- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] How to install package in chimera python?
by Jaime Rodríguez-Guerra 04 Nov '16

04 Nov '16

Hi! My favorite way to do this is via pip. 1. First grab the pip installer from https://bootstrap.pypa.io/get-pip.py wget https://bootstrap.pypa.io/get-pip.py 2. Install pip in Chimera chimera --nogui --script get-pip.py 3. Call the newly installed pip to install your package, ie. scipy chimera --nogui --script `chimera --root`"/bin/pip install scipy" That's it!

1 0

How to install package in chimera python?
by Michał Kadlof 04 Nov '16

04 Nov '16

Hello, how can I add a python package to chimera python? I would like to use scipy inside chimera script. -- pozdrawiam serdecznie Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

1 0

MultiFit is not working
by Smirnova, Julia 03 Nov '16

03 Nov '16

Dear Chimera-team, I was trying to use a MultiFit service of Chimera (to fit two models into my cryo density map), and it gives me the following error: Wrote /tmp/tmp_rSyaW/INSRT_model2.pdb Wrote /tmp/tmp_rSyaW/1x1n.pdb Traceback from web service request (connection setup): Traceback (most recent call last): File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/opal_client.py", line 11, in __init__ self._setup(serviceName, opalURL, sessionData) File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/opal_client.py", line 52, in _setup md = self.sudsClient.service.getAppMetadata() File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/site-packages/suds_jurko-0.6-py2.7.egg/suds/client.py", line 280, in __getattr__ port = self.__find(0) File "/opt/UCSF/Chimera64-1.11.2rc/lib/python2.7/site-packages/suds_jurko-0.6-py2.7.egg/suds/client.py", line 315, in __find raise Exception, 'No services defined' Exception: No services defined Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Traceback from web application request: Traceback (most recent call last): File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/appWebService.py", line 48, in _initApp self.backend = Backend(service, url) File "/opt/UCSF/Chimera64-1.11.2rc/share/WebServices/opal_client.py", line 21, in __init__ raise NonChimeraError("Web service appears " NonChimeraError: Web service appears to be down. See Reply Log for more details. Service 'opal:MultiFitWebService' is unavailable. See Reply Log for more details. Could you please give me a clue what might be a problem. I do have an internet connection (checked by 'Fletch by ID... ' function) Thank you for your support, Julia

4 5

Re: [Chimera-users] How to accurately and proportionally adjust structure size
by Cathy Lawson 03 Nov '16

03 Nov '16

Hi Xiaoyan, Tom Goddard had provided some useful hints when I asked a similar question last month. This has worked really well, though does require fitting a set of coordinates into each map that you want to compare. After following the suggestion set the focus always to all (or some element) of the aligned model for a consistent view across a set of maps. see http://www.cgl.ucsf.edu/pipermail/chimera-users/2016-October/012767.html

1 0

How to accurately and proportionally adjust structure size
by Zhu, Xiaoyan 02 Nov '16

02 Nov '16

Hello, I am trying to compare the cryoEM structures of radial spoke from different organisms. In the mean time, I want to display the same structure from different views. I have trouble to adjust the size accurately and proportional within the same and between different models.? For example, when I adjusted the structure from distal view and then rotated to the proximal view, the distance from screen changed and so the size changed. If I manually adjust the structure after rotation, I don't know how to make the structures from both views identical size. Similar thing troubles me when I want to adjust the size of two independent structures proportionally. Hope I made myself clear. Thank you a lot! Xiaoyan Zhu Ph.D. Candidate Department of Biological Sciences, Marquette University

3 3

select atoms near at least one other atom in original selection?
by Oliver Clarke 01 Nov '16

01 Nov '16

Hi, I’d basically like to perform the equivalent of “hide dust” on an atom selection. I have a bunch of mutation positions that I’ve mapped onto a structure, and I would like to create a subselection containing only those positions which are within lets say 10Å of at least one other postion in the original selection - basically to represent structural clusters of mutations on the structure. Does anyone have any suggestion how to create such a selection using Chimera’s atom selection language? It seems like zr should do it but I can’t quite figure out how. Cheers Oli.

