- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] fitting models into maps
by Tom Goddard 20 Dec '07

20 Dec '07

Hi Dan, The Chimera fit model in map tool doesn't give a correlation value. To get a correlation requires you have two maps to compare, so first a map needs to be calculated from the PDB model that matches the resolution of the experimental map. Although I'd like to have that in Chimera, it is not currently there. I have used the EMAN pdb2mrc program to compute the map. Then you can use the Chimera fit map in map tool to get a correlation value, or you could use fit model in map, then open the map calculated for the PDB and find the correlation for the orientation obtained for the PDB model. You're right that reported correlation values depend on some often unreported parameters. First there is the method used for producing a map from the PDB model. Then the correlation depends on the part of the volume used. I would guess this is typically the portion within a certain contour level of the PDB map. What contour level? Something like 1 standard deviation is not sensible since it depends on the size of the map (the extent of padding). Probably a contour level that encloses a given volume -- maybe the volume enclosed by the solvent excluded surface of the PDB model with a reasonable probe radius. Would be nice if Chimera automated this calculation starting from the fit model in map position -- some day, hopefully in 2008. Reporting average density value at the atom positions would only make sense if the map is normalized. Maybe reporting that value in standard deviations. But the standard deviation depends on how much empty volume surrounds the structure, so that is not very satisfactory. Chimera reports that number so you can compare different fits in the same map -- only relative values are meaningful. Another value I have seen reported is the number of atoms outside a certain contour level of the experimental map. The fit model in map tool reports that in the reply log (Favorites / Reply Log). Of course it depends on how you set the contour level. Again if you set that as some number of standard deviations that depends on the map size. Alternatively you could set the contour level so the experimental map encloses the expected volume. Menu entry Tools / Volume Data / Measure Volume and Area can help set such a contour level. Seems correlation is the most meaningful number. You can calculate the standard deviation of a map from its mean in newer versions of Chimera with menu entry Tools / Volume Data / Volume Mean, SD, RMS. Tom Daniel Southworth wrote: > Tom: > > Hi. I'm a post-doc in David Agard's lab and I have a question about > the "fit model in map" function in chimera. I'm having some good > success fitting crystal structures into my low-resolution em maps > using this function once I get a global fit either by hand or using > situs. I'm wondering if there is any way to get a correlation value > out of the fits or how people typically report on their confidence of > the chimera fitting in publications? I know correlation values are > often different from program to program so perhaps the best measure is > to state the average map value? Any help would be great - thanks. > > Dan

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superimpose --matchmaker.
by Vinay Kumar 19 Dec '07

19 Dec '07

Hi all, There have been a few posts previously regarding superimposing of molecules. using matchmaker would work for a pdb file. I was curious if small molecules (ligands) could be matched. I did check out the documentation and the command match. But what i am not sure abt is, in wht format should the input file for a small molecule be?? could someone suggest!! regards, Vinay

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Question regarding multiple mutant in the same chimera session
by Jean-Didier Maréchal 18 Dec '07

18 Dec '07

Hi, Is there a way to copy, in the same instance of chimera, a model X time? I'd like to generate different mutant of the same prot and have them stocked in the same session of chimera. Cheers, JD -- Dr. Jean-Didier Maréchal Assistant Professor Computational Bioorganic and Bioinorganic Chemistry @Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona 08193 Bellaterra, Spain Tel: +34.(0)1935814936 Fax: +34.(0)1935812920 e-mail:jeandidier.marechal@uab.es

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rmsd cluster analysis
by Francesco Pietra 18 Dec '07

18 Dec '07

Is it feasible to command a cluster analysis from rmsd? I would like to group for likeliness snapshots from MD with respect to, say, the structure from which MD was started. 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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Problem with Chimera under Windows XP
by Peter Girard 18 Dec '07

18 Dec '07

I am running release 2304 of Chimera under Windows XP with service pack 2 on a Dell Inspiron 9300 laptop. The image disappears from the screen for no apparent reason. With the structures I am currently working on, this has become frequent and often occurs after just a few seconds when I click anywhere in the Chimera window. I have found that if I use Model Panel, I can get the picture back by clicking the 'Shown' box to remove the tick mark, then clicking it again to re-insert the tick. But the picture soon disappears again. Occasionally, it doesn't disappear completely, but part of it collapses, or spurious long lines appear. I had the same problem with a previous release, 2184, and was disappointed that upgrading didn't fix it. I can find no mention of anything similar in the documentation or email archive. Can anyone suggest a possible cause? Peter Girard (University of Nottingham, UK)

