- Chimera-users - RBVI Mailing Lists

Fwd: Re: Bug (?) with EnsembleCluster
by Francesco Pietra 17 Jan '08

17 Jan '08

Yes, the two behave differently, and not only as to importing pdb. I had opened my combined trajectories (protein+ligand in a lipid membrane) in VMD while looking at either the ligand or the protein: both highly distorted at each one of the 550 frames. I only got nearly reasonable structure for the ligand by averaging the frames. That was most discouraging in the last few days. Did the same for the equilibration and got the same discouraging results. This last analysis was not fitting the analysis with ptraj, Therefore I have now done the same for the MD trajectories with Chimera, which runs more slowly along the frames, and surprisingly, "at the naked eye" both the ligand and the protein save their correct structure along the 550 frames, with only the internal displacement on/back that one expects from MD. I repeated without hiding the membrane and water, and "at the naked" the ligand was not wandering around. I looked at RMDS Maps(Start frame 1; End 550; Step size 2; RMSD map of trajectory against itself; Lower rmsd threshold 2.9, higher 3.9: RMSD varied from 0.194 to 1.810 for the ligand and from 0.612 to 2.420 for the protein. Is that variation too much for accepting this MD for good (or fair) and continuing it with same settings? If it is a too large a range, that explains why the ligand encountered so many protein residues when the mask was used. I was unable to find how to get a plot of RMSD against time. I would like to do that for the ligand (which is a single big residue) and selected residues of the protein. Thanks francesco --- Francesco Pietra <chiendarret(a)yahoo.com> wrote: > Date: Tue, 15 Jan 2008 06:44:21 -0800 (PST) > From: Francesco Pietra <chiendarret(a)yahoo.com> > Subject: Re: [Chimera-users] Bug (?) with EnsembleCluster > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > CC: chimera BB <chimera-users(a)cgl.ucsf.edu> > > Got FMI, thanks. That seems a reasonable rationalization. Though, if I > understand, importing pdb files without saturating memory (may be importing > one > "model", analyzing it, and then removing it from memory before importing next > "model", or any other better idea) is something to overcome in order to have > Chimera carrying out cluster analysis. Or I do not understand or cluster > analysis is of minor interest, both equally possible. > > francesco > > --- Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > > > Just FYI, when you open a 5000 MODEL structure with Chimera's normal > > File...Open, you get 5000 completely separate models (and will likely > > exhaust memory unless its a small molecule). Each model can be > > colored individually, moved, mutated, closed, etc. individually. > > When you open the same 5000 MODEL file with the MD Movie extension > > you get _one_ model with 5000 sets of coordinates, which takes much > > less memory. On the other hand, each frame shares colors and so > > forth with all the other frames, cannot be moved with respect to the > > other frames, etc. VMD undoubtedly uses the latter approach. > > > > --Eric > > > > Eric Pettersen > > UCSF Computer Graphics Lab > > http://www.cgl.ucsf.edu > > > > On Jan 11, 2008, at 3:04 PM, Francesco Pietra wrote: > > > > > Yes, 5365. What happened will be discovered. Up to the stage on > > > amber_score_everything, all was perfectly OK. Minimization and > > > heating was also > > > OK. As to MD, the situation could not be clarified so far. > > > > > > In view of your comments below, I carried out a check with proven > > > MD. I went to > > > Amber tutorial B3, took equil1.mdcrd.gz, decompressed, took the > > > related prmtop, > > > and fed the two files to Chimera, last Daily Building. After all > > > 5000 steps had > > > been acquired, saved pdb, all frames. Quit MD Movie. Try to open > > > this pdb. > > > Well, with my modest desktop, Debian Linux i386, 1GB ram, this pdb > > > could not be > > > opened: rapidly the memory was exhausted and to get control of the > > > computer I > > > had to kill gnome. With vmd, this pdb developed rapidly with all > > > 5000 frames. > > > Exactly as with the pdb from MD with my protein. This does not mean > > > that my MDs > > > are OK. I'll look for what may be wrong there. > > > > > > Thanks > > > francesco > > > > > > > > > > > > > > > --- Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > > > > > >> 5365 atoms? Given average atom counts in protonated protein residues > > >> that means your ligand came in