3 5

how to select atom within a rectangular region
by Cherry Dons 01 Nov '16

01 Nov '16

Hi Chimera Developers, This is Dengpan, one of chimera users. I have a question about how to select atoms within a region? For example, I I want to select atoms within a rectangular region x0 to x1, y0 to y1, z0 to z1. Could you please give me a hint how to do it? Thanks. Dengpan Dong -- Department of Materials Science and Engineering, University of Utah

2 1

Headless Chimera Registration Notification
by Healey, Joe 31 Oct '16

31 Oct '16

Hi Chimera Team, For some reason the install I have of headless Chimera as recently started warning me that I'm using an unregistered copy (I have actually registered before via the GUI version installed on my Mac (local machine)). Is there some way I can suppress this message (only purely because it's cluttering the STDOUT in my pipelines and I sometimes want to parse this). Or is there a chimera env variable I can modify to tell it that I am registered? Obviously I can't register in the manner the warning describes, as I'm unable to launch a GUI variant of Chimera on the server I'm using. Thanks! Joe Healey M.Sc. B.Sc. (Hons) 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>

2 1

How I can use extension in chimera
by b.behkamal＠stu-mail.um.ac.ir 27 Oct '16

27 Oct '16

Hello, I need to work with the extension files which is attached. The attached files is related to SSETracer. I didn't know how I can use them in chimera. Would you mind please help me about this matter and say to me the details of work step by step. Thank you very much in advanced. Regards, -- Bahareh Behkamal Ph. D. Candidate of Computer Engineering Researcher in Structural Bioinformatics Dept. of Computer Engineering Ferdowsi University of Mashhad, Mashhad, Iran

2 2

problem regarding saving a file
by gutta ramadevi 26 Oct '16

26 Oct '16

Good day, I am using chimera following tutorials. I saved the processed receptor and ligand files in pdb format.But the files are not being saved.when i open the saved files i am getting the unprocessed receptor and ligand files. please help me to save the files.

3 2

Definition of residues involved in binding ligand
by Maarten Schledorn 26 Oct '16

26 Oct '16

Dear reader, I have a pdb file of a protein with bound ADP and the file contains nothing but atomic coordinates and a few CONECT lines. If I open the file, the residues involved in binding ADP are shown, but I would like to know how Chimera knows this. I assume it is some VdW vicinity/overlap perhaps, or all residues within a certain distance from the ADP molecule, but I would like to know exactly how it is defined. I have tried to look for it in the documentation but haven't been successful so far. Does someone know the answer or a link to where it has been discussed previously? Many thanks in advance! Maarten

2 1

pythonic version of fitmap tool
by Michał Kadlof 25 Oct '16

25 Oct '16

Is there any pythonic way of running fitmap tool? I would like to use it as a function that return parameters that I can assign to variable without parsing the output. I didn't find anything similar in Midas module. -- best wishes, Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

2 1

Re: [Chimera-users] chimera minimization querry
by Elaine Meng 21 Oct '16

21 Oct '16

On Oct 21, 2016, at 2:42 AM, Shumaila Khan <shumailakhan432(a)yahoo.com> wrote: > > Hello, > I am shumaila khan , M.phil student at Quaid-i-Azam University Islamabad, Pakistan. Attached File is my structure and I want to minimize it. But there occurs an error that "Residue #0.1:165.A (ALA/ alanine) should have either atom HN or H, but not both. Kindly please reply me asap and help me out. > Thanks Dear Shumaila, For future reference, you should use the chimera-users(a)cgl.ucsf.edu email address for questions. For the minimization error, it is probably what the message says! I can only repeat the message: the residue should not have both of those atoms that it mentions, so you would need to delete one of them. 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

1 0

Chimera crashes on Mac OS Sierra (10.12)
by Tom Goddard 20 Oct '16

20 Oct '16

The Chimera developers have received 8 Chimera crash reports on the new Mac OS Sierra (10.12) somehow related to scrollbars. You may want to hold off updating to Sierra if you make heavy use of Chimera. We have not yet been able to reproduce the crash. It is very likely a bug in the Mac Tk window toolkit that Chimera uses, so even when we figure out how to reproduce it it may take time to figure out a fix since the problem is not in our code. Tom

