- Chimera-users - RBVI Mailing Lists

Merge the protein sequences of two different chains
by Hsih-Te Yang 05 Apr '12

05 Apr '12

Dear all: I am a new beginner of Chemira software package. By using "Multalign Viewer", I would like to merge the protein sequences of two different chains (200~300 a.a.). After that, I want to map some epitopes (8 ~ 20 a.a.) to this merged sequence. How can I do? Thanks for any kind help further. Hsih-Te

2 4

Solvate models
by Nikolay Igorovich Rodionov 05 Apr '12

05 Apr '12

Hi all, I was wondering if some could explain to me the differences between the water models available under the solvate option. * POL3BOX - POL3 water model * SPCBOX - SPC/E water model * SPCFWBOX - SPC/Fw water model * QSPCFWBOX - qSPC/Fw water model * TIP3PBOX - TIP3P water model * TIP3PFBOX - TIP3P/F water model * TIP4PBOX - TIP4P water model * TIP4PEWBOX - TIP4P/Ew water model Thank you all in advance, Nikolay Rodionov

2 1

Coloring distance labels
by George Tzotzos 05 Apr '12

05 Apr '12

I'm somewhat lost in the manual. I'm measured some specific distances which are clearly shown. Changing to Presets: Publication 3 the distances are shown in yellow in white background. I'd like to change the color of the distances. I'm pretty sure there's a quick solution for this. I simply can't find it. Any help would be much appreciated. Regards George

2 2

Coloring distance labels
by George Tzotzos 05 Apr '12

05 Apr '12

I'm somewhat lost in the manual. I'm measured some specific distances which are clearly shown. Changing to Presets: Publication 3 the distances are shown in yellow in white background. I'd like to change the color of the distances. I'm pretty sure there's a quick solution for this. I simply can't find it. Any help would be much appreciated. Regards George

1 0

color by RMSD
by Thomas Evangelidis 04 Apr '12

04 Apr '12

Dear UCSF Chimera users and developers, Is it possible to color a pair of structures representing different stages of the thermodynamic cycle of a protein by the RMSD, without aligning them? thanks in advance, Thomas

3 6

Re: [Chimera-users] [Chimera] #10638: heme not included in morph trajectory
by Elaine Meng 04 Apr '12

04 Apr '12

Hi Francesco, There is some progress... in the newest daily build (Apr 4) I can run the commands below to successfully show a morph of 1hho and 2hhb that includes heme and iron. 1hho only has two chains, so it is necessary to delete C,D from 2hhb before morphing. To include heme and iron, it is necessary to delete all the other het residues that may be different between the structures. I hope this helps, Elaine Here between "----" are contents of Chimera command file, which you could save as plain text file named something.cmd and open in Chimera to execute the commands. Lines starting with # are just comments/explanation and don't do anything. ------------- open 2hhb open 1hho # # delete 2hhb chains C,D # delete #0:.c-d # # delete het residues that may be different between the structures so that # the HEM residues will be included in the morph (if you want to see those # residues, open another copy of structure not used for morphing) # del :hoh,po4,oxy # # superimpose the structures; I used "mm" with defaults but it could be # done with options, or MatchMaker GUI, or "match" command, # or manually with mouse # mm #0 #1 # # create morph trajectory which will be model #2 # morph start #0 frames 25 morph interpolate #1 frames 25 morph movie ~modeldisp #0,1 --------------------- Then I tried to get fancy and make a tetramer of 1hho so that the morph could be from tetramer to tetramer. However, then only the heme/iron from A and B were included, not from C and D. I don't know why, because they are all in the input structures!! Here is that script in case it might be useful: --------------------- open 2hhb open 1hho # # make 1hho tetramer; #1 is original, #2 additional copy # sym #1 # # combine #1,2 dimers into tetramer model #3, close #1,2 # combine #1,2 name 1hho-tetra newchainids true close true # # delete het residues that may be different between the structures so that # the HEM residues will be included in the morph (if you want to see those # residues, open another copy of structure not used for morphing) # del :hoh,po4,oxy # # superimpose #0 and #3 # mm #0 #3 # # create morph trajectory which will be model #1 # morph start #0 frames 25 morph interpolate #3 frames 25 morph movie ~modeldisp #0,3 ---------------------

1 0

occupancy field
by Darjan Andrejc 03 Apr '12

03 Apr '12

Hey, Is it possible to change occupancy field to 1.0 in Chimera? I need a pdb file of my protein for docking and the file needs to have an occupancy field 1.0. Thanks for the help Darjan Andrejc, Mpharm PhD student, Department of Biotechnology National institute of Chemistry, Ljubljana, Slovenia

2 2

Minimize with fixed atoms
by Hurt, Darrell (NIH/NIAID) [E] 03 Apr '12

03 Apr '12

Hi there, I'm trying to minimize a protein after mutating a residue with the Rotamers panel. I first do a Check Clashes and select the clashing atoms. Then I expand the selection using Zone to <5 A. I use these selected atoms as the non-fixed atoms and the unselected atoms as the fixed ones. When I then run the minimization with the appropriate settings, I get an RMSD of 0.000 A for each step, even though the step size is 0.02 A. Nothing moves. Same thing if I have no fixed atoms. Am I in a local minima? Is that why nothing moves? The energy is very high (from the Reply Log): Potential energy: 222274199.525130, Gradient norm: 833984762.552943 Updated 6029 atoms. RMSD: 0.000000 Finished 1 of 5 steepest descent minimization steps Any ideas? I do have some hetero atoms... Thanks, Darrell Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office 301-402-0095 Mobile 301-758-3559 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public) Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

