March 2011 - Chimera-users - RBVI Mailing Lists

Selection through bond and fragment naming
by Jean Didier Pie Marechal 11 Mar '11

11 Mar '11

Hi, I have a system from which I only have xyz coordinates. What I would like to do is to define myself residue attribute on different fragments of the molecules. Could you tell me how (or if there is a way to ): 1. expand a selection to bonding atoms (i.e. I click on one atom and expand selection through one bond after each actions) This would be of the easiest way for me to select the fragments I want to. 2. set a residue attribute to the given selected fragment. I think I remember how to do so in scripting, but what is the command line to do so? Kind regards, JD Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team 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 www: http://asklipio.qf.uab.es

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error: from DockPrep import prep
by wascm 11 Mar '11

11 Mar '11

Dir sir I try to write a indenpendent python script and run it from command line some global variables was first set: export LD_LIBRARY_PATH=/home/wascm/chimera/lib:$LD_LIBRARY_PATH export PYTHONPATH=/home/wascm/chimera/share:/home/wascm/chimera/lib:$PYTHONPATH export CHIMERA=/home/wascm/chimera the script work well when import following module import chimera from chimera import runCommand, openModels, MSMSModel from WriteMol2 import writeMol2 from WriteDMS import writeDMS however, when add the code: from DockPrep import prep the error information as follows: ####################################### Traceback (most recent call last): File "./xx.py", line 12, in <module> from DockPrep import prep File "/home/wascm/chimera/share/DockPrep/__init__.py", line 15, in <module> from prefs import prefs, defaults, INCOMPLETE_SC, MEMORIZED_SETTINGS File "/home/wascm/chimera/share/DockPrep/prefs.py", line 13, in <module> from Rotamers.prefs import defaults as rotamerDefaults File "/home/wascm/chimera/share/Rotamers/__init__.py", line 574, in <module> from prefs import defaults, CLASH_METHOD, CLASH_THRESHOLD, HBOND_ALLOWANCE File "/home/wascm/chimera/share/Rotamers/prefs.py", line 13, in <module> from DetectClash.prefs import CLASH_THRESHOLD, HBOND_ALLOWANCE, PB_COLOR, \ File "/home/wascm/chimera/share/DetectClash/__init__.py", line 157, in <module> val = getColorByName(val) File "/home/wascm/chimera/share/chimera/colorTable.py", line 87, in getColorByName color = chimera.MaterialColor(r/255.0, g/255.0, b/255.0) ValueError: missing default material ################################################# how can i solve this problem? best wishes Tao Cui

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error: from DockPrep import prep
by wascm 11 Mar '11

11 Mar '11

Dir sir I try to write a indenpendent python script and run it from command line some global variables was first set: export LD_LIBRARY_PATH=/home/wascm/chimera/lib:$LD_LIBRARY_PATH export PYTHONPATH=/home/wascm/chimera/share:/home/wascm/chimera/lib:$PYTHONPATH export CHIMERA=/home/wascm/chimera the script work well when import following module import chimera from chimera import runCommand, openModels, MSMSModel from WriteMol2 import writeMol2 from WriteDMS import writeDMS however, when add the code: from DockPrep import prep the error information as follows: ----------------------------------- Traceback (most recent call last): File "./xx.py", line 12, in <module> from DockPrep import prep File "/home/wascm/chimera/share/DockPrep/__init__.py", line 15, in <module> from prefs import prefs, defaults, INCOMPLETE_SC, MEMORIZED_SETTINGS File "/home/wascm/chimera/share/DockPrep/prefs.py", line 13, in <module> from Rotamers.prefs import defaults as rotamerDefaults File "/home/wascm/chimera/share/Rotamers/__init__.py", line 574, in <module> from prefs import defaults, CLASH_METHOD, CLASH_THRESHOLD, HBOND_ALLOWANCE File "/home/wascm/chimera/share/Rotamers/prefs.py", line 13, in <module> from DetectClash.prefs import CLASH_THRESHOLD, HBOND_ALLOWANCE, PB_COLOR, \ File "/home/wascm/chimera/share/DetectClash/__init__.py", line 157, in <module> val = getColorByName(val) File "/home/wascm/chimera/share/chimera/colorTable.py", line 87, in getColorByName color = chimera.MaterialColor(r/255.0, g/255.0, b/255.0) ValueError: missing default material ---------------------- how can i solve this problem? best wishes Tao Cui