1 1

creating O2 molecule in Chimera
by Elaine Meng 20 Oct '16

20 Oct '16

> Subject: Query about chimera > Date: Thu, 20 Oct 2016 06:47:23 +0000 (UTC) > From: Shumaila Khan <shumailakhan432(a)yahoo.com> > > Hello, > I m student from Quaid-i-Azam University, Pakistan, doing my MS research project and I have some problems while working on chimera. I want some help regarding Attachment of oxygen atom to plant hemoglobin.Kindly please help me out how will I do that. kindly tell me how to draw oxygen molecule on chimera? While drawing Oxygen molecule it has only only Oxygen atom and two hydrogen atoms attached. Kindly help me out. Waiting for your kind response. Hi Shumalia, Your question was forwarded to me — Chimera questions should be sent to this address, chimera-users(a)cgl.ucsf.edu There are several different approaches you could use. One way is to use command: open smiles:oo If you hold the mouse over it you can see a balloon that says the bond length is 1.004. You could change the bond length to a better value by (1) selecting the bond (Ctrl-click on the bond so it has a green outline) (2) using Build Structure to change the length of the bond. Menu: Tools… Structure Editing… Build Structure, and in that dialog change from the “Start Structure” section to the “Adjust Bonds” section. Now you can use the slider or type in a value to change the length to what you want. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h…> That would make the oxygen molecule a separate model from your hemoglobin. You would probably want to first move the oxygen molecule by hand to the right position, and then (optionally) combine it together with the hemoglobin to make a single model depending on what you are planning to do. If you don’t need them in the same model, there is no need to combine. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> Or, another totally different approach is to find some other hemoglobin structure that already has an oxygen molecule and superimpose the two structures to get the oxygen in the right place, and then delete all the other atoms of the other structure except for the oxygen molecule. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.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

1 0

chimera 1.11.2rc crashes
by Yanni Goudeuk 18 Oct '16

18 Oct '16

Hello Chimera developers I've got the latest chimera (1.11.2rc), installed on windows 7 (64bit). My card is Nvidia Quadro K2000 and is using the latest drivers: 369.49 - *3D OpenGL stereo* is *enabled* under "*manage 3D settings"* in *nvidia Control Panel* My problem is that chimera crashes a few minutes after I open a .pyc file. Sometimes it will crash when I add a map in "*model panel*", sometimes when I rotate the structure, sometimes when I go though the tabs under " *Favourites*" --> "*Side view*". This is happening with other .pyc files too. I can also confirm that this is happening with older versions of chimera. Please have a look at the Application error log from event viewer: The program pythonw.exe version 0.0.0.0 stopped interacting with Windows and was closed. To see if more information about the problem is available, check the problem history in the Action Center control panel. Process ID: ab0 Start Time: 01d2246bcf21dbd4 Termination Time: 46 Application Path: C:\Program Files\Chimera 1.11.2rc\bin\pythonw.exe Report Id: 3c965b43-905f-11e6-bd99-b8ca3a8bb0d4 If you have any suggestions please let me know. Many thanks

3 7

Guidance in finding Interactive Aminoacids with a ligand
by Shreyas Iyer 17 Oct '16

17 Oct '16

Respected Sir, I am unable to find the interactive aminoacids with the ligand present in a protein. Please guide me how to determine interatcive aminoacids. Awaiting a positive reply Yours Sincerely, Shreyas M Iyer

2 1

MatchMaker algorithm
by 陈柳青 15 Oct '16

15 Oct '16

Respected Sir/Madam The ucsf matchmaker algorithm is "Needleman-Wunsch" and "Smith-Waterman", but other program use SSM algorithm, such as ccp4mg, cuemol et al., can chimera add SSM algorithm? and whether these algorithm will affect results differently? sincerely 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