3 5

Re: [Chimera-users] morphing
by Elaine Meng 31 Mar '12

31 Mar '12

Hello Francesco! First make sure you are hiding the input conformations, so that you are seeing only the morph (for example, you could show Model Panel from Favorites menu, then uncheck the S(hown) boxes for everything except the morph results). I say that because if you see something not moving, it might be the original structure. As explained here, the morph should contain all of the atoms in the protein chain that are included in all of the input structures. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html#p…> Since your input structures are the same protein, if each one includes the sidechain atoms, the morph should contain all the same sidechains and they should move from one position to the other during the morph. They may not be displayed automatically, however. Try displaying all atoms (again better to hide the other structures first) to make sure of what is there. About the ion: even if the ion is in both structures, it may not be in the morph if you are using an older version of Chimera. However, there have been some fixes, and I believe if you are using Chimera 1.6 or newer, the ion should be included. The fix I'm thinking of was 6 months ago and is described here: <http://plato.cgl.ucsf.edu/trac/chimera/ticket/9886> If you try Chimera 1.6 and the suggestions above but you believe there is a bug, you could use Help... Report a Bug in the menu and describe how to reproduce the problem, attaching session file if necessary. 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 Mar 31, 2012, at 5:24 AM, Francesco Malatesta wrote: > Hello from Rome! > I'm trying to morph 2 different conformations of the same protein. I get a very very nice movie, but I can't get amino acid side chains or heteroatoms (heme iron) to move also. > Is there any way to do this? > thank you for help > Francesco

2 1

How to save VIPER transformation matrix
by snoze pa 30 Mar '12

30 Mar '12

Dear Chimera Users, Is it possible to save the coordinates after the VIPER transformation (xyz-2 fold symmetry) in Chimera. I can create a multiscale biological molecule in chimera but it is not saving the viper matrix in pdb file. Please note that this pdb is a model not the crystal structure and I am trying to save the viper matrix for this pdb. Thank you, S

4 5

Chimera is not loading properly
by Andrea Edwards 27 Mar '12

27 Mar '12

I have not used Chimera in awhile. I just downloaded the new version for Mac-OSX-64-bit and when I open it, none of the buttons on the gui are visible. There are ovals and things where there should be buttons, but not words on them. How can I fix this? attached is a screenshot. Thanks, Andrea

3 2

PDB model merging
by Nikolay Igorovich Rodionov 27 Mar '12

27 Mar '12

Hi all, I'm working on a project that requires me to merge models created through PDB BIOMT records. I have been using the copy&combine feature in the model panel to merge all of my models, and then writing a new PDB of only the combined model. I've noticed that this method deletes a large amount of information about the structure, including secondary structure records. Is there a way to merge models without losing such data? If it is relevant, I am merging 90+ models.

3 5

Trajectory analysis: hbond
by George Tzotzos 26 Mar '12

26 Mar '12

I'm wondering if there's a way to determine hbond formation during a trajectory in a similar way to the way the Plot distances tool in MD Movie/Analysis works. Or dumb values to a file. Many thanks in advance for any suggestions Regards George

3 4

Re: [Chimera-users] Electrostatic Potential using APBS .dx file
by Tom Goddard 26 Mar '12

26 Mar '12

Hi Soca, Sounds like you are doing everything right. That makes me suspect that something is wrong with your APBS file -- like all the potential values are zero. To see what the distribution of the potential values are, open the APBS file and then use menu Tools / Volume Data / Volume Viewer, and click on the histogram (empty rectangle in the middle of the volume dialog). That will show a histogram of the potential values. You can move the vertical bar on the histogram to see what the potential value is at that position. Check if -5 to 5 is a reasonable range. Tom > Hello, > > I have been attempting to generate a electrostatic surface map in > chimera using an external potential file generated from APBS (.dx). > > I understand that Chimera has an internal surface calculation protocol > via Coulombic Surface Coloring, however, I would like to use the > Electrostatic Surface Coloring. > > However, when I open my molecule (PDB), show surfaces, and choose its > MSMS main surface to color by electrostatic potential using the .dx > file, the surface map is not the red, white, blue that I have set in > my parameterts under Surface color. Everything turns to grey. My other > parameters include: > > red -5, white 0, blue 5. Colors 3. Palette Red-Blue. Surface offset 1.4. > > I feel as though I am missing something trivia that would allow me to > generate the surface image I want, however I am lost after may > searches for advice through the forums and tutorials. > > Please let me know what I am missing. > > Thanks > > Soca > > -- > Ardian Soca Wibowo, Ph.D. > Postdoctoral Associate > Dann Research Group > Department of Chemistry > Indiana University

1 1

Dimethyl Sulfoxide Electromagnetic Absorbance
by Nancy 25 Mar '12

25 Mar '12

Hi All, I would greatly appreciate it if anyone could provide a reference or information on the electromagnetic absorbance characteristics of dimethyl sulfoxide, especially in the region of 800-1400nm. Thank you, Nancy

1 1

RMSD plot
by lecan 23 Mar '12

23 Mar '12

Hi everybody. I am interested in plotting RMSD values vs time from molecular dynamics. Is there a way to extract the RMSD values from a the RMSD map in the analysis tool of MD movie. Or maybe exists another way to do this with Chimera. Thank you in advance Luis L.

