- Chimera-users - RBVI Mailing Lists

H-bond analysis in case of TIP4P water model ?
by Marek Maly 04 Sep '12

04 Sep '12

Hello, it seem to me that Chimera is not able to do H-bond analysis between water molecules when TIP4P water model is used. Am I right or I overlooked something ? Thank you very much for the answer in advance ! Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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Ligand parametrization
by Miro Moman 04 Sep '12

04 Sep '12

Hello, When energy minimising protein-ligand complexes, I have observed that Chimera seldom, if ever, complains about missing parameters. However, when I try to generate a Pmrtop file for the same complexes, quite often sLeap is unable to complete the request due to its inability to recognise certain atom types.. Provided that the minimization engine (MMTK) is using the Amber force filed, I was wondering: Are parameters computed in the same way? If not, what are the differences? Maybe a different forcefield version? In addition, is there a way to inspect the parameters that have been generated for minimising a given ligand or non-standard residue? Kind regards, Miro

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saving spheres
by MARY VARUGHESE 04 Sep '12

04 Sep '12

Hi, I saved the combined sph(two clusters) file. But the file contains two clusters with single ID, so i cant create the box including both clusters, since in the box.in file of dock i can give only one cluster number. How can i assign both clusters into single cluster. or any other suggestion. Thanking You.

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Fwd: Installation problems
by prashant kurkute 04 Sep '12

04 Sep '12

Respected sir, Sorry for making you disturb. I am novice to linux. I am trying to install chimera in ubuntu 12.04 LTS. I follow following instruction. sudo chmod +x chimera-1.6.2-linux_x86_64.bin ./chimera-1.6.2-linux_x86_64.bin (I also triied with root sudo ./chimera-1.6.2-linux_x86_64.bin) I got following reply bash: ./chimera-1.6.2-linux_x86_64.bin: cannot execute binary file Sir please help me to solve problem. I will be greatly thankful to your help. With Best wishes and regards.

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volume of an ensemble
by R. Andrew Byrd 31 Aug '12

31 Aug '12

Dear Chimera Team, Is it possible to get the total volume that encompasses an ensemble of structures? For example, if a docking or structure calculation produces an ensemble of structures, can one calculate the volume that encompasses all the members of the ensemble? A docking calculation may have one component superimposable and the second component represent an ensemble, and it is that ensemble that I would I like a measure of the total volume. Thanks! Andy

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adjust resolution of alignment .eps in Multalign viewer
by Gesa Volkers 31 Aug '12

31 Aug '12

Hi all, I would like to extract a high resolution publication quality image from my alignment from the Multalign viewer. Only option I see is to save it a as .eps, but when I open that file the resolution is not sufficient. Is it possible to get a higher resolution image? Thanks, Gesa

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reasonable minimization times
by David Belnap 30 Aug '12

30 Aug '12

I am trying to link the crystal structure of an Fc domain with two Fab structures. I am using the command "minimize spec sel fragment true" on the command line. When various options come up, I've selected "if alternate locations, keep only highest occupancy", "add hydrogens", "add charges", "consider each model in isolation from all others", "also consider H-bonds", and AMBER ff12SB and ANTECHAMBER to assign charges. I've had jobs run overnight that didn't finish. What is a reasonable time for about 8-10 residues to be minimized? Can you suggest any ways to speed this up? Thanks, David

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problem with loading color scheme in Multalign viewer
by Gesa Volkers 29 Aug '12

29 Aug '12

Hi all, I encountered a problem when I tried to open a color scheme (tried it with custom.par from the Chimera website) in the Multalign viewer. I get the following error: "File "C:\Program Files\Chimera 1.6.2\share\MultAlignViewer\PrefDialog.py", line 69, in addColorScheme self._resColorOpt.set(colorFile) See reply log for Python traceback." I reported a bug. Though has anyone found a way to solve this problem and is able to open a .par file again? Thanks, Gesa

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making a movie problem
by Boskovic.Jasminka 29 Aug '12

29 Aug '12

Hi, I am trying to make a movie with chimera but instead of filming just a molecule's movement the program is making the frames of all the chimera window showing the "File, Select, Actions etc" bottoms and the command line? How can I remove this option and film just the molecule window? Thank you in advance! Best regards, Jasminka Boskovic, PhD Centro Nacional de Investigaciones Oncologicas-CNIO (Spanish National Cancer Research Centre-CNIO) Melchor Fernandez Almagro 3 28029 Madrid Spain Tel.: + (34) 917 328 000 (ext 3031) Fax: + (34) 912 246 980 e-mail: jboskovic(a)cnio.es **NOTA DE CONFIDENCIALIDAD** Este correo electr�nico, y en su caso los ficheros adjuntos, pueden contener informaci�n protegida para el uso exclusivo de su destinatario. Se proh�be la distribuci�n, reproducci�n o cualquier otro tipo de transmisi�n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.

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Trivial question
by George Tzotzos 28 Aug '12

28 Aug '12

It seems that a standard feature of Chimera is upon loading a pdb file of a complex, a number of nearby residues also show up. My question is whether there's a rule, let's say a cutoff distance, or other. Thanks in advance for any advice on this Regards George

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