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Regarding getSequence
by Jean-Didier Maréchal 18 Dec '07

18 Dec '07

Hi again, I'd like to return the sequence of the protein I opened in chimera in the python shell. >From what I read through, I thought that chimera.getSequence could be used to do so. I was thinking in a simple script beginning with : import chimera s=chimera.getSequence(0,0) .. However the chimera.getSequence(0,0) comes back with: Traceback (most recent call last): File "<pyshell#50>", line 1, in ? chimera.getSequence(0, 0) File "CHIMERA/share/chimera/Sequence.py", line 614, in getSequence File "CHIMERA/share/chimera/Sequence.py", line 656, in getSequences AttributeError: 'int' object has no attribute 'residues' and chimera.getSequence(0,A) with Traceback (most recent call last): File "<pyshell#48>", line 1, in ? chimera.getSequence(0,A) NameError: name 'A' is not defined Did I understand correctly the role of getSequence? if yes, what would be the correct syntax please? Thanks a lot! All the best, JD -- Dr. Jean-Didier Maréchal Assistant Professor Computational Bioorganic and Bioinorganic Chemistry @Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona 08193 Bellaterra, Spain Tel: +34.(0)1935814936 Fax: +34.(0)1935812920 e-mail:jeandidier.marechal@uab.es

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Re: [Chimera-users] Chimera-users Digest, Vol 56, Issue 14
by Jonathan Hilmer 17 Dec '07

17 Dec '07

Ryan, Try this as a way to figure out what you can do with an object: dir(chimera.selection.currentResidues()[0]) In the above command I've indexed the list of selections to return just one object, and the dir() function will return a list of names defined by the currentResidues module. It should contain something like the following: ... 'addAtom', 'atomNames', 'atoms', 'atomsMap', 'bondedTo', 'count', 'findAtom', 'findRangeAtoms', 'getDefaultRibbonStyle', 'hasRibbon', 'id', 'isHelix', 'isHet', 'isSheet', 'isStrand', 'isTurn', 'kdHydrophobicity', 'label', 'labelColor', 'labelOffset', 'molecule', 'numAtoms', 'oslChildren', 'oslIdent', 'oslLevel', 'oslParents', 'oslTestAbbr', 'removeAtom', 'ribbonBinormals', 'ribbonCenters', 'ribbonColor', 'ribbonData', 'ribbonDisplay', 'ribbonDrawMode', 'ribbonFindStyle', 'ribbonFindStyleType', 'ribbonFindXSection', 'ribbonNormals', 'ribbonResidueClass', 'ribbonStyle', 'ribbonXSection', 'selLevel', 'type' If you try: chimera.selection.currentResidues()[0].type it will return a string with the 3-letter aa code, and the other options displayed by dir() will output useful things such as more strings, lists, or other objects that can be likewise explored. Try this combination: mySel = chimera.selection.currentResidues()[0] print "%s, %s" % (mySel.oslIdent(), mySel.type) On my test structure it returns '#0:127.A, ARG'. The second line is equivalent to 'print str(mySel.oslIdent() + ", " + mySel.type)', but the formatting I used in the above example helps to keep things clean if you have a complicated output that needs to have a specific format. There are some more advanced features of that approach detailed here: http://www.python.org/doc/1.5/tut/node45.html Jonathan > Date: Fri, 14 Dec 2007 19:55:39 -0500 > From: Ryan <pavlovicz.7(a)osu.edu> > Subject: Re: [Chimera-users] printing "zone" search > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <17bf4817f850.17f85017bf48(a)osu.edu> > Content-Type: text/plain; charset=us-ascii > > Hi Eric, thanks for your help. I'm getting closer to achieving the results i'd like. > > So i've been able to properly select the residues within a specified radius of my ligand, but am a little confused as to how Chimera handles the selection list. If i try: > > print chimera.selection.currentResidues() > > i get a list like this: > > > [<_chimera.Residue object at 0x578d2020>, <_chimera.Residue object at 0x578cbfb0>, ... ] > > but if i try: > > for x in chimera.selection.currentResidues(): > print x > > i get output that is much closer to what i'm looking for: > > > #0:499 > > #0:496 > > ... > > What is the reason for the difference between these two forms of output that seem to be accessing the same list? Also, is there a way i can get more detailed output with residue names and numbers, such as ['#0:TYR499','#0:TRP496',...]? > > Sorry if these questions are answered elsewhere, but i could not find the answers online. Is there a document out there that can teach me how to better master the Chimera Python modules for scripting? I'm no Python expert -- i've so far only been learning things as i need them. Thanks again, > > ryan