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Re: [Chimera-users] using chimera command in batch mode
by cuitao＠webmail.hzau.edu.cn 10 Mar '11

10 Mar '11

Dear sir I am so grateful to you for your detailed answer. Thanks a million. best wishes Tao Cui ------------------ 原始邮件 ------------------ >From: Eric Pettersen <pett(a)cgl.ucsf.edu> >Reply-To: UCSF Chimera Mailing List <chimera-users(a)cgl.ucsf.edu> >To: "cuitao(a)webmail.hzau.edu.cn" <cuitao(a)webmail.hzau.edu.cn> >Cc: UCSF Chimera Mailing List <chimera-users(a)cgl.ucsf.edu> >Subject: Re: using chimera command in batch mode >Date: Wed, 9 Mar 2011 13:11:31 -0800 > On Mar 8, 2011, at 5:30 PM, Tao Cui wrote: Dear sir: I have seen one message you posted in dock-fans mail list. http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html The batch mode solution you privided is really helpful to me. I wnat to know if I can complete similar batch mode works for other applation? for example, delete all H atoms, save molecule to pdb format and writedms. Thank you very much! Hi Tao, You can use the same approach outlined in the dock-fans post to write scripts for other purposes. The script in that post uses Python since that is the only way to call DockPrep from a script, but if the things you want to do are available as Chimera commands you can just write a Chimera command script and use it the same way (the script would need to end in .com or .cmd instead of .py though). So deleting all H atoms would just be the command "del H". You would save a file in PDB format with the "write" command (type "help write" in Chimera to see what arguments you would want). Writing a DMS file isn't available as a command, so you would need to use Python scripting for that, along the lines of: from chimera import runCommand, openModels, MSMSModel # generate surface using 'surf' command runCommand("surf") # get the surf object surf = openModels.list(modelTypes=[MSMSModel])[0] # write DMS from WriteDMS import writeDMS writeDMS(surf, "output.dms") You would need to keep in mind that Chimera's surface generation will fail for some structures, more so on Windows than other platforms, so you might want to check that the output file actually has some surface points in it. Alternately, in Chimera, the surface attribute "calculationFailed" will tell you if the surface calculation succeeded or not, so you could do something other than try to write the DMS file if that attribute is False. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Re: [Chimera-users] Internal water molecules
by Tom Goddard 10 Mar '11

10 Mar '11

Hi John, Here's an idea about how to define internal water molecules and identify them in Chimera. Make a density map of the molecule at some resolution, say 5 Angstroms, using the Chimera "molmap" command, then define internal waters to be the ones that are located at a point above a certain density threshold. You can use the Chimera "Values at Atom Positions" dialog (menu Tools / Volume Data) to get the interpolated density map value at each atom position. It assigns the density value to each atom. Then you can use the Render by Attribute dialog (menu Tools / Structure Analysis) to select just those atoms with values above the threshold density. Then you can intersect that list of atoms with waters since it will also include protein atoms. All this is easy to do but since you want to do it for many frames of a molecular dynamics simulation you need a script that can be run for each MD frame. Unfortunately the values at atom positions and the render by attribute selection capability don't have Chimera command equivalents. But those capabilities (like all Chimera capabilities) can be used with a Python script. I could provide you a script if this sounds useful. Also I'll add to our feature request list the need for Chimera commands that would allow you to do it without resorting to Python. Tom > Hello, > > Is it possible, in Chimera, to select only the internal water > molecules of a protein structure? I need to find out how many water > molecules enter the protein structure from the outside during a > molecular dynamics simulation. > > Thanks! > > John

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Re: [Chimera-users] castp visualization
by Elaine Meng 09 Mar '11