2 1

MD trajectory analysis
by George Tzotzos 13 Oct '16

13 Oct '16

My task is to identify ligand interactions with protein residues throughout an MD trajectory. I thought of something along the lines sel ligand z<3.5 #for vdW interactions, etc. I don’t think this can be done using the MD movie interface but I may be wrong. I then tried the following: 1. sel protein/hold selection steady 2. sel ligand 3. calculate occupancy (MD Movie/Analysis) 4. Chimera/select/clear selection 5. turned the Volume Viewer to mesh/level2. What I obtained is a mesh grid enclosing solid surfaces (see attached snapshot). I’m not able to get rid of these surfaces? I think that the problem ma be in step 2 above (sel :ligand). My ligand is N,N-Diethyl-meta-toluamide. Should I select the aromatic ring part separately of the amide part, run the above process and then repeat selecting the amide part? I also tried MD movie/Analysis/Residue interaction network, first selecting the ligand. The results I obtained are not satisfactory. Is there a better way of dealing with my problem? Thanks in advance for your kind help George

2 5

Re: [Chimera-users] question
by Jaynes, Jesse 12 Oct '16

12 Oct '16

Hi Folks: I am having difficulty in converting C-terminal carboxyl to C-terminal amide on a beta sheet of 16 amino acids in length. When I try to get the complete amino acids displayed, it doesn't work. It just displays the main peptide cylinder. Thanks for your help. Jesse Jaynes On Thu, Oct 6, 2016 at 6:11 PM, Jaynes, Jesse <jjaynes(a)mytu.tuskegee.edu> wrote: > Hi Folks: > > I am interested in generating a 23 amino acid peptide with several > ornithines present. Is it possible? If not can I construct it with > glutamine as a replacement for ornithine and then just take the carbonyl > group and replace the oxygen with 2 hydrogens. > > I just renewed my registration. > > Thank You, Jesse Jaynes > > On Thu, Oct 6, 2016 at 3:22 PM, Jaynes, Jesse <jjaynes(a)mytu.tuskegee.edu> > wrote: > >> Hi Folks: >> >> I am interested in generating a 23 amino acid peptide with several >> ornithines present. Is it possible? If not can I construct it with >> glutamine as a replacement for ornithine and then just take the carbonyl >> group and replace the oxygen with 2 hydrogens. >> >> Thank You, Jesse Jaynes >> > >

2 3

Creating a dummy atom on a defined position
by Subha Kalyaanamoorthy 11 Oct '16

11 Oct '16

Hi There, Wondering if there is a way to create a dummy atom on a specified position(xyz coords) using a chimera command line? Thanks, Subha -- Dr. Subha Kalyaanamoorthy Post Doctoral Fellow Faculty of Pharmacy and Pharmaceutical Sciences University of Alberta Edmonton, Canada.