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Re: [Chimera-users] other/5067 (error adding hydrogens)
by Eric Pettersen 17 Dec '07

17 Dec '07

Hi Jean-Francois, I have seen this error reported, but only very rarely (maybe once a year at most). Is there any chance you can tell me how to reproduce it? --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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setting pdb path for local mirror
by Moo Cow 17 Dec '07

17 Dec '07

Sorry for an easy question. Chimera has a hook to use a local mirror of the PDB (preferences-PDB) I am too thick to see what path to give it. If you have the PDB, you have the top level /blah/blah/pdb the structure directory /blah/blah/pdb/data/structures/all and the divided directory /blah/blah/pdb/data/structures/divided/pdb When a non-python reader looks at the code (__init__.py), it seems to be trying out the divided directory IDcode = IDcode.lower() subpath = IDcode[1:3] + os.sep + "pdb" + IDcode + ".ent" pdbDir = systemPDBdir() if pdbDir is not None: ..... but this does not look correct. The PDB divided path would want subpath IDcode[1:2] to get the subdirectory "pt" from a file like "5pti" Many thanks and sorry for a seemingly daft question. -- Got No Time? Shop Online for Great Gift Ideas! http://mail.shopping.com/?linkin_id=8033174

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Loading .dx maps to chimera
by maya shcushan 17 Dec '07

17 Dec '07

Dear sir, I am trying to load a .dx file (electrostatic potential) onto a molecule in chimera. I successfully loaded the map onto a the molecule's surface. The problem is the potentials I get look differently than the original map. That is, the potentials appear different in the visualization tool of PMV, the program which generated the .dx file I tried to e-load on chimera. Thanks, Maya Schushan, Tel-Aviv university, Israel.

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crystallographic symmops and lattice translations in Chimera
by Boaz Shaanan 16 Dec '07

16 Dec '07

Hi, Since the question was raised before, I think I know the answer to my first question about lattice translations but let me verify: 1) Chimera can apply crystallographic symmetry operations to the model as they're listed in the pdb file but it won't apply lattice translations, or in other words, won't display molecules in neighbouring unit cells. Am I correct ? maybe you can surprize me me on this and prove me wrong ? 2) Is it possible to draw the unit cell boundaries after reading in the pdb or should I read in a dummy pdb with coordinates of the unit cell vertices ? Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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Re: [Chimera-users] printing "zone" search
by Ryan 14 Dec '07

14 Dec '07

Hi Eric, thanks for your help. I'm getting closer to achieving the results i'd like. So i've been able to properly select the residues within a specified radius of my ligand, but am a little confused as to how Chimera handles the selection list. If i try: print chimera.selection.currentResidues() i get a list like this: > [<_chimera.Residue object at 0x578d2020>, <_chimera.Residue object at 0x578cbfb0>, ... ] but if i try: for x in chimera.selection.currentResidues(): print x i get output that is much closer to what i'm looking for: > #0:499 > #0:496 > ... What is the reason for the difference between these two forms of output that seem to be accessing the same list? Also, is there a way i can get more detailed output with residue names and numbers, such as ['#0:TYR499','#0:TRP496',...]? Sorry if these questions are answered elsewhere, but i could not find the answers online. Is there a document out there that can teach me how to better master the Chimera Python modules for scripting? I'm no Python expert -- i've so far only been learning things as i need them. Thanks again, ryan

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Multi-scale models and BIOMT
by Ken Jang 14 Dec '07

14 Dec '07

Hello, I work at Boston University working mostly with pili and helical reconstructions. Recently we have been trying to fit our subunit structures into maps generated from EM data. Because what we work with are helical in nature, we use BIOMT symmetry since it is the easiest to generate using readily available data. We wanted to see just how close our subunits get and wanted to use the MSC or Color Zone commands, but we have run into a problem with the Multi-Scale Models command. Since we are using the same BIOMT data, we assumed that Multi-Scale Models would use the same origin and orientation. This appears to be the case if we don't move the subunit structure after opening it, but after we move the subunit, the generated models don't seem to be in any relavent orientation. I have attached two pictures, both from the same view, and one showing the placement of the subunits using the 'sym' command and the other showing the surface models using Multi-Scale models. Both cases were generated off the same selected subunit. Any advice or clarification on how to use Mult-Scale Models and BIOMT information would be greatly appreciated. Be seeing you- Ken Jang -and all places are alike to me