2 1

how to measure the volume of the active site
by Thomas Evangelidis 23 Mar '12

23 Mar '12

Dear UCSF Chimera developers, I am interested in measuring the volume of the active site of a kinase. I have searched through the documentation and the only thing I found was how to measure the enclosed volume of a surface object. Is it possible to do what I want with UCSF Chimera? Could you please point me towards the relevant commands? Thanks in advance for any help. Thomas -- ====================================================================== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tevang(a)bioacademy.gr tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/

2 1

Multi-PDB fitting question
by Tom Goddard 21 Mar '12

21 Mar '12

> Dear Tom, > > ... > Currently we are trying to use a lot of PDBs (hundreds!) to fit one > density map and trying to find out the best fitted PDB, and we found > that fitting the PDBs one by one manually was very time-consuming and > low-efficiency. So we are wondering that if there is any advanced way > or batch file that can speedup this process? > > Thank you so much and we are looking forward your reply. > > Best Regards, > Lei > Hi Lei, Ok, I added a new "eachModel" option to the Chimera fitmap command so that one command can independently fit many molecules in the same map. For example, fit #1-50 #0 resolution 13.5 eachModel true listFits true will fit PDB models with id numbers 1 to 50 into map with id #0 and list the fits in a dialog. Each of the fits is done independently (no account for clashes between molecules). Details on each fit are given in the Reply Log dialog (menu Favorites / Reply Log). This will be in tonight's Chimera daily builds (run at midnight) if they succeed: http://www.cgl.ucsf.edu/chimera/download.html#daily Here is the fitmap command documentation which will be updated later this week or next week. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html You will probably find that you can't open hundreds of PDB molecules in Chimera because it takes too much memory. But you can fit them in a few batches if this happens. Tom

1 0

disulfides: naive question
by George Tzotzos 21 Mar '12

21 Mar '12

Apologies for the earlier message. I need to clarify. Loading the topology and trajectory files onto Chimera and selecting functional group/disulfides shows the bonds throughout the trajectory. The problem I have is that I don't see the bonds in pdb files that I've generated from the topology files. Thanks again George

2 4

disulfides: naive question
by George Tzotzos 20 Mar '12

20 Mar '12

I've built a number of disulfide bonds in Amber topology files. From these, I've generated pdb files. When I load them in Chimera and do Select/Chemistry/Functional group/disulfed, I fail to see the selected residues and/or the bonds between them. Obviously, I'm doing something wrong. Any help would be greatly appreciated Regards George

1 0

depicting secondary structure elements
by Jordi Querol Audi 20 Mar '12

20 Mar '12

Dear Chimera developers, I would like to show a fitting of a pdb into my EM reconstruction but instead of displaying helices and b-sheets I would prefer to use cylinders or tubes. Is there any way to display a pdb this way? Thank you so much in advance, Jordi

3 2

smoothMD.py
by Anne Bowen 19 Mar '12

19 Mar '12

Hello, I would like to smooth an MD trajectory using the script " smoothMD.py" mentioned here (http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-September/006797.html) I can't access the attachment. Could someone send it to me? Thanks! Anne

2 1

Chimera Modeller interface trouble
by Karel Berka 16 Mar '12

16 Mar '12

Dear all, I have a strange problem with Chimera 1.6.1 Modeller (9.10) interface - when I tried to prepare a model based on template 3DDQ (CDK2 kinase), it showed that Modeller locally is running: 0%, but it stayed on this value. When I checked Task list, I have found that although it is still "running", the result was "progress: finished" with no protein model produced. I dwelwed more and I later found that Modeller script was prepared, but Modeller was unable to start due to the misspelling between sequence used for the template (probably from SEQRES) and sequence calculated from template structure. When I deleted residues that Modeller was unable to find in the structure, I was able to build the models. As for the web homology modelling interface - I was also unable to get model from Opal server, probably for the same reason. What to repair in Chimera to get Modeller interface running? because otherwise it seems like homology modelling is not working at all, which is not true. Best wishes Karel "Krápník" Berka P.S.: I have tried both Win64 and Debian64 binaries of Chimera 1.6.1. **************************************************************** RNDr. Karel Berka, Ph.D. Palacký University in Olomouc Faculty of Science Department of Physical Chemistry tř. 17. listopadu 1192/12 771 46 Olomouc tel: +420-585634769 fax: +420-585634769 e-mail: karel.berka(a)upol.cz ****************************************************************

2 1

Calculating partial charges of a charged ligand
by Christos Deligkaris 16 Mar '12

16 Mar '12

Dear Chimera users, I have a charged ligand (formal charge of +2) and I have tried using Chimera to calculate the partial charges of that molecule. Even though Chimera predicts correctly that the net charge is +2, after calculating the partial charges (using the Gasteiger method) I see that the sum of all partial charges is zero. Changing the net charge of the molecule seems to have no effect on the calculation of the partial charges. It also seems that the Gasteiger website does not offer the service of calculating the partial charges any more... ( http://www2.chemie.uni-erlangen.de/services/petra/smiles.html) Do you have any suggestions on how to calculate the Gasteiger charges so that the net charge on my molecule is +2? Thank you for your help, -- Christos

