- Chimera-users - RBVI Mailing Lists

different behavior of the Win and OS-X version seen in case of surface calculations
by Marek Maly 15 Dec '14

15 Dec '14

Hello, I found already several times the differences between OS-X and Win version of Chimera (1.10.). Problem is regarding the ability to calculate molecular surface. There are some cases when Win version of Chimera 1.10 is not able to calculate molecular surface of some more complicated molecular structure (e.g. protein) but on the other hand the OS-X version of Chimera (again 1.10) is able to do it (although writes warning that there was some partial problems). Moreover when I create PY session of such molecule with surface calculated/visualized under OS-X and then I want to open this session under Win version it is opened but without the surface and writes many errors into the log - see below. In both versions I am using default settings (no special changes in parameters important for the surface calc.). How is this different behavior of the same program under Win and OS-X possible ? Do you have any recommendation how to eliminate this problem ? Thank you in advance, Best wishes, Marek Here is the err list after the attempt to load into Win Chimera 1.10 session containing "problematic" molecule with surface calculated under OS-X version of the Chimera 1.10 ***** C:\Program Files\Chimera 1.10\bin\mscalc.exe 1.400000 2.000000 0 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags Surface calculation failed, mscalc returned code 5. Surface calculation frequently fails for large, multi-chain structures. The calculation may be successful if the chains are treated individually, by using the "split" command before generating a surface. If splitting is not desired or the structure is already a single chain, changing molecular surface parameters in the Selection Inspector or (before surface creation) the New Surfaces category of Preferences may allow the calculation to succeed. More details are given at http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html Traceback (most recent call last): File "gB_2G_S16_A.py", line 2669, in <module> restoreCoreModels() File "gB_2G_S16_A.py", line 2654, in restoreCoreModels restoreSurfaces(surfInfo) File "C:\Program Files\Chimera 1.10\share\SimpleSession\versions\v40.py", line 55, in restoreSurfaces elif len(customColors) != len(s.triangleData()[0]): TypeError: 'NoneType' object has no attribute '__getitem__' Error restoring core models: TypeError: 'NoneType' object has no attribute '__getitem__' File "C:\Program Files\Chimera 1.10\share\SimpleSession\versions\v40.py", line 55, in restoreSurfaces elif len(customColors) != len(s.triangleData()[0]): See reply log for Python traceback. Traceback (most recent call last): File "gB_2G_S16_A.py", line 3025, in <module> restoreRemainder() File "gB_2G_S16_A.py", line 3020, in restoreRemainder restoreSilhouettes(silhouettes) File "C:\Program Files\Chimera 1.10\share\SimpleSession\versions\v62.py", line 265, in restoreSilhouettes model = idLookup(modelID) File "C:\Program Files\Chimera 1.10\share\SimpleSession\versions\v23.py", line 162, in idLookup return globals.sessionMap[sesID] KeyError: 27136 Error restoring post-model state: KeyError: 27136 File "C:\Program Files\Chimera 1.10\share\SimpleSession\versions\v23.py", line 162, in idLookup return globals.sessionMap[sesID] See reply log for Python traceback. Warning: Could not restore surface color on surface model with id 0.0 because that surface was not restored. C:\Program Files\Chimera 1.10\bin\lib\site-packages\matplotlib\axes.py:2369: UserWarning: Attempting to set identical left==right results in singular transformations; automatically expanding. left=1, right=1 + 'left=%s, right=%s') % (left, right)) -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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Chimera Published Paper
by Kurt Degabriele 08 Dec '14

08 Dec '14

Dear sir/madame, I am a pharmacy student currently undergoing my 4th year pharmacy project at the University of Malta as part of my 5 year study course; I am currently doing research within the Med. Chem. field and would like to ask if you can send me a copy of the following paper so I can include it in my study: UCSF Chimera—A visualization system for exploratory research and analysisEric F. Pettersen, Thomas D. Goddard,Conrad C. Huang, Gregory S. Couch,Daniel M. Greenblatt, Elaine C. Meng andThomas E. Ferrin* Article first published online: 1 JUL 2004DOI: 10.1002/jcc.20084 Regards Kurt