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Re: [Chimera-users] printing "zone" search
by Ryan 14 Dec '07

14 Dec '07

I am actually currently interested in doing something similar to Francesco's previous question about writing out a list of residue names within a certain zone of a ligand -- however i would like to do this from a Python script. I tried to find the zone selection command to use in a script, but could not. Would it be easiest to just use the runCommand('z<') function to select a zone? Also, when the zone is selected, are the selected residue names stored in a list? If so, how can i access this list to print out the residue names into an output file of my own? Thanks a lot, ryan

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edges
by Vincent Racaniello 14 Dec '07

14 Dec '07

When I display a protein as an edged ribbon, sometimes they have a black line on the edges, other times none. There seems to be no consistency in this behavior. The same also happens with surfaces. Is there a way to regulate this appearance?

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Morphing on small ligand
by Jean Didier Pie Marechal 13 Dec '07

13 Dec '07

Hi everyone, I have a " small" ligand with two substantially different conformations. Just for interest: could we use the morphing module to generate intermediate conformations between those two structures? Cheers, JD Dr. Jean-Didier Maréchal Professor Lector Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es

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printing "zone" search
by Francesco Pietra 13 Dec '07

13 Dec '07

I am looking at the protein residues "responsible" for docking a single-residue ligand. select protein & :ligandname z<# works for various values of #. I would like to print the list of residues instead of having to detect them from the screen, which may lead to errors. Also, which section of the manual concerns RMSD? (I would like to calculate RMSD at various stages of DOCK6.1 and Amber9 MD for the above, i..e. how the ligand adapts and the protein follows it, or vice-versa). Thanks francesco pietra ____________________________________________________________________________________ Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs

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Writing alignment and RMSD out
by shengzhiya＠nibs.ac.cn 10 Dec '07

10 Dec '07

Dear all, I would like to write both the sequence alignment and RMSD out after run “mmaker”, but I do NOT want to do this interactively because I have a batch of structures to deal with. I found Eric’s python script: structAlign.py, which is gui-only, but I do not know how to extract RMSD from the Reply Log in gui mode. Any help would be appreciated. Thanks a lot! Btw, may I know how to run structAlign.py? Is there any command like “chimera structAlign.py” and where should I put the input file structList? I can not run this script right now and here is the error message I got after run “chimera structAlign.py”: Traceback (most recent call last): File "/home/sheng/local/bin/chimera/share/__main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "CHIMERA/share/chimeraInit.py", line 298, in init chimera.openModels.open(a, prefixableType=1) File "CHIMERA/share/chimera/__init__.py", line 1253, in open File "CHIMERA/share/chimera/__init__.py", line 746, in _openPython File "/home/sheng/local/bin/chimera/from_mailinglist/structAlign.py", line 18, in ? pdb1, pdb2, output = line.strip().split() ValueError: need more than 2 values to unpack Error while processing structAlign.py: ValueError: need more than 2 values to unpack (see reply log for Python traceback info) Best wishes, Zhiya

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how to export the volume data which is stored in the memory?
by Zhiheng Yu 05 Dec '07

05 Dec '07

Hi, I loaded some volume data (mrc files) into Chimera remotely from a network hard drive. Unfortunately, the network hard drive crashed so I can not access those mrc files anymore. But in Chimera which was started before the drive crash, I still have the volume data and am still able to manipulate them. Apparently, these are stored in the memory. Does anyone know how can I export these data onto a hard drive. I tried "save as" but there is an I/O error since the computer was simply trying to duplicate data from the crashed drive. Any suggestion is appreciated. Thanks, Zhiheng

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Re: [Chimera-users] how to export the volume data which is stored in the memory?
by Tom Goddard 05 Dec '07