2 1

Match structures and density maps
by Sam Meyer 16 Mar '12

16 Mar '12

Good morning, I have two density maps, which I want to align for comparison. They are associated to 2 different PDB structures that I can use as references. I want to match the two PDB structures, and use the rotation/translation matrix of this alignment to move the density map as well. Is that possible ? Thanks Sam Meyer

2 1

1.6.1 release out
by Eric Pettersen 14 Mar '12

14 Mar '12

Hi all, We have put out a 1.6.1 release which, along with some minor fixes, corrects these problems: - Graphics would be corrupted or chimera would crash on recent versions of Linux, e.g., Ubuntu 11.10 and Fedora 16 - Planes (of Axes/Planes/Centroids tool) failed to start - Inappropriate "file types" (e.g. PDB ID) included in the file-type list of the main File→Open dialog - Very old sessions (pre-2006) would not restore on 64-bit Windows Please download 1.6.1 if these problems are affecting you. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

plz ans the ques
by rashmi gupta 12 Mar '12

12 Mar '12

Sir, I am working on insilico metabolomic and genomic study of edible cyanobacteria. What plan should i do to accomplish my goal. -- Rashmi research scholar School of Biomedical Engineering IT BHU

1 0

resolution for volume fitting
by Bala subramanian 07 Mar '12

07 Mar '12

Friends, I am a newbie to fitting molecular structures on a volume map. I would appreciate if someone could suggest me some guidelines to choose an optimal resolution of the map before fitting. Thanks, Bala -- C. Balasubramanian

3 4

Increasing the mesh thickness in Chimera Volume Viewer
by Pradeep Pallan 07 Mar '12

07 Mar '12

Hi, I wanted to know whether there is an option to increase the mesh thickness in Chimera? I have loaded the map in Volume Viewer, but do not know how to increase the thickness of the mesh. Thanks for your help, Pradeep -- -------------------------------------------------------------------

2 2

Linux and Chimera 1.6
by Greg Couch 07 Mar '12

07 Mar '12

If you have are running a recent version of Linux, for example, Ubuntu 11.10 or Fedora 16, then you should wait for Chimera 1.6.1 before updating or use a daily build. -- Greg

2 1

Re: [Chimera-users] [Dock-fans] Help with antechamber
by Scott Brozell 07 Mar '12

