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Problem with added ions in Amber
by George Tzotzos 08 Aug '17

08 Aug '17

In MD movie I loaded complex.prmtop and complex.inpcrd files In Tools/Amber/Add ions I selected Ion types Na+ to neutralise complex.inpcrd using AMBER ff14SB for standard residues and AM1-BCC for other residues (I’m attaching a snapshot showing the Na+ ions in red). I then proceeded to solvate the complex using TIP3PBOX and Box size: 9 NOTE: I unticked the Removed existing ions/solvent box I obtained the following Warning “Could not determine charges for pre-existing solvent/ions from added solvent/ions for: NA NA I generated complex_solv.prmtop and complex_solv.inpcrd files When I checked the complex_solv.prmtop file in cpptraj, I did not see any of the Na+ions (see below). > resinfo #Res Name First Last Natom #Orig #Mol 1 ASP 1 14 14 1 1 2 THR 15 28 14 2 1 ——————— 250 LEU 3988 4006 19 250 3 251 VAL 4007 4023 17 251 3 252 KBR 4024 4062 39 252 4 253 WAT 4063 4065 3 253 5 ———— 10272 WAT 34084 34086 3 10272 10024 10273 WAT 34087 34089 3 10273 10025 Is this what should be expected? Should I consider the solvated complex charge neutralised? Antechamber generated exactly the corresponding complex_solv.prmtop file with Na+ ions Thank you in advance for any suggestions.

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chimera batch process
by y.turgay＠bioc.uzh.ch 08 Aug '17

08 Aug '17

Dear chimera users, I was wondering if you could help me automate the following procedure in order to batch process all my tomograms. What I want to do is to open a segmented tomogram, apply parameters like surface, the step size (1 of 8) to increase the connectivity of what has been segmented, to hide the dust (size: 50) and to threshold the tomogram to 0.5. Afterwards I would select all remaining objects and open a script to invert the surface and execute "mask #0 sel invert true" using the command line in chimera to substract the background from the tomogram. Finally I would save this as new map. Can anyone help me with the commands I have to write in the Terminal to iterate through 200 tomogram folder and automate and batch process this. Best Yagmur Turgay

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looking for help in UCSF Chimera
by Ch Bilal 07 Aug '17

07 Aug '17

Respected Sir/Madam. Its Bilal here and i m doing research on a protein "rstA". I am UCSF Chimera user and i am facing an error while energy minimization i got a pop up windows with this error "No MMKT name of atom "HN1" in standard residue "LYS", please help me out i am attaching my complexes with this mail as well please find the attachment. Thank you!

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Automatically changing rotamers
by Ali Malay 07 Aug '17

07 Aug '17

Dear all, I have a large, capsid-sized structure. Is there an easy way (e.g. using a script) to automatically change all of the rotamers of a particular residue type? For example, I would like to modify all cysteine residues such that they all correspond to the Dunbrack rotamer with Chi1= -61; could this be done using the swapaa command? Thank you in advance! Ali

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surface calculation failed on new laptop
by Paul van Erp 03 Aug '17

03 Aug '17

Dear chimera users and developers, Recently I purchased a new laptop. One of the primary uses of this laptop is rendering structures using chimera and running VR simulations of these structures. I've used the new ChimeraX successfully for this. However I also use the old version of chimera for structure visualization, coloring according to attribute lists and I create morph models between structures. The new laptop is unable to calculate virtually any surface. I've gone through the various troubleshooting pages and tried many things. None seem to be effective. Is it possible that the surface calculation would be more successful on a different computer? Also would this depend on the hardware? or might a similar computer from a different brand suffice? Any help you could offer would be greatly appreciated. Thanks in advance, Regards, Paul van Erp

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Volume transparancy
by Matzov Donna 02 Aug '17

02 Aug '17

Hello, I'm trying to make a movie such that a ribbon model would appear while its maps (represented as surface) is already shown and is partially transparent. For that I wanted to set the ribbon transparency to 100 and then use the following command: transparency 0,r frames 100 The problem is that when when the ribbon in 100% transparent, the shape is still apparent in the partially transparent map. the ribbon shapes are not seen only when the map is not transparent at all. Is there a way to fix that? Thanks, Donna

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put outline box at the center of a marker
by Dieter Blaas 01 Aug '17

01 Aug '17

Hi, I'd like to put an outline box with, say 100 x 100 x 100 px around the position of a marker so as to have the marker exactly in the center of the box. Is this possible? Thanks a lot for help, best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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QUESTION
by Arthur Szabo 31 Jul '17

31 Jul '17

I am working with a stretch of dna oligos bound to proteins. I selected all the nucleotides on one strand, showed the atoms as sticks. Then I realized I had wiped out the original colors of the atoms, oxygen, red and nitrogen, blue. How can I restore the atom colors by selecting those nucleotides, and changing the atoms back to their typical colors - as a group. I know how to change the colors of the atoms by first showing them as balls and sticks and then selecting the atoms I want to color. But with 10 nucleotides that is a bit of a pain, selecting them on the screen image. I seem to recall that there is a way to do color all the same atoms at once, but forget how. If I hide the nucleotide side chains, then show them again, I get back to the view where the atoms are not selectively colored. Thanks Arthur G. Szabo

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Re: [Chimera-users] QUESTION
by Rebecca Swett 31 Jul '17

31 Jul '17

Hi Arthur, Select your nucleotides and then you can either use the command line with : color byhet selected Or go to Actions > Color > by heteroatom. Cheers, Rebecca From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu<mailto:chimera-users-bounces@cgl.ucsf.edu>> on behalf of Arthur Szabo <agszabo(a)outlook.com<mailto:agszabo@outlook.com>> Date: Monday, July 31, 2017 at 11:53 AM To: "chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: [Chimera-users] QUESTION I am working with a stretch of dna oligos bound to proteins. I selected all the nucleotides on one strand, showed the atoms as sticks. Then I realized I had wiped out the original colors of the atoms, oxygen, red and nitrogen, blue. How can I restore the atom colors by selecting those nucleotides, and changing the atoms back to their typical colors – as a group. I know how to change the colors of the atoms by first showing them as balls and sticks and then selecting the atoms I want to color. But with 10 nucleotides that is a bit of a pain, selecting them on the screen image. I seem to recall that there is a way to do color all the same atoms at once, but forget how. If I hide the nucleotide side chains, then show them again, I get back to the view where the atoms are not selectively colored. Thanks Arthur G. Szabo This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.

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figured it out from the tutorial pages
by Arthur Szabo 31 Jul '17

31 Jul '17

Disregard my earlier message. Arthur G Szabo

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