surface rolling ball radius algorithm). However, I have been unable to find a command to select only the surface of a protein that works consistently across interfaces. What commands could I do this with both programmatically (in python) and in the GUI command line? Thanks! Ashton

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Installing Chimera and ChimeraX on a CentOS box without root
by Healey, Joe 20 Jun '17

20 Jun '17

Hi Chimera team, I need to install chimera and chimeraX on a server with a GPU which I now have access to assist in visualising larger structures, but I don't have any root privileges. After the first pass installing both, Chimera 1.11 gives me this warning/error when attempting to run: "OpenGL misconfiguration detected. /usr/lib/libGL.so.1 differs from /usr/X11R6/lib/libGL.so.1" And when I close this dialogue box, I get this: "Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 149 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 717 Current serial number in output stream: 718 libxcb: WARNING! Program tries to lock an already locked connection, which indicates a programming error. There will be no further warnings about this issue." ----------- And when running ChimeraX for the first time, I get this: " ChimeraX: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by ChimeraX) ChimeraX: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /cold/chem/msrnbi/bin/chimerax/bin/../lib/libpython3.6m.so.1.0) ChimeraX: /lib64/libc.so.6: version `GLIBC_2.17' not found (required by /cold/chem/msrnbi/bin/chimerax/bin/../lib/libpython3.6m.so.1.0) " Evidently I need 2 different versions of GLIBC for ChimeraX, but assuming I can install these concurrently without root access, how would I go about telling ChimeraX where to look for the libraries? Any advice/documentation you have to get the programs working would be much appreciated. Joe Healey M.Sc. B.Sc. (Hons) MSRB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738

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alter to periodic box
by paul buscemi 17 Jun '17

17 Jun '17

I was experimenting with mixed solvents and found that if you create a box around a molecule say 10A on a side, then de-select "remove solvent" and then create a second box, say 2A on a side, that second box forms around the first. You can then constrain the second box which will for the most part retain the first and the parent molecule during a simulation. This allows visualization of the live trajectory as well. I used MON around water and he process is faster to create than selecting the six outside surfaces of a solvent box. Paul

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Question about Chimera
by Shabnam Nadjafi 17 Jun '17

17 Jun '17

Dear Manager I have a question about "Chimera". Is " "Chimera" free ? Can this program be used without license and complete freely? Thanks, Sincerely Yours, Shabnam Nadjafi

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Re: [Chimera-users] Run procedure
by Elaine Meng 16 Jun '17

16 Jun '17

Hi Paul, (1) please send questions to the chimera-users address, CC’d here. Questions sent just to me may fall through the cracks. (2) all I know about the Molecular Dynamics Simulation tool, I have written in its documentation. You can see it by clicking the Help button on the dialog or viewing the copy at our website: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html> See the sentence containing “clicking Run” about 1/3 of the way down and the last sentence in the page starting with "After the completion of any MD run…” I am guessing that you chose the recording option in the MD Movie dialog. If you are not sure which data it is showing, Quit from the MD Movie dialog. Then from the Tools menu, restart MD Movie and specify the specific MMTK input (trajectory) file that you want, like we discussed earlier. Although I said earlier that if you gave the same output name for both equilibration and production, the production might overwrite the equilibration, I’m no longer sure about whether it overwrites or just gets added to the end. However, you should be able to tell by the number of frames in the output trajectory. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jun 16, 2017, at 12:03 PM, pbuscemi <pbuscemi(a)q.com> wrote: > > Elaine, > > In doing a simulation, does it matter which screen is used to select "RUN" ie, minimize, equilibrium,production, or other. > > i.e If I select equlibrium, is production also run ? When a movie is recorded, is it from equilibrium or production portion ? > > thanks > Paul > >

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structureViz Path problem
by sriram raghavan 16 Jun '17

16 Jun '17

Dear Sir, I find it difficult to troubleshoot the path setting problem, which I am facing while operating with the structureViz plugin. Please kindly help me in installing the app. I have set UCSF chimera path as below but still i am not able to save the setting if default setting is the problem.[image: Inline image 1] I get the following error. [image: Inline image 2] With Regards S.Sriram Ph.D. Research Scholar CAS in Crystallography and Biophysics University Of Madras Mail:hypowergravity@gmail.com

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Re: [Chimera-users] Generate the tranfromation or bio matrix from the docking complex using Chimera
by Elaine Meng 15 Jun '17