07 Mar '12

Hi, On Tue, Mar 06, 2012 at 08:04:51PM -0500, Brad Ridder wrote: > Thanks for the responses, but I am still stuck on antechamber. > > We are holding off on this python scripting; that was the plan before, but > I want to make sure I can get the individual components working properly > before I go to the effort of writing a python script to do dock prepping. > > I cannot get either the DOCK-supplied version of antechamber or the > CHIMERA-supplied version of antechamber to work correctly. ==== dock > First, I tried the DOCK distribution again. $AMBERHOME was not defined. I > used: > > *$DOCK_HOME/bin/antechamber -i $PDBFILES/3GLR.pdb -fi pdb -o > $DESKTOP/3GLRcharged.mol2 -fo mol2 -c bcc* > > This returns the error: > * > Total number of electrons: 0; net charge: 0 > > Running: $DOCK_HOME/bin/mopac.sh > Error: unable to find mopac charges in mopac.out > * It is possible that antechamber is working and that mopac really fails. Did you look in mopac.out ? Are you really trying to run antechamber on 3glr, which is a protein ? antechamber is not the way to assign charges to a protein. Read the AmberTools manual http://ambermd.org/doc11/AmberTools.pdf Here is one way to test your dock's antechamber: cd dock6/install/test/amber_score_181l make ../../../bin/antechamber -s 2 -i lig.1.mol2 -fi mol2 -o lig.1.gaff.mol2 -fo mol2 -nc 0 -c bcc This last command should emit: ... Running: $DOCK_HOME/bin/mopac.sh Running: .../dock6/bin/am1bcc -i ... ... > I then repeated this later with $AMBERHOME defined to $CHIMERA/bin/amber11, > which gives the new error message: > > *Total number of electrons: 0; net charge: 0 > > Running: $AMBERHOME/bin/divcon > sh: > /home/abhay/Desktop/rcg-research/personal-work/CHIMERA/bin/amber11/bin/divcon: > not found > Error: cannot run "$AMBERHOME/bin/divcon" of bcc() in charge.c properly, > exit* This approach - using dock's antechamber with amberhome defined to be inside chimera - is not a good one. However, you might get it to work: It is very likely that sqm, not divcon, is the qm program that should be invoked. So get help to look for the option to force sqm usage: antechamber -h ... -df am1-bcc flag, 2 - use sqm(default); 0 - use mopac ... is probably what you'll find; if so then add -df 2 to your antechamber command line. > Now, a few questions/reflections: > > 1. As per the first error message, why is mopac.out causing trouble? Is > this a file I am supposed to make? mopac.out is the output of the mopac qm program which antechamber invokes and then processes to make am1-bcc charges. > 2. As per the second error message, I have no idea what "divcon" is, or > what it is needed for. There is no divcon file that comes with the CHIMERA > amber11 directory, nor is there any divcon file in the AmberTools amber11 > directory I have on my Desktop. divcon is another qm program. ==== chimera > I then tried the version of antechamber with the CHIMERA distribution. > First I typed: > > *$CHIMERA/bin/amber11/bin/antechamber* > > And antechamber said "AMBERHOME is not set!" > > So, I set $AMBERHOME to be $CHIMERA/bin/amber11. Then I used > > *$CHIMERA/bin/amber11/bin/antechamber -i $PDBFILES/3GLR.pdb -fi pdb -o > $DESKTOP/3GLRcharged.mol2 -fo mol2 -c bcc* > > The Terminal then spams: > > *Warning: detected more than 10 Residue sequence numbers; > this may be a large multiple residue PDB file; > large multiple residue PDB files are not supported. > Continuing, but problems may be encountered.* > > And then finally stops with > > *Segmentation fault* This warning was absent in early versions of antechamber. And it likely right on target. mopac (above) probably failed because you are really trying to run antechamber on 3glr. antechamber is not the way to assign charges to a protein. > So, in short, I am utterly bamboozled. Obviously, antechamber can handle > "large multiple residue PDB files", since the Dock Prep tutorial used the > AM1-BCC charge model on the large 1ABE.pdb protein, and it worked fine. Why > is it not working for me? No, the receptor charges were assigned using residue matching. See step 1 of http://dock.compbio.ucsf.edu/DOCK_6/tutorials/struct_prep/prepping_molecule… and the chimera dockprep docs: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/framecontrib.html "Charges for standard residues ... are taken from Amber (details)." Read the force field chapter of the AmberTools manual and references therein for even more details. scott > On Wed, Feb 29, 2012 at 10:30 PM, Scott Brozell <sbrozell(a)rci.rutgers.edu>wrote: > > Here's another similar ligand prep script: > > http://mailman.docking.org/pipermail/dock-fans/2011-December/002591.html > > While it is a good pedagogical exercise to prep once manually, > > scripting is the only practical approach for lots of ligands. > > > > As far as running antechamber, be careful and be specific about which > > one you run: > > If you are manually running Dock's antechamber then define DOCK_HOME. > > Do not define AMBERHOME. > > See > > http://dock.compbio.ucsf.edu/DOCK_6/faq.htm#Error%20from%20amberize_ligand > > ; > > > > If you are manually running Chimera's antechamber then DOCK_HOME > > is irrelevant but AMBERHOME may be relevant. > > ( I have not manually run Chimera's antechamber, so my advice may be > > wrong. ) > > > > Also note that Dock's antechamber is circa 2006 with some key subsequent > > bugfixes. Chimera's antechamber is much more recent. > > Dock's antechamber uses mopac for qm; > > Chimera's antechamber uses sqm for qm; > > (http://ambermd.org/#AmberTools) > > I have found mopac to be more robust than sqm. > > Your mileage may vary. > > > > scott > > > > On Wed, Feb 29, 2012 at 04:08:22PM -0800, Eric Pettersen wrote: > > > This previous posting to the dock-fans list seems to be more directly > > > pertinent: > > > > > > http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html > > > > > > On Feb 29, 2012, at 2:47 PM, Trent E. Balius wrote: > > > >I am cc'ing this to the chimera list. > > > > > > > >I think that you should write a python script to run DOCK prep on > > > >the command line. See the following: > > > > > > > >http://www.cgl.ucsf.edu/pipermail/chimera-dev/2011/000784.html > > > > > > > >For other example scripts see the following: > > > > > > > > > > http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003539.html > > > > > > > >You should not have to specify the AMBERHOME path. This is done > > > >internally to chimera. > > > > > > > >as an aside, It is unnecessary to run antichamber with sudo. > > > > > > > >-----Original Message----- > > > >From: Brad Ridder <clustro(a)gmail.com> > > > >To: dock-fans <dock-fans(a)docking.org> > > > > > > > >My name is Brad; I am a grad student in the dept. of chemical > > > >engineering at Purdue University. > > > > > > > >We are experimenting with DOCK for various drug discovery work. At > > > >the moment, I am trying to do execute all of the "dock prep" > > > >commands through the Terminal, since it is not practical to do large > > > >volumes of Dock Prep by hand through the CHIMERA GUI. > > > > > > > >Corresponding to what is in the DOCK tutorial, I am on "Receptor and > > > >Ligand Preparation." I got reduce to work, in order to add hydrogens. > > > > > > > >Now, I am trying to get antechamber to work, in order to add the > > > >charges, but it is not working. Here is the command I am running: > > > > > > > >sudo ./antechamber -i $DESKTOP/3GLR.pdb -fi pdb -o $DESKTOP/ > > > >3GLRcharged.mol2 -fo mol2 > > > > > > > >Which returns the error: > > > > > > > >Warning: $AMBERHOME and $DOCK_HOME enviornment strings are not set, > > > >use "mopac.sh" in the work directory > > > > > > > >Cannot open CONNECT.TPL , exit > > > >The atom number exceeds the MAXATOM, reallocate memory > > > > > > > >I looked around in the dock6 directory, and found a folder called > > > >"parameters/antechamber", which contains CONNECT.TPL. I figured this > > > >is what should be the $AMBERHOME directory. > > > >For DOCK_HOME, I figured it should be the dock6 folder. > > > > > > > >Here is what I have in my .bash_profile file in my home folder. > > > > > > > >export AMBERHOME='/home/.../DOCK6.5/dock6/parameters/antechamber' > > > >export DOCK_HOME='/home/.../DOCK6.5/dock6' > > > > > > > >I also tried using the "amber11" folder that comes with CHIMERA as > > > >AMBERHOME, but to no effect. > > > > > > > >I don't actually have AMBER installed on my computer, but since > > > >CHIMERA can add charges without actually requiring the purchase of > > > >AMBER, I do not think that is the problem. > > > > > > > >I did not know what to do with "mopac.sh." I ran the script, but it > > > >says it needs input files. > > > > > > > >What am I doing wrong that is preventing antechamber from executing > > > >correctly?