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Re: [Chimera-users] How to use a colour-valued attribute?
by Elaine Meng 04 Dec '14

04 Dec '14

On Dec 3, 2014, at 1:30 AM, Mungo Carstairs (Staff) <g.m.carstairs(a)dundee.ac.uk> wrote: > Thanks all. > Tom, your suggestion of comma- instead or or-delimiter improves speed several times! > Elaine, your point about specifying the chain is noted. > > Conrad, I didn't explain too clearly: my 'real' command is the 'non-contiguous' example (think Zappo colouring with some custom features colours on top). The 'contiguous' example was just what I was using to explore behaviour of setattr / defattr / rangecolor. > (Also by the way the REST API is working fine for me.) > > Instead of 'color' I am now using 'setattr' followed by 'rangecolor'. > I tried both 'setattr' and 'defattr' (passing a temporary file) and didn't see any significant performance difference between them, at the scales I am testing so far (up to 3 models of 1600 residues). > > So I have what I need for now. But I'm still curious to know if / how you get Chimera to 'act on' (display) a colour-valued attribute. > > Best regards, > Mungo Hi Mungo, Setting the color attribute with setattr or defattr does change the color immediately. The problem in what you sent earlier: setattr r color green #0:1-84.B … is that there is no residue attribute named “color". There are atom and molecule-model attributes by that name (setattr a color …) but the only per-residue color setting is ribbon color, name “ribbonColor” … thus you would want something like: setattr r ribbonColor green #0:54.a,76.a … and that would only color the ribbon, not the atoms/bonds. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#respr…> Actually I am mystified as to why this would be any faster than using the color command with the same atomspec (#0:54.a,76.a in the example above), but maybe the others who know more about the “guts” of Chimera can comment. Best, 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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Commands for multiscale models?
by Hurt, Darrell (NIH/NIAID) [E] 03 Dec '14

03 Dec '14

Hi Chimera friends, I was reading this post from 2009 that indicates that there are no Chimera commands for multiscale models: http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-June/004009.html Is it still the case that there are no Chimera commands for manipulating the multiscale models? I saw the blue-tongue virus example script for doing something similar using Python itself: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/blueto… I want to script the loading of an arbitrary VIPERdb model and then create multiscale model surfaces for every chain (not just the copies). Can it be done with Chimera commands? Or do I need to work up my Python-fu? 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 Bethesda office: 301-402-0095 Rockville office: 240-669-2741 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> , @NIH3Dprint<https://twitter.com/nih3dprint> 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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volume viewer step value
by Ludovic Renault 03 Dec '14

03 Dec '14

Hi, When I load different EM volumes into Chimera, depending on the size of the box the display step value changes from 1 to 4. Is it possible to force chimera to always load the 3d map with a step value of 1? Or at least change some parameters in preferences to have step 1 loaded with my routine volumes (up to 300 pixel boxes for example). Thanks, Ludo

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show surface fails
by Hartzell Jr., Criss 02 Dec '14

02 Dec '14

I am struggling to show an electrostatic surface on the solvent accessible surface for several related proteins. It works fine in Pymol with APBS but with Chimera I continue to get "surface calculation failed, mscalc returned code 5". I have read posts going back at least 5 years about this problem and I have tried all of the various work-arounds (vdwdef, split, probe radius and vertex density). Has this problem been solved? I am using version 1.8.1 on a PC. Is there a way to identify which part of the protein is causing the problem? Criss Hartzell Professor Department of Cell Biology Emory University School of Medicine Atlanta, GA 30322 ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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regarding distance measurement
by abhishek jamwal 02 Dec '14