15 Jun '17

> On Jun 14, 2017, at 9:35 AM, Elumalai Pavadai <epavadai(a)fiu.edu> wrote: > > Dear Meng, > > I have a cylindrical symmetry protein complex modeled with the protein-protein docking. Since the docking complex is very big in terms of size and number of atoms, I would like to generate the transformation matrix from it. Using the matrix , I can be able to generate the complex with Chimera. So, my question is that how to generate the transformation matrix from the protein complex with Chimera? > > Thank you, and I look forward to hearing from you. > > Kind regards, > Elumalai Dear Elumalai, I’m CC-ing chimera-users(a)cgl.ucsf.edu … it is the recommended address for Chimera questions, to ensure you get a response and allowing others to make suggestions. I’m guessing that you mean your large complex is several copies of the same protein, arranged in some symmetrical way, and instead you would like to have a file with only one copy but also the matrices describing the whole thing. If you had such a file, you could open it in Chimera and then generate the whole thing from the matrices. However, Chimera does not have the tools to go in the opposite direction, to figure out all the matrices from the whole complex. So if I understood your problem correctly, you would need to find some other program to do this. I haven’t done it myself, so I don’t know what you could use. If your protein-protein docking program created this symmetrical structure, maybe it can output the needed matrices. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Smooth "Rocking" Loop Movie
by Andrew Oliver, II 14 Jun '17

14 Jun '17

Dear Chimera, I am trying to create a "rocking" movie of a molecule that will continuously loop. I am using the command: movie record; rock y 10 68; wait; rock y -10 68; wait; movie stop; movie encode However, when I do this, there is always a slight pause at the end of the movie, before it starts the next loop -- which means it doesn't loop smoothly. Is there a way to create the movie so that there will be no pause before each successive loop? Many thanks, Andrew Oliver

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region bounds for pdb
by Edoardo D'Imprima 14 Jun '17

14 Jun '17

Dear Chimera users, I find very handy the function “Region bounds” to cut the EM maps in order to better visualise some part of the volume. I was wondering if there is an equivalent for PDBs. Many thanks in advance, Edoardo --------------------------------------------------- Edoardo D'Imprima PhD Student Max Planck Institute of Biophysics Structural Biology Department Max-von-Laue Straße 3 60438 Frankfurt am Main Germany Tel: +49 (0) 69 6303 3015

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Files generated by UCSF Chimera as .MRC format do not open with AMIRA 5.3.3
by Savriama, Yoland F 13 Jun '17

13 Jun '17

Greetings, I am a researcher working at the University of Helsinki (Finland) and I have used the software UCSF Chimera to process 3D CT-Scans data. I saved the process files as a single .MRC file. When I tried to open it with Amira 5.3.3 it displays the following error message: "No valid licence found for extension Amira Microscopy Option 5.3 Please contact us". The console also says "Access denied for 'readMRCFileStack'" I thought that Amira could read these standard .MRC files? Could it be there was an issue during the file export with Chimera? Best wishes, Yoland Savriama, PhD P/O Jernvall Institute of Biotechnology P.O. Box 56 (Viikinkaari 5) FIN-00014 FINLAND

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Helix represented as sheet, dispite best efforts
by Matthias Vorländer 13 Jun '17

13 Jun '17

Hi everyone, for some reason, chimera displays one helix in a structure as a messed up beta sheet. I am attaching the PDB file and an image (same structure as backbone and ribbon representation). I have tried adding HELIX records manually, ksdssp or the setattr command, but the result is always the same. I would be very grateful for suggestions what could be causing this problem, as I will have to remake all my figures in pymol otherwise (which displays the helix correctly). Many thanks Matthias Vorländer PhD student EMBL Heidelberg - Müller Lab Meyerhofstraße 1, 69126 Heidelberg

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sphere transparency
by Thomas Pochapsky 12 Jun '17

12 Jun '17

Is there any command corresponding to surft (surface transparency) that will modulate the visibility of a sphere representation of a ligand? I want to change it in the course of a morph between substrate-bound and substrate free forms of the same enzyme. I will probably have other questions, but this seems like a good place to start... Thanks, Tom Pochapsky

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Re: [Chimera-users] Axis Of Symmetry
by Elaine Meng 09 Jun '17

