- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] [Chimera-announce] new Chimera release (v1.10)
by Elaine Meng 01 Dec '14

01 Dec '14

Dear Debasish Banerjee, There may have been changes in the ModBase website, or maybe even the UniProt website -- you would need to ask those developers. The ability of Chimera to show ModBase models did not change. Today looking at the ModBase website, I'm having a problem where it always says there are no models for some sequence, even when I know there are models. I don't know if this is the same problem you were having. I know there are models because I can fetch them using Chimera menu: File…Fetch by ID, choosing database: Modbase and entering a sequence ID (UniProt or other). The same can be done with a command, for example: open modbase:P33533 So maybe you can use that approach instead. Regards, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Nov 29, 2014, at 2:39 AM, "Debasish Banerjee" <dbanerjee(a)banerjee.net.in> wrote: > 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

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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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Re: [Chimera-users] [Chimera-announce] new Chimera release (v1.10)
by Elaine Meng 26 Nov '14

26 Nov '14

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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Adding sugars to protein at specific amino acid glycosylation site
by T T 25 Nov '14

25 Nov '14

Dear Mr/Ms, Good morning. My name is Tommy from San Diego Biomedical Research Institute. I am currently learning to use the chimera software. Great work in creating a program for protein and DNA visualization. I have one question to ask regarding the subject above. Is there a way to manually add sugar component onto an existing pdb file? To be precise, I am currently working with HIV-1 envelope. I have the pdb files that features the structure of HIV-1 trimer Env. I wanted to add glycan at specific sites to show steric hindrance to antibody binding. Another question. Is there a way to superimpose 2 pdb files into one image? For example, I have one pdb file for HIV-1 Env and another pdb file for antibody. Can I "merge" these two pdb files as one image? Also, assuming that it is possible to "merge" two different pdb into one image, is there a way to rotate one protein without affect the orientation of the other protein? Any advice/tip is greatly appreciated. Thank you. Sincerely, Tommy

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ribbon options disappeared after upgrade
by Bala subramanian 25 Nov '14

25 Nov '14

Hi, Within the ribbon option under action tool: i used to have additional choices like aitch,wave, octave, etc etc. After an ubuntu upgrade, with chimera 1.9 and 1.10 (i tried both). These extra options dont appear under ribbon. What is going wrong ?. Do i need to install something ? Bala -- C. Balasubramanian

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PDB Header via command line?
by Korbin West 20 Nov '14

20 Nov '14

Hi, I'm trying to find missing atoms in certain residues. I know they are in the pdb header information, but is there a way I can use Chimera or python script to access this using the command line only? I have a large number of proteins to go through, so checking them all individually is not really efficient. Korbin West

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