02 Dec '14

Dear All, I have created a stereoview using chimera where I am showing distance between sidechain atoms of a protein. when I save an image of this stereoview (tiff, 600dpi), the connector lines showing the distances are fading, they are not of same quality in the image as in the original view ! Is there a way to save image without disturbing quality of the connector lines showing distances ? thnx abhishek

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How to use a colour-valued attribute?
by Mungo Carstairs 02 Dec '14

02 Dec '14

Hi, This feels like a basic question but it has stumped me for a day now so here we go... I'm exploring ways of programmatically setting colours to find the most efficient method. This is for the 'custom coloured' case (residue-based colour schemes are not a problem). The simple version is to send as many 'color' commands as there are colours in my (Jalview) sequence: color #ffafaf #0:1.B|#0:5.B|#0:7-8.B|....;color #ffff00 #0:39.B|#0:44.B|#0:47.B|#0:77.B; This works, but doesn't seem to scale up well for large/many structures - I start to see Chimera using 100% CPU for minutes at a time. I'm trying instead to see whether setting a colour-value attribute is faster. I can set the attributes ok with commands like setattr r color green #0:1-84.B etc and confirm they are set with list residues spec #0:1-84.B attribute color but I can't figure out how to get Chimera to use the attribute value as the display colour. 'Render by Attribute' only seems to consider numeric (range-valued) attributes, not colour-valued. I thought perhaps 'my' colour was just hidden in the colour hierarchy, but removing other colours doesn't seem to help. What am I missing? Thanks, Mungo Carstairs Division of Computational Biology University of Dundee http://www.jalview.org The University of Dundee is a registered Scottish Charity, No: SC015096

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Display atoms after multiscale model
by vamsee 02 Dec '14

02 Dec '14

Hello, I am working on a virus capsid and trying to figure out the buried surface area between subunits (similar to what ViperDB has. I have to do this for a few capsids and I am trying to automate this to the maximum possible extent. I have been able to follow the steps in this link Buried surface area calculation <http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-December/001131.html> and manually calculate the information. Are there commands available to do the same? Also, what is the difference between the surfaces created using a multiscale model and surfaces computed from the atom-spec? Would this difference in the surface affect the calculation of the buried surface area? And if it does affect it which one be a more accurate representation? Thank you Vamsee

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select chain and elements simultaneously
by Jacob Lewis 02 Dec '14

02 Dec '14

Hi all, I am new to chimera is it possible to select chain and element for a structure? for instance select chain A and element carbons so they can be coloured red for example? thanks in advance. Jacob

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Re: [Chimera-users] [Chimera-announce] new Chimera release (v1.10)
by Elaine Meng 01 Dec '14

01 Dec '14

Dear Debasish Banerjee, There may have been changes in the ModBase website, or maybe even the UniProt website -- you would need to ask those developers. The ability of Chimera to show ModBase models did not change. Today looking at the ModBase website, I'm having a problem where it always says there are no models for some sequence, even when I know there are models. I don't know if this is the same problem you were having. I know there are models because I can fetch them using Chimera menu: File…Fetch by ID, choosing database: Modbase and entering a sequence ID (UniProt or other). The same can be done with a command, for example: open modbase:P33533 So maybe you can use that approach instead. Regards, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Nov 29, 2014, at 2:39 AM, "Debasish Banerjee" <dbanerjee(a)banerjee.net.in> wrote: > To > Elaine Meng, > May be I didn't explain properly. Most UniprotKB database entries have used Modbase in the 3D structure database section. In any entry where Modbase is used, clicking on search button next to the Modbase entry used to open that structure entry page using Chimera. With the current version that doesn't seem to happen (as it was happening with the earlier versions). Please advice. > Thanking You, > Debasish Banerjee > > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Sent: Wed, 26 Nov 2014 23:02:40 > To: Debasish Banerjee <dbanerjee(a)banerjee.net.in> > Cc: Mailing List <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-announce] new Chimera release (v1.10) > On Nov 25, 2014, at 4:17 PM, Debasish Banerjee <dbanerjee(a)banerjee.net.in> wrote: > > > To, > > Elaine Meng, > > I had downloaded Chimara 1.10 but it doesn't seem to operate on other sites like UniprotKB. Can you please comment. > > Debasish Banerjee > > > Dear Debasish Banerjee, > Not sure I understand your question. UCSF Chimera is a molecular modeling/graphics program that you use on your own computer. > > The only relationship to UniProtKB is that you can fetch sequences and annotations from that site while using Chimera. Maybe you mean you had trouble fetching data from the web (Chimera menu: File… Fetch by ID)? > > We haven’t heard reports of a problem. For example, I can start UCSF Chimera 1.10, use menu: File… Fetch by ID, choose database “UniProt” and then get the sequence for NGF_HUMAN shown in Chimera. Of course, you have to be connected to the internet. Otherwise, if you have some specific problem you can use Chimera menu: Help… Report a Bug and give enough information about the steps you tried so that somebody else could reproduce it. > > Best, > Elaine