2 1

Surface charge density!
by IONEL , ALINA ELENA 06 Mar '12

06 Mar '12

Hi, My name is Alina Ionel and I am PhD student. I have a pseudoatomic model (in pdb format) for a capsid protein. I did a representation of the electrostatic potential in Chimera with the option “Coulombic Surface Coloring” for a hexamer, for example. The unit of this potential are in Kcal/mol*e and the surface is colored in a range of values -10 to 10 Kcal/mol*e. I want to know the surface charge density for this hexamer (in C/m2). I need the value. Can you help me, please? Thank you, Alina

3 3

Atom distances
by Kyle Morris 05 Mar '12

05 Mar '12

Hi, Is there a way in chimera to search a PDB (or any structure file..) for a particular distance and report back in text or visually between what atoms this occurs, i.e. query whether a structure contains atoms spaced at between 5.5-5.6 Å and which ones? Thanks in advance for your help, appreciate it! Kyle

3 2

how to show backbone carbonyl oxygen
by james09 pruza 03 Mar '12

03 Mar '12

Hi All, I am using latest Chimera v1.6. I want to show the backbone carbonyl oxygen of one of the residue. The backbone is in ribbon representation. Also, how to make dotted line representation of the missing residues joining two domains of the same chain. Thanks. James

2 5

How to show the electron density of just selected residues? Thanks
by Pingyang Liu 02 Mar '12

02 Mar '12

Hi, How to show the electron density of just selected residues? Thanks I followed the Chimera tutorial, but still the electron density of the whole protein was displayed. Another question: what does the convexity of a protein structure tell? I did not find much information about convexity online. Thanks a lot. Best, Andy --

2 2

segmentation fault
by nauton lionel 02 Mar '12

02 Mar '12

Hello I send this Email, because I can't used chimera-1.6 for linux 64 bits ( 2-29-2012 version) it crash with this comment "segmentation fault", everytime I tried to load pdb or mol2 files. and I don't have this problem with chimera-1.6rc for linux-32 bits or chimera-1.6( 2-29-2012 version) and chimera-1.5.3 for linux 64bits works well on the same PC I used fedora 16... regards

2 1

Chimera 1.6 officially released
by Eric Pettersen 02 Mar '12

02 Mar '12

Hello everybody, A new production release of UCSF Chimera (version 1.6) is available: <http://www.cgl.ucsf.edu/chimera/download.html> Download is free for noncommercial use. Platforms: Windows, Mac, Linux, including 64-bit versions (recommended for working with large datasets on machines with at least 4GB memory). This will be the last Chimera release supporting Mac PowerPC platforms and OS X 10.5 (Leopard). New features include a Rapid Access interface to frequently used data and tools, new ribbon spline options, improved transparency rendering, new fetch type: Uniprot protein sequence and annotations, and several options for fitting atomic structures into density maps: global search, iterative sequential fitting, symmetric fitting, etc. More details are given below; see release notes for the full list: <http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.6.html> Graphics, Depiction: * new spline options for ribbon closer to backbone atom positions * new initial model colors, pastel rather than saturated * improved transparency rendering (global single-layer on by default) * 3D labels drawn on top by default * fancy backgrounds: images from files, color gradients from Palette Editor * options for cleaner pocket/tunnel surface display (see "sop" command) Structure Analysis and Modeling: * AddH allows specifying less common states of Asp, Glu, Lys, Cys * FindHBond can label H-bonds with distances * Blast Protein shows more info for PDB hits (ligands, resolution, etc.) * Build Structure improvements for joining peptides, swapping substituents * tools to change chain IDs, renumber residues * minimization: - can be conjugate gradient (previously steepest descent only) - parts of structures can be ignored * distance and angle plotting for trajectories * Cage Builder tool for generating polyhedral cage models <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/cagebuilder/cagebu… > * interface to MultiFit web service (simultaneous rigid fitting of multiple structures to density, developed by the Sali Lab, UCSF) * "fitmap" command: - global search with random initial placement - iterative sequential fitting - symmetric fitting * "measure" command options: - map symmetry - surface contact area - center of mass User Interface and I/O: * Rapid Access interface to frequently used data and tools shown at startup, can be hidden/shown at any time by clicking the lightning-bolt icon <http://www.cgl.ucsf.edu/chimera/1.6/docs/UsersGuide/rapid.html> * caching fetched data is turned on by default * scaling with mouse/touchpad scrolling can be turned off (Mouse prefs) * Model Panel: - group/ungroup function, such as for NMR ensembles - functions reorganized into favorites/all * new input types: SPHGEN spheres, Maestro/Glide docking output (ViewDock) * WebGL export (experimental feature) Sequence-related: * new fetch type UniProt: protein sequence and feature annotations * Multalign Viewer: - UniProt features can be mapped onto already open sequences - Region Browser improvements for handling feature annotation regions - calculation of region overall RMSD - interface to Modeller homology modeling allows including water, other HET Enjoy! On behalf of the Chimera team, --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