09 Jun '17

Hi Catherine, Please send Chimera questions to chimera-users(a)cgl.ucsf (CC’d here) to ensure a response. This "measure rotation” command does not use any atoms, it merely reports how a model is currently rotated and translated relative to the another model. The rotating/translating is done by the matching command before that measurement. From our previous emails I see you were using the “matchmaker” command (same as “mmaker”) which, as described in the manual, uses only CA atoms: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html> If you want to use other atoms in the fitting, you have to instead use the “match” command with the specific atoms given in the command. See the manual: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html> See also the page on “Superimposing Structures” <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> and for a specific example, the “Matching” section in the Glycoside Hydrolases tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/frameimages.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jun 9, 2017, at 12:02 PM, Catherine Jenifer Rajam Rajendran <catrajen(a)umail.iu.edu> wrote: > > Hi Elaine, > > Can you tell me how Axis is configured? after using the command measure rotation, it gives me the reply log with information like axis, axis point, rotation angle etc., But I want to know specifically if Axis is calculated by just using the CA atoms of the chains or All atoms? Is there a way to find axis only using CA/All atoms. > > Thanks, > Catherine > > On Tue, Jun 6, 2017 at 4:33 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Catherine, > (Cc’ing chimera-users(a)cgl.ucsf.edu which is the recommended address for Chimera questions) > > As the message suggests, your models #0 and #1 are not rotated from each other. I’m guessing that you opened the same dimer structure twice and then matched it to itself. For example, if your structure contains chains A and B, it sounds like A was matched to A and B to B, so there was no rotation (zero degrees). You have to make sure that the matching is A to B and B to A. To do this with the “mm” command, for example, you would have to specify the chains AND use the “pair ss” option. > > There is a specific example of commands for structure 5hvp in this previous post. > <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2017-April/013290.html> > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > > On Jun 6, 2017, at 1:22 PM, Catherine Jenifer Rajam Rajendran <catrajen(a)umail.iu.edu> wrote: > > > > Hi Eric, > > I am trying to find Axis of Symmetry in Dimers. I executed mm command, and then tried to execute measure rotation #0 #1 command. It throws me an error: > > > > <image.png> > > > > I am using chimera version 1.11.2. Can you please help me with this? > > Thanks, > > Catherine > >

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model recordings
by P. Buscemi Ph.D. 08 Jun '17

08 Jun '17

Dear Users groups. I've been struggling with this issue for some weeks. I will describe the problem and then as what information I should supply to help me solve the issue. It's a prototype adsorption experiment. Water onto polyethylene oxide. Each component, when run individually in a simulation will complete in a normal fashion with a good recorded video. All simulations were run with live presentation. However when the two models are run together, the story is different. The sequence below represents 1) the two loaded files ( water and PEO) 2) the PEO selected for later constraint ( control drag) 3) moving the water into positon. At this state the " live" simulation aappears normal. The peo does not move, and the water more or less jiggles into position on the PEO. However, in running the movie, molecules of the PEO are disrupted (4) and occupy the space in fragments originally occupied by the water molecules when it was first loaded. The same phenomenon occurs with a PE surface and with models of EtOH. The temperature is set to 0->100K, Hydrogents added Gasteiger charge calculation, 0 charge total, no periodic box. Again, I do not expect any suggestions ( although none would be refused !) only to ask the proper channels and information needed to approach the issue. Regards Paul Buscemi cid:image002.jpg@01D2DED8.C01C06501 cid:image001.jpg@01D2DED8.C01C06502 cid:image002.jpg@01D2DED8.64FCD8803 cid:image003.jpg@01D2DED8.64FCD8804

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PDB file opens from chimera GUI but not from python script ( )
by Nikolaos Bismpikos 07 Jun '17

07 Jun '17

Hello, I am having a problem with trying to open a .pdb file using a python script. The file opens and the protein structure is displayed properly when I open the file using the Chimera GUI. However, when I try to run the code from a python script, using the demo script for looping through .pdb files I get the following error: ---------------------------------------------------------------------- File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/re.py", line 251, in _compile raise error, v # invalid expression ---------------------------------------------------------------------- This is the code I am trying to run: ---------------------------------------------------------------------- import sys import os from chimera import runCommand as rc # use 'rc' as shorthand for runCommand from chimera import replyobj # for emitting status messages # change to folder with data files os.chdir("/home/nick/Python/pdb") print >> sys.stdout, retval # gather the names of .pdb files in the folder file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")] # loop through the files, opening, processing, and closing each in turn for fn in file_names: replyobj.status("Processing " + fn) # show what file we're working on rc("open " + fn) replyobj.status("Opened " + fn) # show what file we're working on rc("align ligand ~ligand") # put ligand in front of remainder of molecule rc("focus ligand") # center/zoom ligand rc("surf") # surface receptor rc("preset apply publication 1") # make everything look nice rc("surftransp 15") # make the surface a little bit see-through # save image to a file that ends in .png rather than .pdb png_name = fn[:-3] + "png" rc("copy file " + png_name + " supersample 3") rc("close all") ---------------------------------------------------------------------- The error in more detail, including the traceback from the terminal is the following: ---------------------------------------------------------------------- Processing prediction[NoEnergy-K:0-BS:0.00]-21(20.310186).pdb Traceback (most recent call last): File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimeraInit.py", line 683, in init chimera.openModels.open(a, prefixableType=1) File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py", line 1929, in open models = func(filename, *args, **kw) File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py", line 1299, in _openPython loadFunc(sandboxName, fileName, f) File "test1.py", line 23, in <module> rc("open " + fn) File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py", line 2747, in runCommand makeCommand(*args, **kw) File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/Midas/midas_text.py", line 69, in makeCommand f(c, args) File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/Midas/midas_text.py", line 1552, in doOpen paths = testPath(text, wildcarding) File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/Midas/midas_text.py", line 1538, in testPath return glob(expanded) File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/glob.py", line 27, in glob return list(iglob(pathname)) File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/glob.py", line 49, in iglob for name in glob1(os.curdir, basename): File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/glob.py", line 83, in glob1 return fnmatch.filter(names, pattern) File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/fnmatch.py", line 56, in filter _cache[pat] = re_pat = re.compile(res) File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/re.py", line 194, in compile return _compile(pattern, flags) File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/re.py", line 251, in _compile raise error, v # invalid expression error: bad character range Error while processing test1.py: error: bad character range File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/re.py", line 251, in _compile raise error, v # invalid expression See reply log for Python traceback. ---------------------------------------------------------------------- The error obviously appears at the 2nd line of the for loop ( rc("open " + fn) ) Any tips on why this might happen? I am using Ubuntu 14.04 LTS and the Chimera version I installed is chimera-1.11.2-linux_x86_64.bin

