- Chimera-users - RBVI Mailing Lists

Followup to my last question on MatchMaker
by John Rose 25 Aug '11

25 Aug '11

It looks like there is something going on with PDB entry 1HPB that is causing the problem. John John Rose Ph.D. Associate Professor B204B, The Fred C. Davison Life Sciences Complex 120 Green Street Department of Biochemistry and Molecular Biology University of Georgia Athens, GA 30602-7229 ========================================= Phone: 706-542-1750 Fax: 706-542-3077

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molecular surface isolated to chain
by Jeffrey Kentner 24 Aug '11

24 Aug '11

Hello, I am trying to create a nice aesthetic model of a protein binding to DNA. When I show molecular surface, the program doesn't seem to be able to differentiate between the DNA chain and the protein chain. I either end up with a surface on the DNA which is not fully closed, or if I extend the surface via the 'surface zone' it simply begins to cover the protein as well... I have consulted the documentation and can not find any description of how one would isolate the molecular surface to a particular chain. Is this not possible in Chimera? Cheerio, Jeffrey

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SSEHUnter and SSEBuilder questions
by Kristin Parent 24 Aug '11

24 Aug '11

Hello, I was hoping you could help me out. I am trying to locate secondary structure elements in an individual subunit of an icosahedral virus from a cryo-reconstruction. I have the entire virion in pif format and would like to use the density from a single subunit using SSEHUnter and SSEBuilder. I am not sure how best to get the volume data as a useable mrc input for this tool. I tried using the volume eraser to eliminate other areas in the map that are not the subunit I'd like. When I save the map and then the session, the subunit looks fine in the session, but if I open the subunit mrc file in a new session, I get what appears to be inverse density (the stuff I erased), and in the volume viewer, the density looks inverted. If I move the slide bar to the left, I end up with a solid cube. I am either doing something horribly wrong, or this is maybe not the best method for excising my subunit??? Please advise the best approach to creating a subunit mrc file that can be used by SSEHunter. Thanks in advance! Kristin Kristin Parent, Ph.D. University of California, San Diego Department of Chemistry and Biochemistry 9500 Gilman Drive, NSB 4104A, MC-0378 La Jolla, CA, 92093-0378 (858) 534-8038

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(no subject)
by a kauz 24 Aug '11

24 Aug '11

I am currently trying to extract data (x,y,z coordinates) from a PDB file generated by Chimera (pdbrun command) The file looks like this: MODEL 1 HETATM 1 **** 1 7881.2318439.71911918.53 1.00 0.00 H HETATM 2 **** 2 7878.3608863.83911538.22 1.00 0.00 H HETATM 3 **** 3 7362.1978948.58411340.85 1.00 0.00 H HETATM 4 **** 4 8109.6319067.12510778.80 1.00 0.00 H HETATM 5 **** 5 8512.9689160.81011582.47 1.00 0.00 H HETATM 6 **** 6 8368.0819128.66911020.52 1.00 0.00 H HETATM 7 **** 7 7260.6139750.88411592.71 1.00 0.00 H HETATM 8 **** 8 5841.5699031.23313127.43 1.00 0.00 H HETATM 9 **** 9 6579.8098604.13912097.33 1.00 0.00 H HETATM 10 **** 10 7584.5978302.09511466.04 1.00 0.00 H HETATM 11 **** 11 8520.92710251.0411690.68 1.00 0.00 H HETATM 12 **** 12 9185.69810212.1111417.11 1.00 0.00 H (this is just an extract) How can I know how many decimal numbers each coordinate has? is there a way to set how many decimal numbers will be reported? or to put some kind of tab separation between the coordinates? thanks, Annamaria

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Re: [Chimera-users] creating a peptide bond between two fragments
by Eric Pettersen 23 Aug '11

23 Aug '11

On Jun 7, 2011, at 2:30 PM, Glenn Millhauser wrote: > Hi Folks, > I am trying to add a four amino acid segment to the N-terminus of > a protein in the pdb. I can generate the four residue stretch and > move its C-term close to the N-term of the structured protein. I > can then select the C' and N atoms, which are about 1.0 Angstrom > apart. At that point, I am stuck. Not sure how to add a bond and > then create a proper structure. I've played around with Join > Models, but no luck. Without a peptide bond recognized by Chimera, > ribbons are discontinuous. Any ideas? > Many thanks, > glenn There is now a section of the Join Models page specifically for joining two peptides, so this problem should be easy to solve in the future. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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a simple question about multiple sequence alignment
by Lan Hua 22 Aug '11