close contact with ~340 residues over > > >> the course of the trajectory -- so it's wandering all over the > > >> place. I can see why you want to use cluster analysis. Oh well, I > > >> guess we're stuck until I have time to coordinate with Conrad and > > >> integrate his clustering code with MD Movie. > > >> > > >> --Eric > > >> > > >> On Jan 10, 2008, at 6:38 AM, Francesco Pietra wrote: > > >> > > >>> Eric: I followed previous route from combined mdcrd from ptraj. > > >>> > > >>> Removed remaining water. > > >>> > > >>> select ligand z<2.5 > > >>> > > >>> as Chimera command; (this was the minimum, selecting 244 atoms, 118 > > >>> of which > > >>> for the ligand; with z<2.0 the ligand only is selected) > > >>> > > >>> On playing the pdb (saved for selected atoms only) (with LOOP > > >>> deselected) the > > >>> atom selection increased, reaching 5365 atoms at the last (549) > > >>> frame. In > > >>> another run, with z<4.0 the course of atom selection was similar, > > >>> reaching 5993 > > >>> atoms at frame 549. > > >>> > > >>> This huge number of atoms proved problematic for opening pdb. For > > >>> the z<2.5 > > >>> case I left the computer on for 4h and half, with python occupying > > >>> 98% of the > > >>> available MEM (nearly 1GB). I had to kill gnome to recover command. > > >>> > > >>> May be with much more MEM it will work, though I can't check that > > >>> now. > > >>> > > >>> I did not try to combine the trajectories with Chimera as I have no > > >>> indication > > >>> that those from ptraj are faulty. The pdb files for both z<2.5 and > > >>> z<4.0 open > > >>> in vmd. > > >>> > > >>> francesco > > >>> > > >>> --- Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > > >>> > > >>>> On Jan 9, 2008, at 3:32 PM, Francesco Pietra wrote: > > >>>> > > >>>>> In the "Define script.." I defined "select ligand z<10", then OK > > >>>>> and a BUG > > >>>>> window was presented. Attached is the reply log (bug). I tried > > >>>>> with > > >>>>> z<4 with > > >>>>> the same result (actually, I don't remember if attached bug file > > >>>>> refers to z<10 > > >>>>> or z<4). > > >>>> > > >>>> In the script-definition dialog you need to have "Interpret script > > >>>> as" set to "Chimera commands". You had it set to "Python". > > >>>> > > >>>>> Still found difficulties in loading more than one mdcrd, though > > >>>>> this should be > > >>>>> my fault. I was not sure if the list of mdcrd is to be given at > > >>>>> beginning or if > > >>>>> the other mdcrd files after the first one are to be given > > >>>>> subsequently from the > > >>>>> menu. I tried with the "list" option but only the first mdcrd was > > >>>>> opened. > > >>>> > > >>>> When you run MD Movie and the dialog comes up where you specify the > > >>>> prmtop/trajectory files, you can use the "Add..." button to add as > > >>>> many trajectory files as needed. I think this means you "give > > >>>> it at > > >>>> the beginning" rather than "subsequently from the menu" in your > > >>>> terminology. > > >>>> > > >>>> You can also just list the files in a "metafile" for the command > > >>>> line. For instance, this file works for me: > > >>>> > > >>>> amber > > >>>> leap.top > > >>>> md01.crd > > >>>> md02.crd > > >>>> md03.crd > > >>>> md04.crd > > >>>> md05.crd > > >>>> md06.crd > > >>>> > > >>>> Note that there _still_ seems to be something funky with Amber > > >>>> compressed trajectories, so don't use them for now but I should > > >>>> have > > >>>> things fixed in a day or so with that. > > >>>> > > >>>> --Eric > > >>>> > > >>>> > > >>> > > >>> > > >>> > > >>> > > >>> > > >>> ____________________________________________________________________ > > >>> __ > > >>> ______________ > > >>> Be a better friend, newshound, and > > >>> know-it-all with Yahoo! Mobile. Try it now. http:// > > >>> mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ > > >>> > > >> > > >> > > > > > > > > > > > > > > > ______________________________________________________________________ > > > ______________ > > > Looking for last minute shopping deals? > > > Find them fast with Yahoo! Search. http://tools.search.yahoo.com/ > > > newsearch/category.php?category=shopping > > > > > > > > > ____________________________________________________________________________________ > Be a better friend, newshound, and > know-it-all with Yahoo! Mobile. Try it now. > http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ > > ____________________________________________________________________________________ Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping