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MatchMaker with betapeptides
by 러셀 29 Nov '14

29 Nov '14

Dear Chimera users, I would like to use the MatchMaker utility to superimpose a family of beta peptide conformers calculated through Xplor-NIH. Unfortunately, MatchMaker does not recognize these molecules and tells me the "chains are incompatible". Furthermore, I would like to specify that only certain residues in the beta peptides be used in the global alignment. I know how to match specific selections in 2 models through the Match utility using the command line (sel #0:1,2,3,4,5@CB,N,C,CA #1:1,2,3,4,5@CB,N,C,CA and then match sel) but I am unsure how to superimpose all of the models at the same time. For instance: models #1-20, residues 2-8, atoms C, N, CA, CB. If anyone could offer me help on the appropriate syntax I would be grateful. Thank you and best regards, Russell

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centroids mutual distance etc. ?
by Marek Maly 29 Nov '14

29 Nov '14

Hello, is there any possibility to measure distance between the two centroids ? It is also possible to define somehow centroid which will be automatically updated when position of the atoms (which are represented by this centroid) are changed - e.g. for different frames from the Amber MD trajectory ? Thank you in advance for your comments, Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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Re: [Chimera-users] [Chimera-announce] new Chimera release (v1.10)
by Debasish Banerjee 29 Nov '14

29 Nov '14

To Elaine Meng, May be I didn't explain properly. Most UniprotKB database entries have used Modbase in the 3D structure database section. In any entry where Modbase is used, clicking on search button next to the  Modbase entry used to open that structure entry page using Chimera. With the current version that doesn't seem to happen (as it was happening with the earlier versions). Please advice. Thanking You, Debasish Banerjee From: Elaine Meng <meng(a)cgl.ucsf.edu> Sent: Wed, 26 Nov 2014 23:02:40 To: Debasish Banerjee <dbanerjee(a)banerjee.net.in> Cc: Mailing List <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-announce] new Chimera release (v1.10) On Nov 25, 2014, at 4:17 PM, Debasish Banerjee <dbanerjee(a)banerjee.net.in> wrote: > To, > Elaine Meng, > I had downloaded Chimara 1.10 but it doesn't seem to operate on other sites like UniprotKB. Can you please comment. > Debasish Banerjee Dear Debasish Banerjee, Not sure I understand your question.  UCSF Chimera is a molecular modeling/graphics program that you use on your own computer. The only relationship to UniProtKB is that you can fetch sequences and annotations from that site while using Chimera.  Maybe you mean you had trouble fetching data from the web (Chimera menu: File… Fetch by ID)?   We haven’t heard reports of a problem.  For example, I can start UCSF Chimera 1.10, use menu: File… Fetch by ID, choose database “UniProt” and then get the sequence for NGF_HUMAN shown in Chimera.  Of course, you have to be connected to the internet.  Otherwise, if you have some specific problem you can use Chimera menu: Help… Report a Bug and give enough information about the steps you tried so that somebody else could reproduce it. Best, 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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FW:8debbie
by giovanni.ortosecco 28 Nov '14