22 Aug '11

Hi all, I want to use chimera to create a multiple sequence alignment which will be used to build a model. From elsewhere, I know the pdb id of desirable templates, but I don't know how to create the alignment in the Chimera. Any inputs will be very much appreciated. Thank you! Best, Lan

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Fwd: Showing more than a single centroid trace
by Francesco Pietra 22 Aug '11

22 Aug '11

There is still a problem that had previously escaped my attention. I.e., after the centroid sequence is obtained for model 0 and residue 1, I run the movie for model 1 and residue 2. That's OK, however the second series of centroids starts with progressive number where the first one had ended plus one (if the first series was 1-250, the second series starts from 251). This means that the first part of centroids for model 1 (corresponding to the centroids for model 0, i.e., 250) is not shown. I used define centroid radius ... color ... #modelnumber:residuename & :residuenumber where the residuename is the same for the two series of centroids. Can the command be modified so that both complete series of centroids is shown? I am using chimera production version 1.5.3 (build 33475) 2011-05-24 17:23:26 GMT on Debian i386 (I found this more stable than on Debian amd64 with GTX-580 as the sole graphic cards) Thanks francesco pietra ---------- Forwarded message ---------- From: Francesco Pietra <chiendarret(a)gmail.com> Date: Thu, Aug 18, 2011 at 8:08 PM Subject: Re: [Chimera-users] Showing more than a single centroid trace To: Eric Pettersen <pett(a)cgl.ucsf.edu> On Thu, Aug 18, 2011 at 7:48 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > Try selecting just the one ligand first with this: > sel #0:residuename & #0:residuenumber > then it and the environment around it with: > sel sel z<5 > --Eric That works fine, thank you very much francesco > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > On Aug 18, 2011, at 10:36 AM, Francesco Pietra wrote: > > On Thu, Aug 18, 2011 at 7:07 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > HI Francesco, > > Just put the model number wherever you need it, with no space before residue > name or number, maybe something like: > > sel #0:residuename & #0:residuenumber z<5 > > For me that works between the three ligands only. I.e, with a large > z<20, all the three residues are highlighted, while with z<3 only the > residue with the specified residue number is highlighted. The number > of atoms at the bottom line correspond. For example, with z<20, 6 > atoms, 3 bonds (three diatomic molecules) > > francesco > > > Elaine > > On Aug 18, 2011, at 9:46 AM, Francesco Pietra wrote: > > Hi Elaine: > > Thanks a lot. Could you also help me as how to find the environment of > > the moved ligand, when there are three of them with the same residue > > number? > > While define centroid works nicely with: > > define centroid radius# color # :residuename & :residuenumber > > sel #modelnumber :residuename & :residuenumber z<# > > does not. Could the command be modified to refer to only one of the > residues? > > Thanks > > francesco > > On Wed, Aug 17, 2011 at 7:34 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hi Francesco, > > If your movies are different model numbers, you can put model number before > residue name, for example: > > #0:hem > > You can see what models you have in the Model Panel (under Favorites in > menu). > > Elaine > > On Aug 17, 2011, at 7:11 AM, Francesco Pietra wrote: > > Hi Elaine; > > I selected with line command the molecule that was giving the centroid > > sequence. I was interested in the surroundings of that biatomic > > molecule at various frame numbers. What I said, is that this is > > possible only for the first movie. On subsequent movies, superimposed > > to the first one, the line command always refers to that molecule of > > the first movie. > > francesco > > On Tue, Aug 16, 2011 at 7:38 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hi Francesco, > > You cannot select centroid objects with a command -- they do not have > residue or atom names. You can only select them by clicking their lines in > the Axes/Planes/Centroids dialog, or by Ctrl-clicking on them in the Chimera > graphics window. > > Elaine > > On Aug 16, 2011, at 9:36 AM, Francesco Pietra wrote: > > Hi Elaine: > > I'll try your advice as soon as possible. However, turning mode1 out > > of view in model window while playing movie for model 1, the centroid > > for mode1 is still seen above model 0 and the trace for centroid for > > model 0 . What I could not do was to select the centroid for model 1, > > in order to highlight it. Command "sel :residuename" always selected > > the centroid for model 0. > > francesco > > On Tue, Aug 16, 2011 at 5:51 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hi Francesco, > > I'm not sure I understand what you are asking. Maybe you are saying that > when you hide a model, the centroid is also hidden? > > Instead of hiding the model with the Model Panel "Shown" checkbox or command > "~modeldisplay", which hides everything in the model, you can undisplay the > protein parts and leave the centroid displayed. For example, if I had > protein models #0 and #1 and also centroids for each of those, I could > undisplay the protein part only of #0: > > ~display #0 > > ~ribbon #0 > > ~surf #0 > > (commands to undisplay atoms/bonds, ribbon, and molecular surface of model > #0). Then, you would have the protein #1 plus the centroids of both #0 and > #1 displayed. 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 > > On Aug 15, 2011, at 11:36 PM, Francesco Pietra wrote: > > Hello: > > I would like to show several centroid traces for model 0, 1, 2, .. > > Actually, it is the same model, differing, in the movies, for the > > protein fluctuations. > > What I did, was to superimpose movie for model 1 to the already done > > movie for model 0, hiding the protein for model 1 and choosing a > > different color for the centroid. Doing that, the instant position of > > the centroid can only be color-highlighted for model 0. > > I wonder whether there is a better procedure to show the various > > centroid traces above a single protein model. > > thanks > > francesco pietra > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > >

