March 2012 - Chimera-users - RBVI Mailing Lists

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

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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

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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.

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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/

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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

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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

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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

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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

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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

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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 ****************************************************************

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Chimera-users March 2012