- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] [Dock-fans] How to get the charged mol for the ligand
by Eric Pettersen 04 Feb '08

04 Feb '08

Hi Carlos, There are basically three things you can do: 1) Download the latest daily build and try that. I have been working hard on atom typing for ring systems recently (and am still working on it) and there's a pretty good chance that it will type (and therefore protonate) the phenyl oxygen correctly now. You get a daily build by going to the Chimera home page (www.cgl.ucsf.edu/ chimera) and following the "Daily Builds" link. 2) Directly edit the structure (after adding hydrogens but before adding charges). Control-double-click the oxygen and select "Modify Atom" from the pop-up menu. In the resulting dialog change the element type to O, the geometry to tetrahedral, and the number of bonds to 2. You should also probably change the atom name field to be the same as what the atom's name is. Then click the Change button and the hydrogen will be added. 3) Before doing any processing, change the bond length. Control double-click on the C-O bond and choose "Set Bond Length" from the pop-up menu. Type in a bond length appropriate for a C-O single bond and then run the rest of your processing. --Eric Eric Pettersen UCSF Computer Graphics Lab On Feb 2, 2008, at 5:19 PM, cpsosa(a)comcast.net wrote: > > Hello, > > We have the opposite problem, our PDB has one oxygen that is part > of a phenyl group and after using addH in Chimera, hydrogen does > not get added to that oxygen. Is there a way to add hydrogen to a > single atom? using Chimera. For Chimera to add a hydrogen to that > O... perhaps making the C-O bond larger. > > Any suggestions? > > Thanks, > > -- > Carlos P. Sosa > > -------------- Original message ---------------------- > From: Eric Pettersen <pett(a)cgl.ucsf.edu> >> I assume this is IMZ from 1rv1? Chimera is adding a proton to the N3 >> nitrogen that it shouldn't. After adding hydrogens and before saying >> OK to the charge calculation, type this command to Chimera's command >> line to delete the extra hydrogen: >> >> del :IMZ@h3 >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> http://www.cgl.ucsf.edu >> >> >>> I could not get the charges for my molecule (ligand in x-crystal >>> structure). how to do that? >>> I am getting the following error message. >>> I am using chimera to do these funtions. >>> >>> Running ANTECHAMBER command: C:\Program Files\Chimera\bin >>> \antechamber\exe\antechamber -i c:\docume~1\thomas\locals~1\temp >>> \tmpkzw4il\ante.in.mol2 -fi mol2 -o c:\docume~1\thomas\locals~1\temp >>> \tmpkzw4il\ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 >>> (IMZ) >>> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe >>> \bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC - >>> f ac -j part >>> (IMZ) >>> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe >>> \atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff >>> (IMZ) Total number of electrons: 351; net charge: 1 >>> (IMZ) INFO: Number of electrons is odd: 351 >>> (IMZ) Please check the total charge (-nc flag) and spin >>> multiplicity (-m flag) >>> Failure running ANTECHAMBER for residue IMZ >>> >>> >>> Thomas >> >> > > > > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Date: January 31, 2008 12:54:24 PM PST > To: dock-fans(a)docking.org > Subject: Re: [Dock-fans] How to get the charged mol for the ligand > > > I assume this is IMZ from 1rv1? Chimera is adding a proton to the > N3 nitrogen that it shouldn't. After adding hydrogens and before > saying OK to the charge calculation, type this command to Chimera's > command line to delete the extra hydrogen: > > del :IMZ@h3 > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > >> I could not get the charges for my molecule (ligand in x-crystal >> structure). how to do that? >> I am getting the following error message. >> I am using chimera to do these funtions. >> >> Running ANTECHAMBER command: C:\Program Files\Chimera\bin >> \antechamber\exe\antechamber -i c:\docume~1\thomas\locals~1\temp >> \tmpkzw4il\ante.in.mol2 -fi mol2 -o c:\docume~1\thomas\locals~1 >> \temp\tmpkzw4il\ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 >> (IMZ) >> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe >> \bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC >> -f ac -j part >> (IMZ) >> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe >> \atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff >> (IMZ) Total number of electrons: 351; net charge: 1 >> (IMZ) INFO: Number of electrons is odd: 351 >> (IMZ) Please check the total charge (-nc flag) and spin >> multiplicity (-m flag) >> Failure running ANTECHAMBER for residue IMZ >> >> >> Thomas > > > _______________________________________________ > Dock-fans mailing list > Dock-fans(a)docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans > >

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Aligning two residues same name
by Francesco Pietra 04 Feb '08

04 Feb '08

Task: compare/align a single-residue molecule before docking (naked molecule, mol2 or pdb file) with same residue as ligand in a protein after docking/MD (pdb file of a snapshot for complex embedded in a bilayer membrane). Should I change the residue name in one of the two models? Same name poses to me problems. Or there is a direct way? 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: Aligning two residues same name
by Francesco Pietra 04 Feb '08

04 Feb '08

Changing residue name works. Deleted membrane, saved pdb without membrane. Loaded the two models. Command line: match :XXX :YYY How to put the difference in quantitative terms (rmsd)? Thanks francesco --- Francesco Pietra <chiendarret(a)yahoo.com> wrote: > Date: Mon, 4 Feb 2008 06:59:25 -0800 (PST) > From: Francesco Pietra <chiendarret(a)yahoo.com> > Subject: Aligning two residues same name > To: chimera <chimera-users(a)cgl.ucsf.edu> > > Task: compare/align a single-residue molecule before docking (naked molecule, > mol2 or pdb file) with same residue as ligand in a protein after docking/MD > (pdb file of a snapshot for complex embedded in a bilayer membrane). Should I > change the residue name in one of the two models? Same name poses to me > problems. Or there is a direct way? > Thanks > francesco pietra > > > > ____________________________________________________________________________________ > Be a better friend, newshound, and > know-it-all with Yahoo! Mobile. Try it now. > http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ > > ____________________________________________________________________________________ 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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Permission to use Chimera created image
by Seymour Yang 01 Feb '08