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register file extension .xmp for volume data
by Dieter Blaas 22 Aug '11

22 Aug '11

Hi, I routinely visualize spider format volume data that are output from Xmipp with the extension .xmp. This extension is not registered in Chimera and I have to scroll through the formats page each time to select 'spider volume data' or open the file with 'chimera spider:xxx.xmp'. Is there a way to make Chimera recognize this extension as 'spider format' automatically? There was an older Windows version that allowed to tell Chimera that all following data were of the same format as the first one but I have not seen this in any of the recent Linux versions. Thanks for hints, D. - ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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<no subject>
by Sacha De Carlo 22 Aug '11

22 Aug '11

unsuscribe

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Morph with Chimera: how to make visible connection/interaction in Morph
by WENHE ZHONG 19 Aug '11

19 Aug '11

Dear all, I would like to show the visible metal-residue interaction during the Morph movie. Anyone knows how to do that in Chimera? Thank you. King regards, Wenhe

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Showing more than a single centroid trace
by Francesco Pietra 18 Aug '11

18 Aug '11

Hello: I would like to show several centroid traces for model 0, 1, 2, .. Actually, it is the same model, differing, in the movies, for the protein fluctuations. What I did, was to superimpose movie for model 1 to the already done movie for model 0, hiding the protein for model 1 and choosing a different color for the centroid. Doing that, the instant position of the centroid can only be color-highlighted for model 0. I wonder whether there is a better procedure to show the various centroid traces above a single protein model. thanks francesco pietra

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XPLOR volumetric data not shown as a volume
by matthias.gutmann＠stfc.ac.uk 18 Aug '11

18 Aug '11

Dear all, having succeeded in writing an XPLOR data file and importing it into CHIMERA, I was expecting to see a cube like volume. Instead, I'm only seeing a thin plane. Is this to be expected? The header for the XPLOR file is as below: 1 SXD2001reciprocal_space_volume 301 0 300 301 0 300 301 0 300 30.10000 30.10000 30.10000 90.00000 90.00000 90.00000 ZYX 0 0.57280 0.05125 0.25826 0.23192 0.47232 0.40565 0.28667 0.06406 0.13678 0.22750 0.22332 0.11380 -0.02432 0.32358 0.22395 0.06303 0.22736 0.27504 0.30512 0.21062 0.26810 0.15033 0.25180 0.39434 0.85280 0.25197 0.07160 0.22430 0.28253 0.11386 0.34160 0.32177 -0.03150 0.22739 0.47072 -0.00241 0.26013 0.20844 0.20823 0.30089 0.40608 0.23863 -0.13479 0.28377 0.08277 0.25996 0.23550 0.09638 How can I get the entire volume to display as a volume rather than a single plane? Is the XPLOR format not a good one to use for this purpose? Many thanks and best wishes, Matthias ---------------------------------------------------------------------------------------------- Matthias Gutmann Instrument Scientist SXD Rutherford Appleton Laboratory Phone: +44 (0)1235 44 6397 ISIS Facility Fax: +44 (0)1235 44 5200 Chilton Didcot Office : R3, 1.28 Oxfordshire OX11 0QX Email: Matthias.Gutmann(a)stfc.ac.uk UNITED KINGDOM -- Scanned by iCritical.