05 Dec '07

Hi Zhiheng, Here is a script to write out the maps in memory using Chimera 1.2199. You open this script with menu entry File / Open... from the main Chimera window. It will write the files to /tmp. Of course be sure to check those files before closing Chimera. Tom Zhiheng Yu wrote: > Hi Tom, > > I got the following information: > > Beta Version 1 build 2199 2006/01/24 > Platform: linux 2. Windowing system:x11. > > Apparently, it is an older version. > > Thank you very much for your generous help. I really appreciate it. > > Zhiheng > > Tom Goddard wrote: >> Hi Zhiheng, >> >> You must be using an older version of Chimera. Old versions read >> the original file even if the map was in memory when writing out the >> data. Maybe I can give you a script that will write the maps out >> from memory if you tell me what version of Chimera you are running >> (menu entry Help / About UCSF Chimera). >> >> Tom >> # # Write maps to files. For Chimera 1.2199. Only use in-memory copy. # Written for Zhiheng Yu to recover maps lost to failed disk. # from VolumeData import Array_Grid_Data from VolumeData.mrc.writemrc import write_mrc2000_grid_data from VolumeViewer import volume_dialog from os.path import join dir = '/tmp' # Location to write maps. d = volume_dialog() for v in d.data_regions: m = v.full_matrix(read_matrix = False) if not m is None: a = Array_Grid_Data(m, v.data.origin, v.data.step) path = join(dir, v.data.name) write_mrc2000_grid_data(a, path)

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(no subject)
by Julien Orts 04 Dec '07

04 Dec '07

Dear Chimera people, I would like to save a lot of pdb. I have for example 500 pdb. Each saved pdb file should contains 2 pdbs of these 500 pdbs. I can write a script for this but the command write does not work for more than two pdb. Is there any other way? thank you Julien

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question about the model panel
by jean-francois menetret 04 Dec '07

04 Dec '07

Is there is way to reorder the position of the models in the model panel ? (For example putting the mrc files on top and the pdb files at the bottom) Jean-Fran�ois M�n�tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street

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Re: [Chimera-users] Question regarding Chimera usage
by Tom Goddard 03 Dec '07

03 Dec '07

Hi Navya, If you have a 3-button mouse you move the atomic model with the middle button. If that is not working then you probably have the mouse modes assigned differently. You can look at and change what the mouse buttons do with menu entry Features / Preferences category Mouse. Usually button 2 is assigned to translate in x and y (second column of table). It may not be assigned to that operation if you have used other tools like volume path tracer or volume subregion selection that reassign mouse button 2. Tom swetha davuluri wrote: > Hi, > > Thanks for your reply. I am trying to move the atomic model using the > mouse. But I can only rotate the model but not transitionally shift it > i.e. I am not able to move the model either up/down and sideways. Not > sure how to do this. Please let me know. > > Thank you, > Navya. > > ----- Original Message ---- > From: Tom Goddard <goddard(a)cgl.ucsf.edu> > To: swethadn(a)yahoo.com > Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> > Sent: Friday, November 30, 2007 9:27:37 AM > Subject: Re: [Chimera-users] Question regarding Chimera usage > > Hi Navya, > > The first step is to move the atomic model using the mouse close to > the correct location in the EM map. The Fit Model in Map tool will not > move the atomic model if its initial position lies outside the map. > Here are instructions on how to do the fitting. > > > http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#fitmod… > > Tom > > > > ------------------------------------------------------------------------ > Be a better pen pal. Text or chat with friends inside Yahoo! Mail. See > how. <http://us.rd.yahoo.com/evt=51732/*http://overview.mail.yahoo.com/>

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Remove steric clashes
by Francesco Pietra 02 Dec '07

02 Dec '07

I would like to delete all water residues that are in steric clash with lipid residues. What I have is a single pdb file that includes both types of residues. Can't have the two as different models. Therefore I can't apply the zone tool that I know how to manage for two different models. The only alternative I can figure out is through the "Find Clashes,Contacts", writing a file for all WAT at a specified distance from the lipid residues and then manually deleting, or inventing a script for that (at <=0.6A there are 386 clashes). Hope to have missed an automatic tool from Chimera. If not, I suggest that as a most useful additional tool for cleaning systems. I dropped into the problem when at the first minimization, in view of MD, the system met segmentation fault after a few steps, with gradient decreasing by eight orders of magnitude along those few steps. Then I recognized not to have been careful enough before making the coordinate files for the MD suite. I should have not relied too much in the membrane builder and I had better spent time in checking for steric clashes. Thanks francesco pietra ____________________________________________________________________________________ Get easy, one-click access to your favorites. Make Yahoo! your homepage. http://www.yahoo.com/r/hs

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distance measurement
by sette＠uniroma2.it 30 Nov '07

30 Nov '07

Dear all, I would like to measure the distances between all atoms in a molecule, in particular between all hydrogens. I added the H but it seems to me that is possible to measure only the distance between two selected atoms and not between all atoms in a single command. How is possible to do? Thanks for your help, Marco Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it Tel.: +39-0672594424 Fax: +39-0672594328

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