28 Nov '14

http://thewebmaker.coolromania.ro/nvmp/odvovssbmjpkdokxvhtwdf.uonvpngrmzjax… giovanni.ortosecco(a)libero.it

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recent malfunction of reading ConSurf .chimerax files
by Alec Zander 28 Nov '14

28 Nov '14

Hello world of Chimera users, I use Chimera to visualize results from the ConSurf server. I ran some ConSurf jobs a while ago, downloaded the .chimerax files for offline viewing, and was happily using Chimera to do so. However, a few days ago, Chimera started hanging upon trying to load these very same files, and I get Chimera Launcher Error chimera exited abnormally; the exit code was: -805306369 I've gotten this same error for both Chimera v 1.9 and 1.10; Windows 7 Pro reports that pythonw.exe is not responding. I don't understand the cause of this error, and the Chimera debug executable seems to hang too. What to do? Best regards, Alex

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Re: [Chimera-users] [Chimera-announce] new Chimera release (v1.10)
by Elaine Meng 26 Nov '14

26 Nov '14

On Nov 25, 2014, at 4:17 PM, Debasish Banerjee <dbanerjee(a)banerjee.net.in> wrote: > To, > Elaine Meng, > I had downloaded Chimara 1.10 but it doesn't seem to operate on other sites like UniprotKB. Can you please comment. > Debasish Banerjee Dear Debasish Banerjee, Not sure I understand your question. UCSF Chimera is a molecular modeling/graphics program that you use on your own computer. The only relationship to UniProtKB is that you can fetch sequences and annotations from that site while using Chimera. Maybe you mean you had trouble fetching data from the web (Chimera menu: File… Fetch by ID)? We haven’t heard reports of a problem. For example, I can start UCSF Chimera 1.10, use menu: File… Fetch by ID, choose database “UniProt” and then get the sequence for NGF_HUMAN shown in Chimera. Of course, you have to be connected to the internet. Otherwise, if you have some specific problem you can use Chimera menu: Help… Report a Bug and give enough information about the steps you tried so that somebody else could reproduce it. Best, 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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Adding sugars to protein at specific amino acid glycosylation site
by T T 25 Nov '14

25 Nov '14

Dear Mr/Ms, Good morning. My name is Tommy from San Diego Biomedical Research Institute. I am currently learning to use the chimera software. Great work in creating a program for protein and DNA visualization. I have one question to ask regarding the subject above. Is there a way to manually add sugar component onto an existing pdb file? To be precise, I am currently working with HIV-1 envelope. I have the pdb files that features the structure of HIV-1 trimer Env. I wanted to add glycan at specific sites to show steric hindrance to antibody binding. Another question. Is there a way to superimpose 2 pdb files into one image? For example, I have one pdb file for HIV-1 Env and another pdb file for antibody. Can I "merge" these two pdb files as one image? Also, assuming that it is possible to "merge" two different pdb into one image, is there a way to rotate one protein without affect the orientation of the other protein? Any advice/tip is greatly appreciated. Thank you. Sincerely, Tommy

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ribbon options disappeared after upgrade
by Bala subramanian 25 Nov '14

25 Nov '14

Hi, Within the ribbon option under action tool: i used to have additional choices like aitch,wave, octave, etc etc. After an ubuntu upgrade, with chimera 1.9 and 1.10 (i tried both). These extra options dont appear under ribbon. What is going wrong ?. Do i need to install something ? Bala -- C. Balasubramanian

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PDB Header via command line?
by Korbin West 20 Nov '14

20 Nov '14

Hi, I'm trying to find missing atoms in certain residues. I know they are in the pdb header information, but is there a way I can use Chimera or python script to access this using the command line only? I have a large number of proteins to go through, so checking them all individually is not really efficient. Korbin West