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MolMol file format for electrostatic potentials
by Esther Bullitt 16 Jan '08

16 Jan '08

Hi, Is there a way to import into Chimera the results of MolMol's calculation for electrostatic potentials? I like MolMol because it shows the charge without the surface hydrogens (so the results show the same thing as with, the hydrogens, but 'more strongly'), and equally important, the program is very easy to use. Is there a format conversion script, or would it be possible to make one? I can send sample files, if this would be helpful. thanks, Esther --- Esther Bullitt, Ph.D. Dept. of Physiology & Biophysics, Room W302 Boston University School of Medicine 715 Albany Street (mail only; couriers use 700 Albany Street) Boston, MA 02118-2526 Email: bullitt(a)bu.edu Telephone: 617-638-5037 Facsimile: 617-638-4041

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coloring by property
by Elaine Meng 15 Jan '08

15 Jan '08

Hi everybody, There is another set of possibilities I neglected to mention. These simply categorize residues into discrete sets which could be colored differently, as opposed to coloring continuously over a numerical range. There are amino acid categories that can be specified with "Select... Residue... amino acid category... [category-name]" where category- name is hydrophobic, positive, negative, etc. These names could also be used in the command line, e.g.: color blue positive color red negative We took the default categorizations from a paper, http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/aacat.html but you can change which residues are in which category as well as create entirely new categories with the ResProp tool. The new categories will show up in the menu and can be used in the command line too. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/resprop/ resprop.html A similar approach is to use the "alias" command, for example: alias myres :phe,tyr,leu col hot pink myres alias thezone ligand z<4 rep stick thezone Aliasing can use any type of specification and is not limited to amino acids like ResProp. To color by some continuous numerical property, however, attributes would definitely be the way to go. Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Re: [Chimera-users] Questions about homology modelling
by Elaine Meng 15 Jan '08

15 Jan '08

Hi Jim, You can color by any attribute, once it is assigned. New attributes will be listed in the Render by Attribute (coloring) tool. You can create attributes arbitrarily with Define Attribute, as mentioned, and various different tools in Chimera create tool-specific attributes: (1) A "charge" attribute could be created by reading in a Mol2 file with charges or by running the Add Charge tool (an example of use is included in the Attributes tutorial). This uses Cornell et al. AMBER charges for standard residues and calculates charges for nonstandard residues with Antechamber. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/ addcharge.html You could use Attribute Calculator to create a residue attribute from those atom attributes, or if you used the Define Attribute approach, you could define the residue charge directly. That would be quite simple to do for the standard amino acids, for example. (2) Electrostatic potential: Currently Chimera does not calculate the potential for you, but reads several formats of maps. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp If you have opened an electrostatic potential map and a structure, you can use the "Values at Atom Positions" tool to create an atom attribute of the potential value at its position. This can be used with other kinds of maps as well, such as electron density. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/density/ density.html Alternatively, you could color a surface directly by potential or density without going through atomic attributes. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/ surfcolor.html (3) Docking scores: the ViewDock tool automatically assigns whatever DOCK scores are in the ligand file as attributes. (4) Residue conservation: if you have a sequence alignment and associated structure(s) open in Chimera, the structure residues get various conservation attributes according to the columns in the alignment. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ multalignviewer/framemav.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ multalignviewer/multalignviewer.html#mavAttributes There are probably additional examples, but that may already be more than you wanted to know. I would be happy to provide more specific assistance with whatever you would like to do - let me know, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jan 15, 2008, at 12:01 PM, Nicholson, Jim wrote: > Elaine: > > Thanks for the reply. My comment about coloring refers to using a > table > of residue hydrophobic index to color atoms or surfaces. I used it > all > the time for docking. I also want to color things by residue > charge or > electrostatic field. Most modelling packages offer something like > that, > and, I couldn't find it in Chimera, so, I thought would ask. > > -Jim Nicholson >