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Unrecognized command: "minimize"
by Viachaslau Bernat 18 Aug '11

18 Aug '11

Dear Chimera developers, I've got a problem with scripting in chimera. By analogy with your example I've written a python script for geometry optimization of small library of ligands. In GUI mode all commands run smoothly as I type them into chimera command line. Nevertheless, when I try to run a script containing the same commands I get the error `unrecognized command: "minimize"`, no matter if I run it from GUI interface menu or with --nogui parameter. Here is my testing script (test.py): import os import chimera from chimera import runCommand as rc from chimera import replyobj os.chdir("/home/viachaslau/sybyl/sublib/") fn = "lib1.mol2" rc("open " + fn) rc("miminize nsteps 70000 stepsize 0.001 interval 100 freeze none nogui true") rc("write format pdb 0 min/" + fn + ".pdb") rc("close all") rc("stop now") And here is the output from Python: ~/sublib> ~/chimera/bin/chimera --nogui test.py Executing test.py... Opening lib1.mol2... UNQ1 opened Traceback (most recent call last): File "/home/viachaslau/chimera/share/chimeraInit.py", line 677, in init chimera.openModels.open(a, prefixableType=1) File "/home/viachaslau/chimera/share/chimera/__init__.py", line 1541, in open models = func(filename, *args, **kw) File "/home/viachaslau/chimera/share/chimera/__init__.py", line 973, in _openPython loadFunc(sandboxName, fileName, f) File "test.py", line 8, in <module> rc("miminize nsteps 70000 stepsize 0.001 interval 100 freeze none nogui true") File "/home/viachaslau/chimera/share/chimera/__init__.py", line 2235, in runCommand makeCommand(*args, **kw) File "/home/viachaslau/chimera/share/Midas/midas_text.py", line 78, in makeCommand 'Unrecognized command: "%s"' % cmd MidasError: Unrecognized command: "miminize" Error while processing test.py: MidasError: Unrecognized command: "miminize" File "/home/viachaslau/chimera/share/Midas/midas_text.py", line 78, in makeCommand 'Unrecognized command: "%s"' % cmd See reply log for Python traceback. I run SUSE 11.3 as operating system and chimera is installed into ~/chimera/ I also tried to run commands row by row in IDLE window of chimera and found out that python suspends on runCommand("minimize ...") command -- Viachaslau Bernat, PhD-student Department Chemistry and Pharmacy Schuhstrasse 19, 91052 Erlangen -- Germany Phone: +49-9131-8522588 www.medchem.uni-erlangen.de

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delete volume densities
by Hernando J Sosa 17 Aug '11

17 Aug '11

A while ago I remember using a Chimera function to delete map densities that were outside a given distance from selected atoms in a structure. I can't seem to find this utility anymore. Can somebody please remind me where to find it. Is this utility still there in the new chimera versions? Thanks Hernando

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Re: [Chimera-users] suggested feature/model panel
by Eric Pettersen 17 Aug '11

17 Aug '11

On Jan 22, 2009, at 3:15 PM, Eric Pettersen wrote: > On Jan 21, 2009, at 5:05 PM, Matthew Dougherty wrote: > > > 1) ability to create folders in the model panel so models can be > > grouped > > 2) ability to have a model in multiple folders > > 3) ability to show/hide in a folder by a a single checkbox > > 4) ability to name the folder > > These are good suggestions, and we have discussed adding some kind of > grouping mechanism in Chimera given that there are a lot of situations > where you want to treat a set of models as a single entity (e.g. > multiple structures fit into a EM map). > > I think #2 and #3 are in conflict though. Really, I don't think you > want #2 -- it's too confusing. Say a model is in two groups: you > close one group -- what happens? You hide one group -- what happens? > You deactivate one group and move the other -- what happens? Perhaps > if you elaborated on the motivation for putting a model in multiple > groups then some other alternative could be devised that provides what > you need. > > I'll open a change-request in our Trac database for "grouping > mechanism" and include the above. I don't really want to promise a > timeline, but the issue is a concern of ours. Seems like I never opened that ticket, at least I can't find it searching the database. A year later I did open a very similar ticket (#8253) which has now been implemented. So the Model Panel now supports grouping (and ungrouping) models in the current daily build, which at least minimally satisfies points 1, 3, and 4 above. The groups can be named as you wish, and changing active/shown/color/etc. for a group changes the corresponding attribute of all the models in the group. Right now if multiple models are opened from a single data source they are automatically grouped. This comes into play most often when opening NMR ensembles. If anyone has any strong opinion as to whether this is a good default behavior or not, please speak up! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Calculation of Hydrophobicity
by Magnus Andersson 17 Aug '11