09 Mar '11

On Mar 9, 2011, at 9:06 AM, Irene Newhouse wrote: > Remember a few days ago, I sent you an image from a Chimera castp visualization & it looked really weird, with strips connecting two apparently disconnected regions? Well, I put up PyMol & its castp viewer & it manages to plot the surface understandably - blackish represents the 'outside' of the cavity... I think my protein is nonetheless somewhat pathological, because if I try to render the same surface in mesh, it swells to occupy nearly the whole molecule, which is not right - mesh & solid should enclose the same volume. However, the solid rendering does reproduce where the substrate goes, and how on earth it gets in there is now my problem:-) > > I just tried something else -- I have the new Chimera on my linux station, & that's where I was seeing the odd renderings. On my PC, I have the previous version of Chimera & it shows the same surfaces as PyMol! The image chasurfs.png shows the odd effects [from the current release on my linux station], for only one of the dimer units [I thought maybe the dimer was the issue. No.] Possibly the surface rendering of cavities in the current release of Chimera is correct most of the time, but it looks as if it's not for a protein as odd as this one. For debugging purposes, the PDB is 1X09 [I used Chimera to generate the other dimer unit]. > Hi Irene, Given your observations, it may be a graphics driver problem on your linux machine. I.e. the salient difference may be the platform, not the Chimera version. However, wasn't what you sent before from Surfnet, not CASTp? In any case, my understanding is that the same Chimera code is used on the different platforms, and I don't think these tools have been changed for months. I just tried "open castp:1x09" in the 1.5 release and a recent daily build (v1.6 Feb 24) and looked at a few pockets, and the surfaces seemed fine. Since I deal with the user interface and not programming or hardware issues, I included the list in case others have suggestions or comments. Best, Elaine

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Re: [Chimera-users] using chimera command in batch mode
by Eric Pettersen 09 Mar '11

09 Mar '11

On Mar 8, 2011, at 5:30 PM, Tao Cui wrote: > Dear sir: > > I have seen one message you posted in dock-fans mail list. > > http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html > > The batch mode solution you privided is really helpful to me. I > wnat to know if I can complete similar batch mode works for other > applation? for example, delete all H atoms, save molecule to pdb > format and writedms. > > Thank you very much! Hi Tao, You can use the same approach outlined in the dock-fans post to write scripts for other purposes. The script in that post uses Python since that is the only way to call DockPrep from a script, but if the things you want to do are available as Chimera commands you can just write a Chimera command script and use it the same way (the script would need to end in .com or .cmd instead of .py though). So deleting all H atoms would just be the command "del H". You would save a file in PDB format with the "write" command (type "help write" in Chimera to see what arguments you would want). Writing a DMS file isn't available as a command, so you would need to use Python scripting for that, along the lines of: from chimera import runCommand, openModels, MSMSModel # generate surface using 'surf' command runCommand("surf") # get the surf object surf = openModels.list(modelTypes=[MSMSModel])[0] # write DMS from WriteDMS import writeDMS writeDMS(surf, "output.dms") You would need to keep in mind that Chimera's surface generation will fail for some structures, more so on Windows than other platforms, so you might want to check that the output file actually has some surface points in it. Alternately, in Chimera, the surface attribute "calculationFailed" will tell you if the surface calculation succeeded or not, so you could do something other than try to write the DMS file if that attribute is False. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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select by atom number
by Francesco Pietra 09 Mar '11

09 Mar '11

Hello: Is any trick to select by atom number? Having NAMD files with CHARMM FF, i.e., SEGID and no chain ID, I find now difficult to use CHIMERA the way I used it. Thanks francesco pietra

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color bond distance, angle and so on
by Jean-Didier Maréchal 09 Mar '11

09 Mar '11

Hi guys, How can I change the color of the labels associated to distance between atoms, angles etc (both the for the text and the dashes). Thanks a lot JD **************************** Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team 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 www: http://asklipio.qf.uab.es

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Re: [Chimera-users] How to model a 4Fe4S cluster on conserved Cys residues
by Elaine Meng 08 Mar '11

