- Chimera-users - RBVI Mailing Lists

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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Calculating partial charges of a charged ligand
by Christos Deligkaris 15 Mar '12

15 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

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Match structures and density maps
by Sam Meyer 15 Mar '12

15 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

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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

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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

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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

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