17 Aug '11

Hi, I'm a new user to Chimera and found it very useful really fast. I have a question however, is possible to make a calculation of the hydrophobicity of a surface or the electrostatic potential, not only show it visually? Best regards Magnus ------------------------------------------------------------ Magnus Andersson, PhD Assistant Professor Department of Physics Umeå University SE-901 87 Umeå, Sweden Phone: +46 90 786 63 36 Mobile: +46 706 460 602 Email: magnus.andersson(a)physics.umu.se<mailto:magnus.andersson@physics.umu.se> ------------------------------------------------------------

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Problem with volumetric data in XPLOR format
by matthias.gutmann＠stfc.ac.uk 17 Aug '11

17 Aug '11

Dear all, I'm trying to write volumetric data in XPLOR format in order to import it into Chimera for displaying. The volumetric data set is a general volume data set, not necessarily an electron density map. However, it keeps on failing as Chimera keeps on thinking there are only 262 data values, whilst expecting 90601 numbers (which is the correct number). I'm trying to write the XPLOR file in the format given on the CNS web page: Format of CNS maps The grid size of the map is determined by the GRID parameter in the FFT statement. The following lines show the beginning of a typical electron density map file: 2 !NTITLE REMARKS FILENAME="" REMARKS DATE:18-Jun-98 12:24:08 created by user: 30 4 12 15 5 10 16 2 12 0.40960E+02 0.18650E+02 0.22520E+02 0.90000E+02 0.90770E+02 0.90000E+02 ZYX 0 -0.97086E+00-0.49927E+00-0.82774E+00-0.13491E+01-0.57034E+00-0.71253E-01 -0.19491E+00 0.61017E+00 0.10064E+01-0.22888E+01-0.94020E+00 0.77451E+00 0.57539E+00-0.31211E-01-0.27430E+00-0.36526E+00 0.34772E+00 0.81884E+00 -0.19954E+01-0.10117E+01 0.18038E+01 0.19008E+01 0.11886E+00-0.41646E+00 0.47560E-01 0.48855E+00 0.57606E+00-0.22320E+00-0.12787E+01 0.47590E+00 .... -9999 0.2044E-09 0.9999E+00 Is this correct or is Chimera expecting a different format? Looking forward to your replies! Many thanks and best wishes, Matthias ---------------------------------------------------------------------------------------------- Matthias Gutmann Instrument Scientist SXD Rutherford Appleton Laboratory Phone: +44 (0)1235 44 6397 ISIS Facility Fax: +44 (0)1235 44 5200 Chilton Didcot Office : R3, 1.28 Oxfordshire OX11 0QX Email: Matthias.Gutmann(a)stfc.ac.uk UNITED KINGDOM -- Scanned by iCritical.

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suggestion
by Dougherty, Matthew T 16 Aug '11

16 Aug '11

It would be good to have a session description window that I could type text into. The typical method is to generate a session file name that is the description, but as the complexity of a session file increases it would helpful to be able to write a couple sentences/paragraph as to the subtle differences it has over a near identical session file. It would also allow me to pass messages/instructions in the session file to other users so they can properly implement the session file on their computer (e.g., "be sure to change the directory name and update your density files", "the related command files that work with this session file are ....") Later on such information could be extracted in mass from closed session files, allowing for searches using database-like queries. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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BIOMT
by Ludovic Autin 16 Aug '11

16 Aug '11

Hi there, I am wondering if its possible to access the matrices computed by the sym command and/or if its possible to save the multiscale structure as a PDB with the BIOMT fields instead of the full structure? thanks in advance Ludovic

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Residue.uniprotIndex
by Eric Pettersen 16 Aug '11

16 Aug '11

I thought some of the script writers out there might want to know that in the latest daily builds residues have a "uniprotIndex" attribute which gives the position of the residues relative to their UniProt sequence, if the correspondence can be determined. To determine the correspondence the structure must have valid PDB HEADER and SEQRES records, and the PDB web site must be reachable (to use their UniProt mapping service). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Surface point types in WriteDMS
by Ken Shimo 11 Aug '11