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Axis Of Symmetry
by Catherine Jenifer Rajam Rajendran 06 Jun '17

06 Jun '17

Hi Eric, I am trying to find Axis of Symmetry in Dimers. I executed mm command, and then tried to execute measure rotation #0 #1 command. It throws me an error: I am using chimera version 1.11.2. Can you please help me with this? Thanks, Catherine

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measure surface area
by 陈柳青 06 Jun '17

06 Jun '17

Hi! i want measure several selected residues surface area and volume, but in the reply log, it always give the total surface area and volume of the protein, how can i get only the selected residues surface area? because this residues make a cavity , which may binding substrate. in addition, the castP server can't give me the pocket i wanted, because it give a bigger pocket than i wanted. thanks in advance！ liuqing chen -- Liuqing Chen School of Life Science & Biotechnology Minhang Campus Shanghai Jiao Tong University No. 800 Dongchuan Road Shanghai 200240 P.R. China Tel: +86 21 34207247

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extracting real numerical values for steric energies
by Fenton Heirtzler 06 Jun '17

06 Jun '17

Hello, I'm using Chimera to optimize the structures of several small-molecule transition metal complexes. The goal is to compare the steric energies of different diastereomers. I 've searched the local documentation on version 1.11.2 (Macintosh) for the term "Minimize structure" but found nothing which actually described the meaning,number format, reference points and units which are produced by the "Minimize Structure" command and appear in the "Reply log". For example, the potential energy values which are returned can be either < 0 or > 0 (!!) If a minimization is occurring, then the force field will describe those parameters - but the preceding values make no sense. Some advice and instruction would be appreciated. Thanks *Dr. Fenton Heirtzler* ------------------------------- Phone: +1-301-312-5145 LinkedIn <http://www.linkedin.com/in/fentonhorgchem/>

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Chimera files to be read in Pymol?
by Tuli Mukhopadhyay 05 Jun '17

05 Jun '17

Hello, Is there a (simple) way to read Chimera session in Pymol or vice versa? Tuli -- -- Tuli Mukhopadhyay Department of Biology Indiana University Simon Hall MSBI, Room 220C 212 S. Hawthorne Drive Bloomington, IN 47405-7003 Phone 812.856.3686 Fax 812.856.5710 sumukhop(a)indiana.edu | Tuli Lab Webpage <http://www.bio.indiana.edu/~tulilab/> | @TuliLab <https://twitter.com/TuliLab>

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Re: [Chimera-users] Chimera how to question
by Elaine Meng 05 Jun '17

05 Jun '17

> On Jun 5, 2017, at 5:59 AM, Egor Tchesnokov <tchesnok(a)ualberta.ca> wrote: > > Hello, > Is there a way to delete a set of residues in the beginning of the sequence, so these residues disappear from the sequence in the pdb file? > I am working on the structure-base alignment and the exogneous residues in the protein sequence (eg. affinity-tag) interfere with the nubmering of the endigenous residues. > Thank you > Egor Hi Egor, Of course you can delete atoms. You can select them and then use menu: Actions… Atoms/Bonds… delete, or you can use the “delete” command ...either with selection (delete sel) or with some other kind of specification of what you wanted to delete, e.g. delete :1-20.A ...to delete residues 1-20 of chain A. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/delete.html> Maybe in your case it would be easiest to use the sequence window (Favories… Sequence) to select the set of residues you want to delete by dragging a box around them, and then using the menu or command. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/delete.html> However, this will not change any sequence numbering. Chimera just uses the numbers that are in the input file. Sometimes but not always, affinity-tag residues are given negative residue numbers in the input file. If you want to renumber residues, see menu: Tools.. Structure Editing… Renumber Residues, or the command “resrenumber”: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/renumber.…> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/resrenumber.html> Chimera questions should be sent to chimera-users(a)cgl.ucsf.edu (CC’d here) to ensure that they will be answered. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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