- Chimera-users - RBVI Mailing Lists

using IDLE
by Ben Keshet 07 Feb '08

07 Feb '08

Hi, I am interested in performing the same actions several times on several different structures. For example: open a file, select the histidines, delete them, save and close. Is IDLE the right tool for that? I opened the python shell (Tools-> General Controls-> IDLE) but could not open files or manipulate them using the shell. I have no knowledge in python. What is the best way to write scripts to execute commands repeatedly? If IDLE is the tool, how can use it to do that? Is there a written source for that? Do I need to master python first? Many thanks, Ben

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clipping related models identically
by Eric Pettersen 06 Feb '08

06 Feb '08

Raven Huang asks (paraphrased): > I have four related structures that I want to show in cutaway view, > with the cut being in the same place in all the structures. How > can I do that? The technique varies depending on whether you are clipping using the global clip planes (i.e. the ones shown in the Side View), or with per-model clip planes (from the Per-Model Clipping tool). Both techniques share the same setup step though: open all your models and get the parts you care about superimposed. If the starting coordinates are already "in the same reference frame" then you don't have to do anything but open the models. Otherwise you will have to superimpose them either with the MatchMaker tool or the "match" command. There is a discussion of using those here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/tutorials/ images.html#matching To view just one of the structures at a time, use the Model Panel (Favorites->Model Panel) and use the buttons in the Shown column (or the Show Only button in the button list) to show one structure/ surface. Now for adjusting the clip plane... Global clipping: open the Side View and adjust the near clip plane until it is cutting where you want it to. Per-model clipping: use the Per-Model Clipping tool to adjust the clip plane of the visible model until it is cutting where you want it to. Then choose one of the other models you want to cut from Per- Model Clipping's "Model:" menu. Enable clipping and click the "Align plane" button once you have chosen the original model in the menu next to the button. The model clip planes will now be aligned. Once the models are all clipped, you can either show then individually (the Model Panel again) and save separate images, or move them apart using the "move" command and save one combined image. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Planes feature in the Volume Viewer
by William Jeffrey Triffo 05 Feb '08

05 Feb '08

hi, when using the Planes tool in Volume Viewer, are the planes numbered from 0 or 1? I loaded a contour using the IMOD import, where I had drawn the contour on slice 12 of a volume; however, it appears that the plane that transects the contour in Chimera is '11' when using the Planes tool. I tried to test the enumeration by exceeding bounds (150 slices are in the volume, so was expecting an error for an entry of '150' if it was enumerated from zero), but it appears that slice indices outside the range of the loaded volume just default to the limit in either direction (typing in '200' just sets it to the highest-enumerated slice). -- ------------------------------------------------------------- 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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Contact/clash detection for HETATMs
by Jonathan Magasin 05 Feb '08

05 Feb '08

Hello, I'm trying to use the clashes/contacts tool to explore valid phi/psi angles for L- and D-Ala (as part of a homework assignment; developing a Ramachandran plot for each). The tool worked great for L-Ala but does not report any contacts for D-Ala. (For each, I've snipped just the relevant sections out of a larger PDB. I'm using default params for collision detection, with detection calculated for any movement.) The difference in the PDB's for L-Ala and D-Ala is that the latter are in HETATM records. I did include the CONNECT info (to explicitly tell Chimera how HETATMs bond) but that did not help. Perhaps there's something else I must include, or some modification I can make to the HETATMS (element labeling?) so that collision detection will work as with peptides? Or is this a known limitation? (Is there a list of known limitations? I'm a new user.) I'm not Note that the distance tool works for D-Ala. If I can get collision detection to work, it take much less time. Thanks in advance. -Jonathan

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Aligning two residues same name
by Elaine Meng 05 Feb '08

05 Feb '08

> Changing residue name works. Deleted membrane, saved pdb without > membrane. > Loaded the two models. Command line: match :XXX :YYY Hi Francesco, You can still use the name without changing it, for example open 4hhb open 4cpp preset apply interactive 1 match #1:hem #0:hem.a ~ribbon This matches the single heme residue of 4cpp (#1) to the chain A heme of 4hbb (#0 - it has four heme residues, in chains A-D). The protein parts are totally different but I just used this as an example because they both have heme. It takes a little time, but I recommend learning about the command- line specification language because it is used in so many commands, and can be very powerful yet flexible. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ frameatom_spec.html Or, for some quick hints see the examples on the second page of the "Quick Reference": http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/quickref.pdf 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] [Dock-fans] How to get the charged mol for the ligand
by cpsosa＠comcast.net 04 Feb '08

04 Feb '08

Thanks. We tried that but after the hydrogens were added. We saved it and "vi" the mol2 file. I'll try this. -- Carlos P. Sosa -------------- Original message ---------------------- From: Eric Pettersen <pett(a)cgl.ucsf.edu> > I forgot, there's actually a fourth thing you can do: change the > atom type directly. Select the oxygen atom and open the command line > (Favorites->Command Line) and type: > > setattr a idatmType O3 sel > > which will set the selected atom's "idatmType" attribute to sp3 > oxygen ("O3"). > > Do this before hydrogens are added. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > On Feb 3, 2008, at 1:27 PM, Eric Pettersen wrote: > > > 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 > >> > >> > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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Fwd: Loading prmtop/mdcrd with partial workout
by Francesco Pietra 04 Feb '08

04 Feb '08

What I asked below has no sense. Deleting residues does not freed memory. Of course, because those residues can be resumed. francesco --- Francesco Pietra <chiendarret(a)yahoo.com> wrote: > Date: Fri, 1 Feb 2008 12:49:22 -0800 (PST) > From: Francesco Pietra <chiendarret(a)yahoo.com> > Subject: Loading prmtop/mdcrd with partial workout > To: chimera <chimera-users(a)cgl.ucsf.edu> > > 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 > > ____________________________________________________________________________________ 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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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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