01 Feb '08

Hi, I wish to obtain permission to use one or two of the virus images shown on your Chimera image gallery (Semliki forest Virus and Sindbis Virus). We are writing a feature article about 3D molecular imaging and would like to include some Chimera images. May I ask whom to contact regarding permission and obtaining higher resolution files? Hope you can help. Seymour Seymour Yang Producer - Science Feature Stories Email: seymour(a)sciencephoto.com Website: www.sciencephoto.com Blog:http://sciencephoto.blogspot.com/

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Loading prmtop/mdcrd with partial workout
by Francesco Pietra 01 Feb '08

01 Feb '08

I am experiencing difficulties with Amber ptraj in removing solvent/lipid/box (i.e., unexpected problems of prmtop fitting after that, though I used a prmtop before creating solvent/lipid/box). Otherwise, I have memory problems with Chimera in loading such an extensive MD (many ns, in various coordinate files) with all the burden of solvent/lipid/box. My question: is that feasible with Chimera to load a coordinate file, remove solvent and lipid, load a second coordinate file, remove solvent and lipid, and so on for all coordinate files? 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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screening
by snoze pa 01 Feb '08

01 Feb '08

In continuation to my previous question, Is it possible to use chimera in virtual screening?

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graphics card question (survey?)
by William Jeffrey Triffo 31 Jan '08

31 Jan '08

hello, anyone out there using a Radeon HD 2600 XT or GeForce 8800 GT? Just wanted to know if there are any driver issues out there that are known - these are the two 'lower-end' options on the current Mac Pro line, and I am evaluating that as a potential purchase (so technically, my question may only be relevant if you are also using a Mac machine). likewise, if you have a current-generation Mac (Tiger/10.4 or Leopard/10.5) and have bought a third-party card that you have had success with, I am all ears. best, -Jeff -- ------------------------------------------------------------- Jeff Triffo Auer Group, Donner Lab, Lawrence Berkeley National Laboratory Raphael Group, Bioengineering Department, Rice University Medical Scientist Training Program (MSTP), Baylor College of Medicine phone (Berkeley): 510-486-7940 fax (Berkeley): 510-486-6488

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fourier transforms
by Matt Shawkey 31 Jan '08

31 Jan '08

Hi, I'm doing fourier transforms of 3d volumes and noticed that they are computed in Chimera using only a small portion of the actual data available (e.g. 128 ^3 pixels rather than the 512^3 pixels in the volume). Is there a way to do a fourier transform using all of the available data? THanks, Matt

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Surface color
by James Fethiere 30 Jan '08

30 Jan '08

Hi, I'm using the volume path tracer and color zone to highlight regions of a map. I would like to display a model within this region but it is not visible when I color the region with color zone. How can I make this zone transparent but still a different color that the rest of the map? Thanks James

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Re: [Chimera-users] mac pro theoretical question
by Tom Goddard 29 Jan '08

29 Jan '08

Hi Jeff, I don't know much about any of the current Apple graphics cards (Radeon HD 2600 XT 256Mb, Nvidia GeForce 8800 GT 512Mb, Nvidia Quadro FX 5600 1.5Gb). My first concern would be whether bugs in the drivers for these cards are going to cause trouble in Chimera. We have a web page that lists problems with graphics drivers observed using Chimera: http://www.cgl.ucsf.edu/chimera/graphics/graphicsbugs.html#cards There was a recently reported problem (squashed atom spheres) with GeForce 8800 GTX (not GT) on Windows. The Apple driver may be much different. The Quadro FX 4500 which was Apple's high-end offering before the 5600 crashed with solid volume rendering. Don't know if the current 5600 would have the same problem -- but there is a fair chance it does. Chimera uses many different OpenGL calls and I'd guess 1 in 10 drivers exhibit bugs of varying severity when using Chimera. Some of Chimera performance is related to graphics card speed and memory, and some is related to CPU speed and memory. When the displayed models rotate slowly that is the graphics card except if you are using transparent volume surfaces or meshes which are sorted by depth on the CPU for every new view angle. Everything else is the CPU, main memory, memory cache performance, and hard-drive speed. Solid style volume rendering makes a lot of textures which usually will be stored in graphics card memory. More graphics card memory could make larger volume rotate faster because they fit on the card. 256^3 volumes (16 million voxels, 4 bytes per voxel) typically rotate at 10 frames per second with graphics memory sizes 128 Mb and up. Textures have to have power of 2 sizes so just knowing that can get you better performance if you trim your 550x550x100 region to 512x512x100 you'll get a factor of 4 speed-up. I don't know if a single application using one display can use more than one graphics card in Apple's multicard options. Chimera has no special code to do that. For large volume data, hard-drive speed, main memory size, and CPU speed are likely to be noticable factors in Chimera performance, each of about equal importance to graphics card speed. Tom > hi Tom, > > if you were considering a Mac Pro at some point in the future, what > graphics card would you pick when thinking of chimera (if you don't > mind peeking at some point at the list at > http://store.apple.com/1-800-MY-APPLE/WebObjects/AppleStore.woa/9354001/wo/… > > > are rendering bottlenecks in chimera largely a processor-limited thing > (and thus one of the 'lower end' cards listed would be fine), or > something that benefits dramatically from spending $2000 on a graphics > card (I am not in that kind of market, just wondering what kind of > decision you would make if evaluating that platform) > > best, > > -Jeff > > >

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