3 3

Re: [Chimera-users] reading SMILES description into Chimera
by Elaine Meng 01 Mar '12

01 Mar '12

Hi Boaz, You can just use the command line, for example: open smiles:CC1=CC=C(C=C1)S(=O)(=O)[O-] I'm thinking it may be a mistake that SMILES shows up as a file type in the "Open File" dialog. The only other place I can think of is in Build Structure (under Tools... Structure Editing), where the Start Structure section includes a SMILES option. In that case you would just type or paste in the SMILES string in the indicated field. 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 Mar 1, 2012, at 7:08 AM, Boaz Shaanan wrote: > Hi, > > I'm trying to read a small molecule for which I have a SMILES description into Chimera. I selected 'smiles' from the input options but it's not clear to me how to proceed. Do I have to generate a text file with the smiles description in it? do I paste the smiles description in the file name line? or what? > > Thanks for your help. > > Boaz > > > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > E-mail: bshaanan(a)bgu.ac.il > Phone: 972-8-647-2220 Skype: boaz.shaanan > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

3 3

how to copy partial charges from a .mol2 file to another
by Thomas Evangelidis 29 Feb '12

29 Feb '12

Dear Chimera community, Is there any straight forward way to copy the partial charges from one .mol2 file to another? Thanks in advance. Thomas -- ====================================================================== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tevang(a)bioacademy.gr tevang3(a)gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/

2 3

partial conservation coloring
by Eric Pettersen 28 Feb '12

28 Feb '12

Jill Voreis wrote: > I'm trying to use chimera to show conservation maps. Using pdb files > that I fetch from the database using the pdb id number and > alignments created in clustal that contain the sequence of the pdb > file, I select render by conservation. For some reason, the > conservation colors only go onto my model when it's in ribbon form. > When I try to show the surface representation or use spheres so that > I can use commans to show the SAS, the colors of my model do not > match the conservation model but rather are stuck on some sort of > coloring scheme related to the compounds that are there. The > majority of the map looks brown, like the default color before > rendering by conservation. If you could help me, I'd really > appreciate it! Hi Jill, There are a few possibilities here, though it's impossible to be certain what the problem without access to a concrete example. My best guess is that much of the surface region of your protein is poorly conserved and those areas have columns where the rows are more than 50% gap characters. For such columns no conservation score is assigned. That means that when you use Render By Attribute with default settings, those atoms / surface parts will retain their original colors. If in Render By Attribute you use the "No-value color" color well to assign a color to such regions (perhaps gray) you will be able to tell if this is what is happening. Two other possibilities are that you don't have the "Color atom" and "Color surfaces" check boxes checked [though I image you would have noticed this!] or that your protein has multiple chains and that only one is associated with the alignment and only that one is getting colored. If none of these are "it", if you can provide me with a specific example so I can reproduce the behavior then I will investigate. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

Not crossfade but coinciding bond command...
by Kevin D. Walker 28 Feb '12

28 Feb '12

I temporarily disabled a bond command and found this to be the cause of the selected bond problem I am having. I don't think crossfade has anything to do with it.

1 0

Animate a Reacton Mechanism?
by Kevin D. Walker 28 Feb '12

28 Feb '12

I constructed a movie for the first part of a reaction mechanism (substrate docking). I would like the animated mechanism to continue as follows. The substrate donates a proton to a tyrosine residue of the enzyme, forming an intermediate. The intermediate rotates 180 (I have accomplished this part) and the proton rebounds to the intermediate forming a new product, which is released. I can animate the product release -- it's the reverse of substrate docking. The part of the animation I cannot envisage is how to smoothly show or morph the bond transitions (bond breaking and making) during the reaction progression. IAny advice on whether Chimera or other ancillary software can do this is appreciated.

4 6

using CalcAttr from a Python script
by Roger L. Chang 28 Feb '12

28 Feb '12

Hi, 1) I need to get residue.areaSES for two separate selections (all polar amino acids and all nonpolar amino acids). I have successfully generated a list of residue.areaSES using the GUI simply by selecting the residues of interest and then using the attribute calculator typing "residue.areaSES" in the formula box of the Attribute Calculator, which outputs the list to the Reply Log. This is the data that I need, but I need to get it for >2000 PDB structures and would like to automate this analysis through a Python script. I am somewhat new to Python and Chimera and don't yet know all the ins and outs yet. I dug through the code and found a method "getResidueAttr" in the "ResidueDataWrapper" class from "CalcAttr". This seems to be what I need, but I don't know the proper syntax to call it from my Python script. Could someone please provide an example? 2) I would like to sum the residue.areaSES values once I have them. I tried "sum(residue.areaSES)" in the formula box of the Attribute Calculator in the GUI, but this returns the error "Formula evaluation error: expecting vector argument in function". I'm not sure again on the proper syntax to use "sum()" in the Attribute Calculator. If I knew how to generate/save the residue.areaSES data from the command line, I could just parse the saved file and sum the values in Python. How can Attribute Calculator formulas be used from the command line, and if they can't, how can I save the residue.areaSES data to file from a Python script? Thanks in advance, Roger -- Roger L. Chang Graduate Student Bioinformatics and Systems Biology Graduate Program University of California, San Diego

