November 2014 - Chimera-users - RBVI Mailing Lists

Constrainted fitting
by Christoph Wigge 22 Mar '19

22 Mar '19

Dear all, I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance. Bests Christoph Wigge

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volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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layering problem
by Joseph Atherton 20 Aug '15

20 Aug '15

Hi! I'm trying to make videos at the moment but I have a problem with layering, as in the model seems to be 'hiding' behind the density even when the density is transparent. This occurs when I set transparency also in the model, even at low transparency (e.g command #19:transparency 5,a,r #0:259-271). See the example attached- the left hand most part of the model, and the ADP is hidden when their transparency is non-zero. Can I prevent this? Cheers, Joe

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mmaker usage with md-movie perframe
by Bala subramanian 02 Jan '15

02 Jan '15

Friends, I have a crystal structure of a protein (370aa). I have a trajectory of a similar protein (not same) with (210aa). I opened the crystal structure and the trajectory via md-movie tool. In the perframe analysis, i gave the following command (#1 my traj, #0 crystal.pdb) *mmaker #1 #0 computeSS false* mmaker uses different number of atom pairs for rmsd calculation. If there are say 150aa that match between my target and crystal, then mmaker should make the rmsd firt for 150 atom pairs in every frame. Why does it use different no. of atom pairs. Do i need to give some extra options ? Thanks, Bala -- C. Balasubramanian

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Display atoms after multiscale model
by vamsee 02 Dec '14

02 Dec '14

Hello, I am working on a virus capsid and trying to figure out the buried surface area between subunits (similar to what ViperDB has. I have to do this for a few capsids and I am trying to automate this to the maximum possible extent. I have been able to follow the steps in this link Buried surface area calculation <http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-December/001131.html> and manually calculate the information. Are there commands available to do the same? Also, what is the difference between the surfaces created using a multiscale model and surfaces computed from the atom-spec? Would this difference in the surface affect the calculation of the buried surface area? And if it does affect it which one be a more accurate representation? Thank you Vamsee

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MatchMaker with betapeptides
by 러셀 29 Nov '14

29 Nov '14

Dear Chimera users, I would like to use the MatchMaker utility to superimpose a family of beta peptide conformers calculated through Xplor-NIH. Unfortunately, MatchMaker does not recognize these molecules and tells me the "chains are incompatible". Furthermore, I would like to specify that only certain residues in the beta peptides be used in the global alignment. I know how to match specific selections in 2 models through the Match utility using the command line (sel #0:1,2,3,4,5@CB,N,C,CA #1:1,2,3,4,5@CB,N,C,CA and then match sel) but I am unsure how to superimpose all of the models at the same time. For instance: models #1-20, residues 2-8, atoms C, N, CA, CB. If anyone could offer me help on the appropriate syntax I would be grateful. Thank you and best regards, Russell

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centroids mutual distance etc. ?
by Marek Maly 29 Nov '14

29 Nov '14

Hello, is there any possibility to measure distance between the two centroids ? It is also possible to define somehow centroid which will be automatically updated when position of the atoms (which are represented by this centroid) are changed - e.g. for different frames from the Amber MD trajectory ? Thank you in advance for your comments, Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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Re: [Chimera-users] [Chimera-announce] new Chimera release (v1.10)
by Debasish Banerjee 29 Nov '14

29 Nov '14

To Elaine Meng, May be I didn't explain properly. Most UniprotKB database entries have used Modbase in the 3D structure database section. In any entry where Modbase is used, clicking on search button next to the  Modbase entry used to open that structure entry page using Chimera. With the current version that doesn't seem to happen (as it was happening with the earlier versions). Please advice. Thanking You, Debasish Banerjee From: Elaine Meng <meng(a)cgl.ucsf.edu> Sent: Wed, 26 Nov 2014 23:02:40 To: Debasish Banerjee <dbanerjee(a)banerjee.net.in> Cc: Mailing List <chimera-users(a)cgl.ucsf.edu> Subject: Re: [Chimera-announce] new Chimera release (v1.10) On Nov 25, 2014, at 4:17 PM, Debasish Banerjee <dbanerjee(a)banerjee.net.in> wrote: > To, > Elaine Meng, > I had downloaded Chimara 1.10 but it doesn't seem to operate on other sites like UniprotKB. Can you please comment. > Debasish Banerjee Dear Debasish Banerjee, Not sure I understand your question.  UCSF Chimera is a molecular modeling/graphics program that you use on your own computer. The only relationship to UniProtKB is that you can fetch sequences and annotations from that site while using Chimera.  Maybe you mean you had trouble fetching data from the web (Chimera menu: File… Fetch by ID)?   We haven’t heard reports of a problem.  For example, I can start UCSF Chimera 1.10, use menu: File… Fetch by ID, choose database “UniProt” and then get the sequence for NGF_HUMAN shown in Chimera.  Of course, you have to be connected to the internet.  Otherwise, if you have some specific problem you can use Chimera menu: Help… Report a Bug and give enough information about the steps you tried so that somebody else could reproduce it. Best, Elaine ----- Elaine C. Meng, Ph.D.                       UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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FW:8debbie
by giovanni.ortosecco 28 Nov '14

28 Nov '14

http://thewebmaker.coolromania.ro/nvmp/odvovssbmjpkdokxvhtwdf.uonvpngrmzjax… giovanni.ortosecco(a)libero.it

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recent malfunction of reading ConSurf .chimerax files
by Alec Zander 28 Nov '14

28 Nov '14

Hello world of Chimera users, I use Chimera to visualize results from the ConSurf server. I ran some ConSurf jobs a while ago, downloaded the .chimerax files for offline viewing, and was happily using Chimera to do so. However, a few days ago, Chimera started hanging upon trying to load these very same files, and I get Chimera Launcher Error chimera exited abnormally; the exit code was: -805306369 I've gotten this same error for both Chimera v 1.9 and 1.10; Windows 7 Pro reports that pythonw.exe is not responding. I don't understand the cause of this error, and the Chimera debug executable seems to hang too. What to do? Best regards, Alex

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