08 Mar '11

On Mar 8, 2011, at 1:03 PM, Ingmar Buerstel wrote: > Dear Elaine, > thanx a lot for your quick answer. In fact I have already a modelled structure (made with swiss model) of the protein. > I was looking for a possiblitiy to fit a 4Fe4S-cluster in the position of the original cluster. The cysteines are conserved, thus, I just need to copy/paste the 4Fe4S-cluster into my structure. I would be glad, if you could help me concerning this problem. Dear Ingmar, You could superimpose your model and the related structure that does contain this cluster (residue SF4) and then merge the SF4 residue into your model. However, the result may be rough, depending on how well the structures match in 3D. It might be better to start over and use Modeller as described in my previous message, because it can make a model that already includes the cluster. However, if you want to try the superimposing approach, here are more details. (a) In Chimera, open your model and then open the known related structure that contains the cluster. (b) Superimpose the two structures, for example with the Matchmaker tool. Here is some discussion of different ways to superimpose structures in Chimera. You will want to make sure that the structures match well at the four cysteines. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html> (c) Delete everything in the known structure except for the part you want to paste into your homology model, and then combine the two models into one. For example, if your model is open as #0 in Chimera and the known structure is open as #1, you could use commands delete #1 & ~:sf4 combine #0,1 The delete command gets rid of all atoms in #1 except the SF4 residue. The combine command creates a new model, #2, by merging the SF4 residue in #1 with the homology model in #0. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> You can save the new model #2 to a file (for example, with File... Save PDB). However, you would hope that the cysteine sidechains in your model are pointing in the correct orientations to bind the cluster. If not, you might have to paste in those residues from the known structure too, and delete them from your homology model, before merging. Then you might have to manually text-edit the PDB to add bonds between the merged cysteines and the rest of the homology model. Again, it might be better just to start over and use a modelling method that can include the cluster in the first place. 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 > > > > Subject: Re: [Chimera-users] How to model a 4Fe4S cluster on conserved Cys residues > > From: meng(a)cgl.ucsf.edu > > Date: Mon, 7 Mar 2011 09:38:45 -0800 > > CC: chimera-users(a)cgl.ucsf.edu > > To: ingmar_b(a)hotmail.com > > > > Dear Ingmar, > > It sounds like you want to model your whole protein including the 4Fe4S cluster, am I right? Or is there a structure of your protein but that does not include the cluster? > > > > I would not recommend modeling this "from scratch" (building one atom by one atom) in Chimera but instead, homology-modeling your protein and cluster from the structure of a related protein that contains the cluster. Of course, this all depends on the existence of a known structure for a related protein. > > > > Chimera includes an interface to the Modeller program for homology-modeling. To use it, you would have to first go to the Modeller website > > <http://www.salilab.org/modeller/registration.html> > > and register to get a license key (free for academic use). In Chimera, you could choose "Tools... Sequence... Blast Protein," paste in the sequence of your protein, and then blast it against the PDB to see if there are any structures related to your protein. If there is a hit that seems good enough to you, you could use the Blast results dialog to open the structure and also the alignment of the two sequences. > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/blast.html> > > Then, in the sequence alignment window, choose "Structure... Modeller Tools" to show the interface to Modeller. Use "Advanced Option" to "Include non-water HETATM residues from template" so that the FeS cluster will be included in the model. > > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mo…> > > > > Or, you could simply see if there is already a model of your protein available in ModBase by using "File... Fetch by ID" in the Chimera menu. However, those models probably wouldn't contain the FeS cluster. > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/fetch.html> > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modbase.html> > > > > Some related references I just saw but didn't read in detail: > > > > Fee, J. A.; Castagnetto, J.M.; Case, David A.; Noodleman, L.; Stout, C.D.; Torres, R.A.; "The circumsphere as a tool to assess distortion in [4Fe-4S] atom clusters". J. Biol. Inorg. Chem. 2003, 8: 519-526. > > <http://dx.doi.org/10.1007/s00775-003-0445-8> > > > > Atomic resolution structures of oxidized [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus in two crystal forms: systematic distortion of [4Fe-4S] cluster in the protein. > > (2002) J.Mol.Biol. 315: 1155-1166 > > <http://dx.doi.org/10.1006/jmbi.2001.5292> > > (goes with PDB entries 1iqz, 1ir0 ... I see that the residue name of the cluster is SF4, so you could also use the searching tools at the PDB website to find structures that have this cluster) > > > > I hope this helps, > > Elaine > > > On Mar 6, 2011, at 6:44 AM, Ingmar Buerstel wrote: > > > Dear users, > > > i hope anybody out there can help me. I would like to model a 4Fe4S cluster in between a set of four highly conserved Cys residues. From compoarative analysis with crystal strucutre I know there belongs a 4Fe4S but for my respective protein no such crystal exists, so I would like to model my 4Fe4S cluster by my self. I am not very familiar with Chimera, yet, but the "Build structure" function did not work quite well for me. > > > > > > So would kindly ask those who have experince with this kind of models to give me some hinds to model such a FeS-cluster > > > Thanx in advance, > > > Ingmar > >

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