3 3

Computing 'basic' structure characteristics
by Healey, Joe 11 Oct '16

11 Oct '16

Hi again Chimera Team, I have 2 questions, one specific and one quite general. If you see the emails below, I was speaking with Jaime about computing basic structure characteristics (pKa, net surface charge, proportions/predominance of 2ary structure etc). The general question I have is what suggestions might you have for functions within chimera capable of computing any or all of these features? (ideally commandline based so that I can run this over many PDB structures). The specific question that pertains to the below is that Jaime mentioned each residue has an int value that corresponds to a particular structure designation, ints from -1 to 6. Could you let me know what the correspondence is between these values and actual structure? Joe Healey M.Sc. B.Sc. (Hons) 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> ________________________________ From: Jaime Rodríguez-Guerra <jaime.rodriguezguerra(a)uab.cat> Sent: 08 October 2016 09:55 To: Healey, Joe Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers Hi again Joe! No problem at all; I'll be pleased to help you. For charges, I think Chimera can calculate them as part of the Surface/Binding analysis> Dock Prep wizard. You also have some information about 2nd structure inside chimera.Residue objects, specifically ssId attribute. However, these are int values, and I don't really know which ss is each (ranging from -1 to 6, as I have observed). For pKa, you can use PropKa (https://github.com/jensengroup/propka-3.1) and then I guess you'll be able to get the pI somewhere around the code. I've been designing a GUI to use this in Chimera, but it's not yet ready... Sorry about that! I don't know if you need anything else... but I think the Python community will have you covered one way or another! BioPython.PDB might be useful too (http://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ) Cheers, Jaime. 2016-10-06 15:57 GMT+02:00 Healey, Joe <J.R.J.Healey(a)warwick.ac.uk<mailto:J.R.J.Healey@warwick.ac.uk>>: Hi again Jaime, Hope you don't mind but I had a couple of questions for you. You may have figured out from all the previous correspondance that I have a load of protein structure simulations. The RMSD script you helped me with was to sort of 'broadly' gauge whether the simulations looked realistic or not. For some of them, I'd like to build up a chart of their tertiary structure properties based on the simulations. Things like charge/hydrophobicity, isoelectric point, 2ndary structure dominance and so on. Could I ask you for any advice you might about what tools are available to analyse PDBs? I'm sure chimera is probably capable of it too. I've mostly found webservers at the moment for specific tasks, but I'd like to do most of the analysis locally. My group is full of bioinformaticians, but I'm the only one who really looks at proteins so I need the advice of a computational chemist I think! Cheers, Joe Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620<tel:%2B44%20%280%29%207536%20042620> | Email: J.R.J.Healey(a)warwick.ac.uk<mailto:J.R.J.Healey@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> ________________________________ From: Healey, Joe Sent: 23 September 2016 11:51:40 To: Jaime Rodríguez-Guerra Cc: Eric Pettersen; chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers Not at all! Much appreciated, as I think I mentioned, this is my first go at writing anything remotely complex in python (and not a bad turn out for about a week I don't think...) A lot of the mess comes from copying functional bits from StackOverflow in the interests of just getting it working first, and making it pretty second as I'm sure you can appreciate (you'd hate to see my LaTeX preamble)! Not needed to close the file with 'with' is useful to know (takes some of the headache out of knowing where to place the close). I'll certainly make the tidy ups you've suggested, for my own learning. Thanks again, Joe :) Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620<tel:%2B44%20%280%29%207536%20042620> | Email: J.R.J.Healey(a)warwick.ac.uk<mailto:J.R.J.Healey@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> ________________________________ From: Jaime Rodríguez-Guerra <jaime.rodriguezguerra(a)uab.cat<mailto:jaime.rodriguezguerra@uab.cat>> Sent: 23 September 2016 10:56:38 To: Healey, Joe Cc: Eric Pettersen; Jaime Rodríguez-Guerra; chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers Hi Joe! You're welcome! Glad to see you got it working. I've reviewed your code and would want to point out some details that might be helpful to you in the future, though. These are mostly style-related things, but those will contribute to a cleaner reading experience! 1. You don't need backslashes if you're inside parenthesis. So, in all those parse_argument lines, you can safely delete them. Related to this, you can wrap imports with parenthesis, so that backslashes are not needed. 2. Tuple unpacking does not need parenthesis in you're dealing with 1D-tuples. Only needed if you are dealing with more than one dimension (ie, (animal, fruit), sport = [['tiger', 'pear'], 'soccer'] 3. Since you are opening files with the "with" context manager, you don't need to manually close the file later. It's closed automatically as soon as you leave that with block. 4. Lines 166-170 could be replaced with a (cleaner, but not necessarily more performant) glob.glob() call. Check it out to see if it satisfies your requirements. 5. While you are at it, take a look at the PEP8 docs and the Google Python style guide. You don't need to follow all the rules, but they are really helpful in bringing consistency to your own style! That's it! Hope you don't mind these pieces of advice :) Cheers, Jaime. 2016-09-23 11:27 GMT+02:00 Healey, Joe <J.R.J.Healey(a)warwick.ac.uk<mailto:J.R.J.Healey@warwick.ac.uk>>: > That was exactly what I was after thanks! I figured the object orientation > should provide that somewhere but was barking up slightly the wrong tree! > > > Thank you all for all your help - definitely wouldn't have been able to do > it without you! > > > If it's of any interest, or it helps for any future questions where you > might want to refer back to code segments, I've put the > more-or-less-finished script in this paste: > > > http://pastebin.com/xJNSWJGq > > > Joe Healey > > > M.Sc. B.Sc. (Hons) > PhD Student > MOAC CDT, Senate House > University of Warwick > Coventry > CV47AL > Mob: +44 (0) 7536 042620<tel:%2B44%20%280%29%207536%20042620> | Email: J.R.J.Healey(a)warwick.ac.uk<mailto:J.R.J.Healey@warwick.ac.uk> > > Jointly working in: > Waterfield Lab (WMS Microbiology and Infection Unit) > and the Gibson Lab (Warwick Chemistry) > > Twitter: @JRJHealey | Website: MOAC Page > ________________________________ > From: Eric Pettersen <pett(a)cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>> > Sent: 22 September 2016 20:54:35 > To: Jaime Rodríguez-Guerra > Cc: chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>; Healey, Joe > Subject: Re: [Chimera-users] Recursive structure matching and acquisition of > descriptive numbers > > Thanks Jaime — exactly right. I realized that the “atoms1, atoms2” in my > original example didn’t really give any indication of which atoms were > which, which is why in my later examples I changed to "simAtoms, refAtoms”, > so it’s actually “atoms2” that are the reference atoms. > > —Eric > >> On Sep 22, 2016, at 11:45 AM, Jaime Rodríguez-Guerra >> <jaime.rodriguezguerra(a)uab.cat<mailto:jaime.rodriguezguerra@uab.cat>> wrote: >> >> Hi! >> >> Since you are getting lists of atoms back, you only need to do some >> attribute access (rather than method calling)! >> >> Every chimera.Atom object has an attribute called molecule: a >> reference to its parent chimera.Molecule. chimera.Molecule objects >> have an attribute called 'name', but sometimes this is not very >> informative (depends on your input), so you need to resort to the pdb >> filename, stored in the first element of the openedAs tuple. >> >> In code, this looks like this: >> >> for atoms1, atoms2, rmsd, fullRmsd in match(CP_BEST, [ref, sims], >> defaults[MATRIX], "nw", defaults[GAP_OPEN], defaults[GAP_EXTEND]): >> molecule1 = atoms1[0].molecule # any atom from the list will do >> molecule2 = atoms2[0].molecule >> print molecule1.name<http://molecule1.name>, "\t", molecule2.name<http://molecule2.name>, "\t", rmsd # >> molecule1.openedAs[0] will also work here >> >> I don't know if atoms1 comes consistently from the reference molecule, >> but I'd guess it does. >> >> Hope it helps! >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >