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Questions about homology modelling
by Nicholson, Jim 15 Jan '08

15 Jan '08

Hi: I still love Chimera (if you remember my last message), but, I need to do some homology modelling. I was using Insight/Homology, but, access to that software has been taken away. I'm wondering if anyone on the Chimera project is using an interface to Modeller or has any recommendations commands that might be usefull, like adding amino acids from a sequence, extending the protein, etc. Also, the coloring schemes I can see look a little limited. I regularly color by charge or hydrophobicity. I was wondering if there might be something I'm missing in Chimera? -Jim Nicholson Program in Neuroscience University of Maryland 685 W. Baltimore, St., MSTF 5-11 Baltimore, MD 21201 410-706-3418 410-804-5872 (cell)

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Bug (?) with EnsembleCluster
by Francesco Pietra 15 Jan '08

15 Jan '08

I was trying to carry out a cluster analysis from three mdcrd trajectories from Amber 9. I reported here yesterday that I was unable to input more that one mdcrd (in gz form) to Chimera. Therefore, I combined the mdcrd files with ptraj in Amber 9, while stripping all water molecules, all lipid, and box information, leaving only the protein with ligand. That combined mdcrd loaded perfectly into Chimera MD Movie saving a pdb file (there was no option "save all frames" suggested by Elaine's email; I did not select anything else than "untranformed coordinates") Opened successfully this pdb into Chimera, Tools, MD/EnsembleAnalysis, EnsembleCluster, select the new file, finally click on OK: that resulted in Chimera Error. This was a first trial, though I have right taken the opportunity to submit an alleged bug from the window inviting to do so. From a perusal of Reply Log, I was unable to grasp the nature of the failure. In particular, lacking documentation for ksdssp, I was unable to run it (to assign the lacking secondary structure of the protein) with different parameters from used energy cutoff -0.5 minimum helix length 3 minimum strand length 3 and commands as from Log. Perhaps I should also mention that lack of secondary structure is typical of the long procedure through different programs to carry our (1) model building, (2) docking, (3) MD. Thanks francesco ____________________________________________________________________________________ Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping

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A features-related question
by Dmitri Pavlov 14 Jan '08

14 Jan '08

Dear friends and colleagues, I have not really tried the product yet, but was wondering whether it is possible to "edit" a protein's structure by introducing one or two single mutations with the follow-up minimization using Chimera. If so, could you please hint to the algorithm of actions. Thanks a lot in advance! The project is burning :-( Dmitri

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transparent background
by Krepkiy, Dmitriy (NIH/NINDS) [F] 14 Jan '08

14 Jan '08

Hi, Is it possible to make background transparent? Thanks, Dmitriy ************************************** Dmitriy Krepkiy, Ph.D. Room 3B213 Building 35 - Porter Bldg, 35 Convent Dr Bethesda, MD 20892

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Fit model in map algorithm
by Tom Goddard 14 Jan '08