3 2

Coloring molmap surfaces
by Tom Goddard 24 Feb '12

24 Feb '12

> Greetings Tom > > How can color the molmap surface of certain atoms/residues. > > Many Thanks, Vijay > Hi Vijay, Use the Color Zone dialog to color a molmap surface to match nearby atom colors (menu Tools / Volume Data / Color Zone). You select the atoms you want to use for color (e.g. menu Select / Select All) choose a distance range from those atoms to color in the Color Zone dialog and press the Color button. In Chimera 1.6 (release candidate available on the web) or daily builds there is a command version of color zone. For example scolor #0 zone @ca range 5 says to color molmap surface #0 to match C-alpha atom colors within a distance of 5 Angstroms. To avoid jagged edges in the coloring you should use the molmap gridSpacing option to specify a grid size about 1/5 to 1/10 the map resolution. The default value is 1/3 of map resolution making a fairly coarse surface mesh. Colors are only assigned to the mesh vertices, so a fine mesh is needed for smooth boundaries between different color regions. Tom

1 0

batch peptide builder
by Xiao-Ping Zhang 23 Feb '12

23 Feb '12

Dear Chimera developers, I would like to generate some peptides from a protein sequence. The peptide builder in Chimera is a very nice application. I wonder if there is a stand alone script which I can use to generate series peptides from the command line. Thank you for your help. Xiao-Ping Zhang

2 1

Drawing arrows without using .bild file
by Victor Muñoz 21 Feb '12

21 Feb '12

Dear all, I'm trying to make a script that draws an arrow on every atom and every frame during a trajectory using the MD movie. Right now, the script creates a .bild file to draw the arrows, but it is not a very good approach since it is creating a new file for every frame of the trajectory. I was wondering if there's a way to do the same thing without having to create the .bild file. I already checked the "shape" command but you can´t use it to draw an arrow. Maybe I should make a combination between a cylinder and a rectangle to draw an arrow? Is there any other easy way to do that? Thanks in advance. Kind regards, --

3 2

bug
by Eifler, Jay Q. (UMKC-Student) 21 Feb '12

21 Feb '12

Whew, too much work to get you guys a message. The bug report form was lengthy. Anyway, can't join models in your latest 1.6 version but 1.5 whatever is fine. Should have never updated.

3 2

(no subject)
by Valia Dimitrova 21 Feb '12

21 Feb '12

Hi, I am PhD student, and I am working with program Gaussian, I want ask you some questions. I want to make maps with electrostatic potential, I saw that with this program may be make very beautiful pictures. What type of files I have to have, so I can do these pictures? I have ".fchk" files and ".cube" files. May I use them to make this? I will be very appreciated if some one can help me. thank you in advance Valia Nikolova

2 1

how to find
by Bishwajit Das 18 Feb '12

18 Feb '12

suppose i want so select ARG 188 and TRP 144 and also want to see the distance between them ....how i do this in chimera..please help me. -- BISHWAJIT DAS KOLKATA,West Bengal INDIA* * --

2 3

bug report
by Longfei Wang 16 Feb '12

16 Feb '12

Hi there, For nogui Chimera: Calls with script in nogui mode create the following traceback. terry@daisy[14]% chimera --nogui --script "coord_for_cluster_ATP_ bothChiFlip.py" Traceback (most recent call last): File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1.6rc/share/__main__.py", line 69, in <module> value = chimeraInit.init(sys.argv) File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1.6rc/share/chimeraInit.py", line 618, in init chimera.initializeGraphics() File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1. 6rc/share/chimera/__init__.py", line 2114, in initializeGraphics bgprefs.initialize() File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1.6rc/share/chimera/bgprefs.py", line 211, in initialize onDisplay=_bgPrefDisp, onHide=_bgPrefHide) File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1. 6rc/share/chimera/preferences/base.py", line 567, in register self._loadCategory(category, cat, inherit, convert) File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1. 6rc/share/chimera/preferences/base.py", line 482, in _loadCategory cat.load(self._loadDict[name]) File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1. 6rc/share/chimera/preferences/base.py", line 249, in load opt.set(value, asSaved=True, fromPref=True) File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1. 6rc/share/chimera/preferences/base.py", line 64, in set self._callback(self) File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1.6rc/share/chimera/bgprefs.py", line 53, in _backgroundColorCB Midas.background(color=color, setMethod=False) File "/nfs/turing2/labs/sbgrid/programs/i386-linux/chimera/1.6rc/share/Midas/__init__.py", line 966, in background method = chimera.viewer.Solid AttributeError: '_chimera.NoGuiViewer' object has no attribute 'Solid' Best Longfei -- *Longfei Wang * Postdoctoral Fellow Harvard Medical School 250 Longwood Ave Boston, MA 02115

2 1