3 7

Chimera using problem
by Chonghua Ren 11 Oct '16

11 Oct '16

Dear there, I am learning how to use Chimera now, I like it so much and find it is so awesome. I have one question, if I want to input a DNA sequence like ID "1d86", how can I transfer the DNA sequence to PDB format? Another question, how can I know protein and DNA interaction using this software? Thank you so much! Best wishes, Chonghua Ren

2 1

Assisstance to claculate RMSD value
by Shreyas Iyer 08 Oct '16

08 Oct '16

Respected Sir/Madam, I wanted to know how to calculate RMSD values between any 2 homology models of a protein with the help of USCF Chimera. Please guide me as soon as possible. Awaiting a positive reply. Yours Sincerely, Shreyas Iyer

2 2

fit in map and multimodel pdbs
by Martin Lawrence 07 Oct '16

07 Oct '16

Dear Chimera Users, I have a pdb file for an entire virus (biological assembly) that I can read into Chimera just fine, as either a multimodel PDB with 60 different models, or as a PDB lacking model and endmdl cards, but with the atom number of the multi-model pdb preserved. The model is placed very close to the density for the virus in a tomogram. When I use the fit in map command, the single model pdb moves nicely by a couple of nm and a few degrees into the tomogram density. For the multimodel map I must first use the combine command in the model panel to combine the 60 differernt models, but that then also moves nicely into the density. However, in both cases, when I try to write out the slightly rotated/translated coordinates to a PDB file, I wind up with a semi-corrupted PDB file containing **** in many locations, especially for the last half of the file. Since the virus is pseudo T=31 with 18 chains in the viral asu, the pdb model has more than 2 million atoms and 1048 chains; the chains obviously cannot be uniquely identified with a single letter, the atom numbers exceed the the allowed format, and residues are renumbered and then also exceed the allowed format. I can fix this by hand to some extent, and could write a jiffy to put it back into the multiple model format, but feel like there is a more elegant solution to this problem already embedded in Chimera. Preferably one that will allow high throughput down the road. Any advice would be appreciated! Thanks, Martin Martin Lawrence Department of Chemistry and Biochemistry Montana State University Bozeman, MT 59717 USA

2 1