11 Aug '11

Hello, When I use WriteDMS, a surface point is defined by the 7th field, which should start in 'S'. In the format definition, next to it, should be an 'S', for saddle, 'C', for contact, 'R', for reentrant, that defines de surface type. But in Chimera's WriteDMS the surface points are always set as 'C' (contact). How can I create a DMS file with the correct surface types? I'm thankful for any help, -- Helder Ken Shimo BSc in Biomedical Informatics (University of São Paulo - Brazil) MSc candidate in Bioinformatics (University of São Paulo - Brazil) -- "When I get sad, I stop being sad and be awesome instead." (Neil Patrick Harris as Barney Stinson)

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Large size display system
by jens j birktoft 10 Aug '11

10 Aug '11

Subject: Large size display system: I am looking for some advice regarding a presentation system that permit the display in high definition of interactive molecular graphic sessions (incl. Chimera) to our research group (10-12 people). Ideally we would like a 32"-36" LCD monitor coupled to a computer equipped with the proper graphics card for the large display as well as 24" monitor . Any suggestions would be greatly appreciated Cheers Jens +++++++++++++++++++++++++++++++++++++++++++++++++++++++*/ Jens J. Birktoft, Department of Chemistry, New York University e-mail: birktoft(a)nyu.edu <mailto:jens.knold@gmail.com> slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025 Phone: 212-749-5057

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Problem with a script calculating distance between residues in a single pdb file with several models
by Damien Larivière 09 Aug '11

09 Aug '11

Dear all, Here is a single pdb file called modetest_14.pdb. It contains 6 structures: 1 protein MutS (only chain B) with 5 different conformations + another protein MutL (chains A and B). In Chimera, the protein with the 5 different conformations is displayed as model 0.1 to 0.5. The other protein is model 0.6. I would like to calculate the distance between the residue 239 of MutS chain B (for the 5 conformations) and the residue 169 of MutL chain A. I wrote this script which reports this error message: expected an indented block (scriptdistance.py, line 4) *from chimera import runCommand as rc rc(r"open C:\Program Files (x86)\Hex 6.3\examples\New Hex run_SL_250211\FirstRun_S_Ldimer\New_filtering\Eucl_Dist_S246-L297\Top solutions\SL0265B\dockLH248\NMA\Test\modetest_14.pdb") for i in range(1, 6): rc("distance #0.%d:239.B@N #0.6:169.A@N" % i)* May you tell me what is wrong? the script correctly opens the file so I suppose it is the python string #0.%d (intended to specify 0.1, 0.2,... 0.5)!? Thanks for your help Damien

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python and MD
by Daniel Gurnon 08 Aug '11

08 Aug '11

Hi everyone, I have a question for the python experts: Suppose I have opened an MD trajectory using MD movie. I want a script that will capture images along the trajectory spaced by user-defined timespans. Problem is, I don't know how to use a script to go to a specific frame in MD movie. As I understand it, coordset, as employed in the following example, requires the user to first play through the entire trajectory. With a million frames, that's not practical. Here's what I have so far, cobbled together from examples and my own limited understanding of Python. ---------------------------- from chimera import runCommand timestep=input ("How many picoseconds pass between frames?") spacing=input ("What spacing, in ps, do you want between structures?") start=input ("Which frame do you want to start with?") end=input ("What frame do you want to end with?") runCommand("coordset #0" + start) runCommand("focus") runCommand("copy file C:\Users\Dan\Desktop" + "\\" +start + ".png" + " width 2000 width 2000 supersample 3") ---------------------------- So in place of coordest, what could I use to jump to frames within MD movie? And while I'm at it, How can I generically specify the desktop in a windows environment (so that I could give this to a student and they wouldn't have to change "Dan" in c:\users\Dan\Desktp") How can I change the filename for the image to reflect framenumber? Thanks as always for your help. Dan -- ____________________________ Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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Python command SaveReplyLog
by Damien Larivière 08 Aug '11

08 Aug '11

Dear all, Within a loop for i in range(1, 5), I would like to save the Reply Log in text file in a specific location. My script fails when I use such syntax, saying Unrecognized command: *from chimera.tkgui import saveReplyLog rc("saveReplyLog('C:\Program Files (x86)\Hex 6.3\examples\replyLog%d.txt')" % i)* I looked at old posts saying the syntax to be saveReplyLog('path') but it does not work. May you tell me what is wrong with it? I can post the whole script if necessary. Many thanks for your help Damien

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