14 Jan '08

Christopher Akey wrote: > Tom- > > I was wondering how the fit model into map works? Is it calculating a > ccf and if so how since a pdb and a map file are quite different > entities. > > > cheers C Akey Hi Christopher, The Chimera fit model in map capability does a rigid rotation and translation to maximize the sum of the map values at the atom positions. It reports the average map value at the atom positions. It doesn't report a correlation coefficient. That would require calculating a simulated map from the PDB at the desired resolution and Chimera currently cannot do that. I would like to add that capability since correlation values are the standard measure of goodness of fit that is reported in the literature. The fit model in map code uses a gradient ascent iterative method to maximize the sum of map values. The Chimera fit map in map capability will report a correlation value. So you could run some external program to compute a simulated map (I've used pdb2mrc from the EMAN package) then fit that simulated map into your experimental map with the fit map in map dialog and get a correlation value. Or you could use the Chimera fit model in map to fit the PDB, then open the simulated map, register it with the fit PDB (using Model Panel / Transform As button), and then have the fit map in map dialog report the correlation without optimizing the simulated map placement. I'd expect very similar results from fitting the PDB versus fitting the simulated map. The fit map in map algorithm maximizes the "overlap" between maps. That is not the same as the correlation. It is a sum of the pointwise products between the two maps at grid points within the contour surface of one of the maps. That differs from the correlation in that it is not normalized by the sum of the squares of each maps' values within the surface. This has important consequences. The Chimera "overlap" optimization will move the map into a nearby high density region even if the pattern of highs and lows in the density does not match. The correlation normalization eliminates the tendency to move to higher density -- instead just optimizing the match of the highs and lows in the density. Both are useful and I will in the future add an option to optimize the correlation. The Tools section of the Chimera User's Guide describes the map and model fitting methods: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmodels/fitmodel… http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.ht… Tom

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Re: [Chimera-users] suppressing warning messages
by Eric Pettersen 08 Jan '08

08 Jan '08

Hi Ryan, Perhaps other Chimera developers can chime in, but I don't know of any good way to selectively suppress the non-status messages that Chimera generates, particularly the "duplicate atom serial number" messages which are being put on standard error by code in the C++ layer. What I can suggest in your situation is that you have your print statements go to standard error (so that they flush through pipes immediately) and that you prefix them with some unique string that you can grep for. Something like: from sys import __stderr__ as stderr print>>stderr, "OUTPUT", "my result:", r and run Chimera with: chimera --nogui myscript.py |& grep OUTPUT --Eric On Jan 8, 2008, at 12:19 PM, Ryan Pavlovicz wrote: > Are there ways just to suppress the chimera output? I'd still like > to see some of my print commands that are part of my python script, > so i can easily debug, follow a process, etc.? > > On Jan 8, 2008 1:24 PM, Eric Pettersen < pett(a)cgl.ucsf.edu> wrote: > Well to suppress all output you would use normal shell redirection > to /dev/null. For csh-style shells, something like this: > > chimera --nogui >& /dev/null > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > On Jan 8, 2008, at 9:28 AM, Ryan wrote: > >> The --nostatus option will suppress messages like: >> >> "Executing xxx.py... Opening xxx.pdb..." >> >> but still, messages like: >> >> "Model 0 (xxx.pdb) appears to be a protein with noe secondary >> structure assignements. Computing assignments..." & "warning: >> duplicate atom serial number found..." >> >> are still printed to the screen. Are there ways to suppress these >> messages as well? Thanks again, >> >> ryan >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

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Re: [Chimera-users] suppressing warning messages
by Ryan 08 Jan '08

08 Jan '08

The --nostatus option will suppress messages like: "Executing xxx.py... Opening xxx.pdb..." but still, messages like: "Model 0 (xxx.pdb) appears to be a protein with noe secondary structure assignements. Computing assignments..." & "warning: duplicate atom serial number found..." are still printed to the screen. Are there ways to suppress these messages as well? Thanks again, ryan

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suppressing warning messages
by Ryan 08 Jan '08

08 Jan '08

Is there a way to suppress warning messages when using Chimera in a python script (--nogui option)? Additionally, is there a way to suppress the additional non-warning Chimera output that prints to screen when running via python script? Thanks, ryan

