- Chimera-users - RBVI Mailing Lists

selection based on ring names
by Bala subramanian 02 Feb '12

02 Feb '12

Friends, I have two ligands with a common benzoxadiazole ring. I want to do the rmsd comparison only on the ring, but the names of the atoms forming the benzoxadiazole ring are different in both the ligands. Is there any way to use ring name as a string the compare the rmsd. ie. rmsd of benzoxadiazole of ligand 1 and benzoxadiazole ring of ligand 2 -- C. Balasubramanian

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stereo with zalman monitor
by Jose Miguel Mancheno 01 Feb '12

01 Feb '12

Dear colleagues, I am trying to see stereo images with chimera (candidate version 1.6 for mac) using a Zalman monitor ZM240W which works OK with COOT, which is connected to an iMac. As far as I know, I have to select (within the camera mode) the option: row stereo, right eye even (or odd). However, none of these options provided stereo images. If I select sequential stereo (or reverse sequential stereo) I see the image flickering, as expected, but this is not synchronized with the zalman glasses. Any suggestion about how to proceed to see in stereo mode? Thank you very much in advance. José Miguel --

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Selecting equivalent surfaces
by Ankush Aggarwal 01 Feb '12

01 Feb '12

Hi, I am opening up a viperDB file of a T=3 virus in Chimera. I want to select the 60 equivalent copies of a protein, so that I can change their color together. I am able to select selecting each of them separately. Is there a smarter way to do it? Also, after I rotate the view, is there a command to reset it to the default. Right now, I am "undoing" the move, but it can be a pain if I have moved the model a few times. Thanks, Ankush.

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Notebook
by Miguel Ortiz Lombardía 01 Feb '12

01 Feb '12

Dear all, Was the notebook feature implemented in Chimera? I found a message from some time ago but nothing else? Any plans to include a session notebook? I would ask for something really simple, just apt for text notes. Currently, I create text files with the same name than sessions but with .txt extension, however I think it would be useful to have this built-in in Chimera. Best regards, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR7257) CNRS, Aix-Marseille Université Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombardia@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

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Re: [Chimera-users] HIV ligands
by Eric Pettersen 31 Jan '12

31 Jan '12

On Jan 30, 2012, at 5:27 PM, Forbes J. Burkowski wrote: > Hi: > > I think I have found a bug or least a small inconsistency... > > If you fetch 3NDW and do the menu invocation: > > Select... Residue... > > The list in the submenu offerings includes RIT. > > In a command line, I can use: > > sel :RIT > > to get the same selection. > > Now, repeat the above invocations for 2FDE. > > The Select... Residue... leads us to believe that the ligand can be > accessed as 385. But when I use: > > sel :385 > > I do not get a selection. > > This alternate strategy to do the selection is important for me > because I > am getting the same problem when I put this command into the > runCommand > string within a script. > > The same problem seems to exist for 3SM2 and 3SO9. Both have the > ligand > designated by a number so I have a suspicion that one must do > something > different in the sel command when a number is used to designate the > ligand > instead of a character triplet (such as RIT). > > Is this a bug or am I missing something in the syntax of the sel > command? Hi Forbes, Pedantically speaking, the single-colon (e.g ":532") syntax takes a residue sequence number afterward, whereas the lesser-known double- colon syntax (e.g. "::ala") takes the residue name. Now, as a convenience, if you type something that is not an integer after the single colon, then it assumes you mean the residue name and switches over to interpreting it like the double colon does. But in your case you have character strings that you always want interpreted as residues names regardless of whether they look like integers, so you should just use "::" all the time. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Re: [Chimera-users] how2 select named selections using command-line [chimera1.5.3]
by Eric Pettersen 31 Jan '12

31 Jan '12

On Jan 31, 2012, at 2:34 PM, frederick lee wrote: > thanks VERY much eric and elaine. > > last question: how do i find out about the alias definitions, if > any, stored > in a session from within chimera instead of looking inside the > python script > (of that stored session). Hi Fred, "alias" with no arguments will list all current aliases in the reply log. --Eric

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how2 select named selections using command-line [chimera1.5.3]
by frederick lee 31 Jan '12

31 Jan '12

dear chimera users, i can defined named selections and they work under the select menu. however, i canNOT use the command line to select them; e.g., i have 4 named selections 0a,0b,1a,1b dis 0a | 1a works sel 1a NOT working sel :1a NOT working (said selection cleared) i like to be able to select multiple named selections and further apply filters on them; e.g., "select 1a and 1b and atoms=side chain atoms" how do i accomplish this? as always thank you very much. fred

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Re: [Chimera-users] structural movement when removing ligand
by Elaine Meng 31 Jan '12

31 Jan '12

On Jan 30, 2012, at 6:24 PM, Benny Lo wrote: > Hi, Elaine: > I am using chimera to remove ligand from the protein structure and am curious why there are structural movement of the protein? > Thank you for your response, > Ben Hi Ben, If you are just deleting some atoms, the other atoms should not move. To say anything else, would need more details on what you actually did. Questions should be sent to chimera-users(a)cgl.ucsf.edu, or if you believe it is a bug, you should use Help... Report a Bug in the Chimera menu to send us everything needed to reproduce the problem (for example attaching your input file and describing each step that you did). 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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Biology infrastructure at the XFEL
by Tim Wiegels 31 Jan '12

31 Jan '12

The European Molecular Biology Laboratory (EMBL) and the European X-ray Free Electron Laser (XFEL) at DESY, Hamburg, Germany, have a keen interest in the development of FEL-based applications in structural biology. Within this framework the EMBL, together with international collaborators from Russia, Sweden and Germany, propose to construct a biology infrastructure at the XFEL facility (expected completion in 2016) to enable biological experiments using the high brilliance, ultrashort pulse duration and high repetition rate coherent X-ray radiation. The proposed biological sample infrastructure facility will provide: - support to the international life-science community in generation and handling of challenging samples in immediate proximity to XFEL instruments. - appropriate selection, quality control and evaluation of samples, including correlative imaging, immediately prior to XFEL experiments. - standardized technology for data interpretation, including computation and validation of structural models. In order to ensure efficient operation of the facility and provide optimal services for the international biological community we seek your input to identify the requirements necessary to support these novel biological imaging experiments. We would appreciate your input in the web-based questionnaire available at http://www.embl-hamburg.de/xfel_cgi-bin/questionnaire The results of this survey will be used to identify the most pressing needs that should be taken into account during planning and construction of the infrastructure. We thank you in advance for your cooperation. __________________________________ Tim Wiegels Predoc @ Lamzin Group, EMBL Hamburg __________________________________ EMBL Hamburg c/o DESY Notkestrasse 85 DE-22603 HAMBURG GERMANY Phone 0049 40 89902-184 Fax 0049 40 89902-149

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Regarding Bonding Pattern and all residue
by Vivek Keshri 30 Jan '12

30 Jan '12

Dear Sir / Madam, I Vivek Keshri writing from Uttar Pradesh India, I am opening docked PDB file in Chimera 1.5.3 and want to identify all residue of receptor and ligand which are involved in binding. Waiting for favorable response... Yours Sincerely, Vivek Keshri +91-8005261512

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