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Split chimera screen
by Ibai Irastorza 19 Nov '14

19 Nov '14

Hello, I want to show 2 structures in chimera. I want them to be in different chimera sessions, but then, I want them to be dependant, so when I move one structure, the other structure also moves accordingly. For that matter, I would also like both structures to be in the "same perspective". How could I do that? Thanks a lot and long live chimera! Ibai Irastorza Azkarate, PhD Student Centro Andaluz de Biología del Desarrollo CABD Universidad Pablo de Olavide, Carretera de Utrera km1, 41013 Sevilla, Spain http://www.cabd.es/en-research_groups-104-247-microbiology-s-platypus-summa…

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Reading Chimera source ...?
by Boris Steipe 17 Nov '14

17 Nov '14

Hi - I'm new to writing Chimera code; I've started poking around in the sample scripts and the modules but and I find it a bit slow to find my way around. For example I would like to perform some simple calculations on the coordinates of a set of selected atoms, and I see many functions that take a "sel" argument, but I can't seem to find documentation on exactly what that argument is expected to contain, or the function that would return such a selection list (is it even a list) of objects. I'm sure if I spend more time, through trial and error and dir() and grep, I'll eventually figure it out, but I wonder if there isn't a more principled approach - a document on the big picture of how the code is structured, and/or a searchable list of all functions? What's the best strategy to start reading and coding Chimera scripts? Thanks! Boris

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aligning molecules
by Elaine Meng 15 Nov '14

15 Nov '14

On Nov 14, 2014, at 7:45 PM, Bhaskar Bagchi <bhaskarbagchi(a)gmail.com> wrote: > Respected Sir > I want to align ligands after docking study. Is it possible in chimera? Please help me. > Thanking you Yours faithfully, > Bhaskar Bagchi > Cheminformatics, Bioinformatics Lab Department of Chemistry, Raiganj College Dear Bhaskar Bagchi, I may not understand your question very well, because if you align the molecules they would no longer be in their docked positions. However, there are several ways to align molecules in Chimera. If non-protein, you would probably want to use the “match” command, but this also requires specifying the atoms to use, in the right order, if the two molecules don’t have all the same atom names. See documentation for ways to align, and the “match” command specifically: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html See also related command “rmsd” and the “ViewDock” tool for looking at docking results. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.…> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html> It is recommended to send Chimera questions to chimera-users(a)cgl.ucsf.edu (CC’d here) rather than to my individual address. Best, 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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Can 'readstdin' capture stderr output?
by Mungo Carstairs 14 Nov '14

14 Nov '14

Hello, I am working on ?driving Chimera from Jalview using the stdin/stdout mechanism (expecting to migrate to REST in future). I have a case where a 'match' command fails, but the stdout response does not show this. Using the Chimera command line I can see a message (I guess to stderr) 'Unequal numbers of atoms chosen for evaluation' but in stdout I just see the same message as for a successful match e.g.: 'Executing match ['#1:1-69.B,96.B@CA', '#0:1-69.A,96.A@CA'], no iteration' Is there a way to detect that the match has failed and/or capture the stderr output? Thanks, Mungo Carstairs http://www.jalview.org The University of Dundee is a registered Scottish Charity, No: SC015096

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Detection of sterical clashes within selection
by James Starlight 13 Nov '14

13 Nov '14

Dear Chimera users! This timeI'm writing of some automatic script aimed on the embedding of the receptors into the membrane consisted of the pre-equilibrated lipids as well as hole for the protein. The main issue that some of the receptors consist of the bulky PHE or TRP side chains on their surface which are overlap with the lipids atoms. As the result subsequent MD simulation of these systems is crushed although of long minimization stage prior to it. I'll be very thankful if someone provide me with some Chimera's command for automatic detection of these steric clashes (overlapped atoms) for a given selection (e.g protein and lipids) based on which I'll be able to write automatic python script. Thanks for help, James

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