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How to input more than one mdcrd file
by Francesco Pietra 07 Jan '08

07 Jan '08

I was unable to input more that one mdcrd file to MD Movie (to get a single pdb file for EnsembleCluster). I tried by either giving the files one to one, or with the following prod.meta: amber my.prmtop prod1.mdcrd.gz prod2.mdcrd.gz prod3.mdcrd.gz Always, I got prod1 trajectories alone. I used compressed coordinate files also when fed one to one. I did not try with non compressed files. Thanks francesco pietra ____________________________________________________________________________________ Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping

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chimera crashes my linux 64 bits PC
by jean-francois menetret 07 Jan '08

07 Jan '08

After I rebooted my linux 64 bits PC this morning, chimera crashes the machine. I tried older versions of chimera ... same result :-( How can I fix that situation ? Jean-Fran�ois M�n�tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street

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mean structure
by sette＠uniroma2.it 07 Jan '08

07 Jan '08

Hi, I don't know if someone already ask for this... It is possible to calculate an average structure having a bundle of structures? I loaded from the pdb a file containing 30 NMR structures but I would like to use only the mean structure... Thanks for your help, Marco Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328

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Slow dealing with pdb files
by Francesco Pietra 03 Jan '08

03 Jan '08

I am dealing with the average structure (a protein complex embedded in a POCP membrane and water solvated) derived with Amber's ptraj from a 1.5 ns MD. Opening this pdb file in 1.2470 Chimera has become extremely slow. The file is 6.4MB. First, below the screen it is warned "Ignored bad PDB record found on line #", for lines from 1 to 114154. This may take some 10 minutes. The pdb records read as in the following examples: For the lipid: ATOM 20 2C21 POP 1 25.569 20.201 48.492 0.00 0.00 For the protein: ATOM 10915 HB2 ALA 117 44.211 74.567 28.832 0.00 0.00 For water: ATOM 22264 O WAT 1771 25.558 39.417 16.580 0.00 0.00 ATOM 22265 H1 WAT 1771 25.582 39.432 16.549 0.00 0.00 ATOM 22266 H2 WAT 1771 25.569 39.482 16.611 0.00 0.00 After that, the warning message changes to "Computed secondary structure assignments (see reply log)" which lasts for longer than 1 hour and 20 minutes. During this time, "top" command shows that python is using 12% MEM and 99% CPU. Then, the graphics appears, with the membrane-protein-complex not centered in the water box. During all that time, I had to avoid doing anything else with the GNOME interface. A second terminal for "top" had to be opened before launching Chimera on another terminal window. Otherwise, spurious graphics become superimposed to the Chimera window. I could then carry out rapid mapping of the protein residues around the single-residue ligand (select protein & :ligandname z<#), which was what I wanted to do. The same events occurred with shorter trajectories. At ca 0.7ns the time taken by Chimera to work out the average-structure pdb was about 15 minutes. Clearly, there is an exponential trend. I can in part compare these events on VMD: the pdb file from 1.5ns MD is opened in VMD in less than 1 minute and the resulting membrane-protein-complex is centered in the water box. Is all that caused by the not-updated atom naming by Amber? Or could the execution be accelerated by calling some C routines by python? Chimera was run on a modest desktop: Athlon 1GHz, RAM 1GB, a poor main board (product: K7S5A, vendor: ECS, version: 1.0), Debian Linux i386. Thanks francesco pietra ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

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Fwd: Re: Slow dealing with pdb files
by Francesco Pietra 03 Jan '08

