- Chimera-users - RBVI Mailing Lists

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

2 4

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

2 2

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

4 3

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

2 1

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

2 1

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

2 1

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

2 2

formal charge or net charge
by snoze pa 26 Dec '07

26 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

2 1

rmsd cluster analysis
by Elaine Meng 25 Dec '07

25 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

2 4

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.

4 4