03 Jan '08

Must add that alternatively to "average structure" I tried a cluster analysis with MMTSB. The program refused to work on my trajectories for unclear reasons: the program is installed correctly and the input is correct (as verified by the program author). Therefore, I am eagerly waiting for Chimera being able to carry out cluster analysis (if I understood correctly your message to this regards) francesco --- Francesco Pietra <chiendarret(a)yahoo.com> wrote: > Date: Wed, 2 Jan 2008 23:04:40 -0800 (PST) > From: Francesco Pietra <chiendarret(a)yahoo.com> > Subject: Re: [Chimera-users] Slow dealing with pdb files > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > CC: chimera <chimera-users(a)cgl.ucsf.edu> > > Eric: > Thanks a lot for this lesson, surely useful to many other guys, too. > > Whether looking at an "average structure" or some other output structure was > a > problem I got no clarification from the Amber mailing list. Unfortunately, Pr > Brozell is not active in this period on Dockfans to ask him. My question was, > is the "average structure" representative of the interactions occurring > between > the protein and the ligand as resulting from the MD carried out? Although > DOCK6.1 does that with amber score, it is only for implicit medium > surrounding > the complex. Ideally, I would have liked to estimate the free energy of > interaction in the presence of explicit surrounding medium but Amber does not > appear to have a way to that for a complex in a membrane (or anyway for a > non-standard ligand). Therefore, what I am relying on, is the distance > between > the protein residues and the ligand. The closest the protein residues are to > the ligand, the more they are considered to be relevant. > > At any event, given the problem Chimera has encountered with an average > structure, do you believe that mapping the protein environment around the > ligand with Chimera's "zone" is correct? From your "lesson" I understand YES. > > I would appreciate any comment or suggestion about that. > > francesco > > --- Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > > > On Jan 1, 2008, at 1:44 PM, Francesco Pietra wrote: > > > > > I am dealing with the average structure (a protein complex embedded > > > in a POCP > > > membrane and water solvated) derived with Amber's ptraj from a 1.5 > > > ns MD. > > > > > > Opening this pdb file in 1.2470 Chimera has become extremely slow. > > > The file is > > > 6.4MB. First, below the screen it is warned "Ignored bad PDB record > > > found on > > > line #", for lines from 1 to 114154. This may take some 10 minutes. > > > > These are for the water ATOM records where the atom serial number and/ > > or residue number were "****" (what FORTRAN inserts when a number > > won't fit inside a field width). > > > > > After that, the warning message changes to "Computed secondary > > > structure > > > assignments (see reply log)" which lasts for longer than 1 hour and > > > 20 minutes. > > > During this time, "top" command shows that python is using 12% MEM > > > and 99% CPU. > > > > Due to the fact that this is an "average" structure, Chimera's > > estimation of the connectivity is bad for many parts of the structure > > -- particularly the POP residues in the membrane. This creates a > > rat's nest of intra-residue connectivity which the ring-finding > > algorithm (designed for "reasonable" structures) takes a long time to > > operate on. Normally Chimera wouldn't run ring-finding as a > > structure opens, but due some interesting naming of hydrogens in the > > POP residues (e.g. RH16) it assigns some of the hydrogens to be other > > elements (e.g. rhodium, as per PDB atom naming rules). Since rhodium > > is a metal, it wants to depict it as a sphere, which means it needs > > to know the radius, which in turn depends on the atom type, which > > needs to find rings... > > > > > Then, the graphics appears, with the membrane-protein-complex not > > > centered in > > > the water box. > > > > This is due to the "****" waters being ignored. > > > > > I could then carry out rapid mapping of the protein residues around > > > the > > > single-residue ligand (select protein & :ligandname z<#), which was > > > what I > > > wanted to do. > > > > If you only care about the protein and ligand in your analysis, you > > should just edit your file to strip the waters and lipids. When I > > did this with the file you sent it only took moments to open. > > > > --Eric > > > > Eric Pettersen > > UCSF Computer Graphics Lab > > http://www.cgl.ucsf.edu > > > > > > > > > ____________________________________________________________________________________ > Never miss a thing. Make Yahoo your home page. > http://www.yahoo.com/r/hs > ____________________________________________________________________________________ Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs

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selection
by Sara Bowen 03 Jan '08

03 Jan '08

Hi, I've been going through the chimera tutorial, but I'm having some trouble selecting anything. I can select atoms, and the bottom corner of the window lists what I've selected, but there is no green highlighting in the image. Then if I try to move anything, the image will move in the side view but not in the main window. It seems frozen. If I select everything or select nothing, I can still only get the image to move in the side view...not the main window. Then if I make the main window full screen, the image is just fuzzy colors like snow on a out of tune t.v. Does anybody know what's going on and how I can fix it? Thanks, Sara B. at ASU

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coloring protein structure according to Order parameters
by rama krishna 03 Jan '08

03 Jan '08

Dear Friends, I need to Paint a protein structure according to generalized parameter values. Is there any way to do that in UCSF-Chimera. Kindly suggest me. Regards Ramakrishna, Dr Ashish Arora Lab, Molecular and Structural Biology lab, Central Drug Reseach Institute, India

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Opening compressed trajectories
by Francesco Pietra 02 Jan '08

02 Jan '08

I found comfortable to deal with mdcrd compressed (gz) files directly in Amber's ptraj. This saves much disk space. I wonder whether this could be made available for Chimera. The scope would be twofold: other that saving disk space, shorted times of ssh transfer from the computing machine to the desktop with Chimera. Happy 2008! francesco pietra ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

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saving complex structure
by bala 02 Jan '08

02 Jan '08

Dear chimera friends, I have a protein-RNA complex pdb structure. I want to remove the RNA in the crystal structure and put my RNA molecule in to the binding site. Since my RNA is very big around 20bp long, i prefer to manually dock my RNA followed by a big simulation than a automated docking. I tried in chimera and i saved the complex structure with the option "save the displayed atoms". But when i see the pdb structure, it has the coordinates of RNA molecule but not the protein. Also when i open the pdb in chimera, it shows me the protein structure. Kindly write me your comments on using chimera i) for such a manual docking and also ii) how to save the complex structure. Wish you all a happy new year, Bala

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Command for volume and area calculation
by shengzhiya＠nibs.ac.cn 27 Dec '07

27 Dec '07

Dear all, May I know if there is some command in chimera for measuring volume and area like in the menus: “Tools…Surface/Binding Analysis…Measure Volume and Area”? Thanks in advance! Happy new year and have a nice holiday! Zhiya

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formal charge or net charge
by snoze pa 25 Dec '07

25 Dec '07

Dear Chimera Users, Is it possible to calculate the net charge or formal charge of unknown residues using chimera. I have a large set of molecules for which i am trying to calculate the net charge on each molecule. Thanks in advance s

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rmsd cluster analysis
by Elaine Meng 24 Dec '07

24 Dec '07

Hi Francesco and others, People with MD trajectories can also use this new EnsembleCluster tool (available in the most recent daily builds) by: - viewing the whole trajectory with the "MD Movie" tool, or at least all the frames you want to cluster - from the MD Movie dialog menu, choosing File... Save PDB and saving "all frames" to a file - quitting from MD Movie and opening the new file with File... Open - choosing Tools... MD/Ensemble Analysis... EnsembleCluster, clicking the line that shows that new file, then OK I just tried this to make sure it works. The clustering calculation may take a while, but eventually another dialog with results should appear. This tool is still under development and may change, but this will at least allow users to try it on trajectory ensembles as well as NMR ensembles. Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Transparent background
by Abbas 20 Dec '07

20 Dec '07

Hi, One feature I really appreciated about chimera was the ability to make pictures without a background, however recently i realized this is not possible anymore I checked out under the effects dialog under tools>viewing controls and it give me an error saying this wasn't supported. I haven't changed my computer since i first started using chimera I have updated to the latest version of chimera available for OSX 10.4, I wonder if this is the cause of the problem. I would really like to have pictures without backgrounds like I used to, I know PyMol lets you do it, but I dislike this program. In any case I would greatly appreciate any help/pointers on this issue. Thanks in advance. abbas.

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