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density maps
by Antonio Coluccia 24 Feb '17

24 Feb '17

Dear all I have computed a molecular dynamic and i would like to have the density maps for some molecules of the system. I tried with isopropanol molecules and I obtain the map for each atom type: H; C3; O3, CH and another called density map_iso.mcr My concerns are about the last one map. What does it mean? Is it the map for the whole molecules, while the other maps are for each atom type? Is it possible to analyse the maps contemporary thus I am able to visualize just three per time? Any help will be really appreciated. Antonio Antonio Coluccia Ph.D. Department of Chemistry and Drugs Technology Rome 00185 Piazzale Aldo Moro 5 antonio.coluccia(a)uniroma1.it

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Two questions about a model
by Steven D. Aird 23 Feb '17

23 Feb '17

Dear Elaine, I have a couple of questions about the attached model set. These are catalytic residues and residues forming the hydrophobic channel in four phospholipases. The first question almost seems silly. I decided to experiment with the label command and labeled one residue in the lower right enzyme of the figure. I didn’t like the position or form of the label. I couldn’t get rid of the “.A” on the label and when I tried to delete the entire label, I couldn’t. Selecting the residue and then selecting LABEL>Off, doesn’t work. In all four plots there are fine lines that resemble the earlier ribspline problem, but they are not resolved by "ribspline cardinal.” Any idea as to what these are? As always, thank you for your tutelage. I am making steady progress. Sincerely yours, Steve Steven D. Aird Technical Editor Faculty Affairs Division Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha, Onna-son Kunigami-gun, Okinawa-ken Japan 904-0495 Phone: 098-982-3584 Cell: 080-4154-9504 Email: steven.aird(a)oist.jp

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Windows & dialogues outside the screen
by Hernando J Sosa 22 Feb '17

22 Feb '17

Dear UCSF-Chimera, I have noticed (perhaps since I upgraded, currently running v1.11.2) that when opening new windows/dialogues many times they pop-up outside the screen. This seems to happen more often when many windows are opened simultaneously. It is more of a nuisance than a real problem but it can get annoying having to continuously search for those elusive windows. So I wonder if there is a way to fix this behavior (e.g. to force newly opened windows to always appear on top and within the screen boundaries) . I am running Windows 64 UCSF-Chimera version 1.11.2 on a Windows 7 and Windows 10 machine (problem occurs in both computers) Thanks Hernando

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Converting a part of a molecule in pdb to xyz format
by Vladyslav Dziuba 22 Feb '17

22 Feb '17

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Re: [Chimera-users] MatchMaker working beautifully, and Transform Coordinates definitely does move things....
by Elaine Meng 17 Feb '17

17 Feb '17

> On Feb 17, 2017, at 3:47 AM, Steven D. Aird <steven.d.aird(a)gmail.com> wrote: > > Dear Elaine, > I apologize for the deluge of Email, but within minutes of writing you, I figured out how to use MatchMaker to align two ribbon models of interest. Again, it’s simple and elegant. > > I also found the transform coordinates command, which I had missed earlier. That enables me to move one of the models relative to the other. But moving a model is tricky because it seems impossible to know what relationship the two models have with a Cartesian coordinate system. I had assumed that x, y, and z would be relative to the monitor surface, but that is not the case. > > Is there a more intuitive way to move molecules while maintaining the same relative orientation? > Thanks very much for your help. > Sincerely yours, > Steve Hi Steve, Thanks for the kind words! After you use Matchmaker (or matrixcopy or the mouse or some other method) to position structures relative to one another, you shouldn’t have to do anything special… now when you move “everything” they will still retain their relationships. I.e. you can rotate and translate everything with the mouse and structures will still be superimposed, docked, etc. as they were after you moved them separately. Personally I never use the Transform Coordinates tool and I don’t understand why you wanted to use it. You can translate and rotate relative to screen coordinates (X horizontal Y vertical Z normal to screen) using commands “move” and “turn” and these can apply to everything or only certain models (they have a “models” keyword option). You can also move only certain models with the mouse by activating/deactivating (freezing) them with the “A” checkboxes in the Model Panel, which can be opened from the Favorites menu. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/move.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> Also, for future reference, we really prefer questions to be sent to chimera-users (CC’d here) so that other people can benefit from the answers, and also give you better support if I don’t know the answer or am away. I hope this helps, 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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Chimera refuses to attach short peptide to protein C-terminus
by Steven Douglas Aird 16 Feb '17

16 Feb '17

Dear Sirs: I am modeling novel proteins on homologous structures from other organisms using SWISS-MODEL. After the model is completed I import the PDB file into Chimera to form disulfides and to produce publication quality graphics. I thought all was going well until I discovered that SWISS-MODEL was actually truncating one or both termini of my target sequences by 1-5 residues. In one case, I created the missing C-terminal tripeptide using MacPyMol, but MacPyMol will not not add the tripeptide to the C-terminus, because it is designed only to create intramolecular bonds. So I imported the protein and the tripeptide into Chimera. I selected the C-terminal oxygen of the protein and the N-terminal nitrogen of the tripeptide and tried to create a peptide bond using Build Structure>Adjust Bonds>Add Bond. Chimera claims that only one atom is selected, but in fact, both are selected. I do not want to try to build a tripeptide one atom at a time. Is there any way to do ligate the tripeptide? Thanks very much! Steve Aird Steven D. Aird Technical Editor Faculty Affairs Division Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha, Onna-son Kunigami-gun, Okinawa-ken Japan 904-0495 Phone: 098-982-3584 Cell: 080-4154-9504 Email: steven.aird(a)oist.jp<mailto:steven.aird@oist.jp>

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Visualisation of membrane proteins
by James Starlight 15 Feb '17

15 Feb '17

Dear Chimera users! I am on the preparation of interactive molecular visualisation, focusing on ligand-binding representation in GPCRs system. Working with the X-ray structures of the receptor bound with the ligand, I wonder to ask some suggestions: 1 - I need to move ligand from ligand binding pocket burried within receptor (as on default in the X-ray structure) towards the selected position outside of it - e.g in case where I would like to depict "vestibule" for the ligand enterance. As I understood for the realisation I should to select ligand within the current model and than to copy it to new model (layer) which then should be moved against the structure, shouldn't it? 2- Is it possible using some Chimera tool to indicate "approximate" membrane plane assuming that GPCRs structure is shown in latteral perspective? Thanks so much for the help! James

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electrostatic surface
by chemocev marker 13 Feb '17

13 Feb '17

Hi I am calculating the electrostatic surface of the protein that has a peptide bound inside the catalytic camber. There are two ways to calculate, either i can split the molecule in indivual chain and calculate their surface indivdually and run the APBS server for the electrostatic potential, or i can do it use the surfcat command. Both of them works but the results are different. To me the results are more logical by splitting the molecule in indivual chain, but u am not sure if its right to do that specially when you want to measure the electrostatic potential. What is your opinion. best Jiri

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Write out coordinates for Centre of mass
by Soumya Govinda Remesh 10 Feb '17

10 Feb '17

Hello, I wanted to know if I can write out the coordinates for the object placed at the 'centre of mass' of selected atoms from a domain. I used the following command to place a marker at the location of interest. - measure center sel mark true Thanks Best, Soumya Govinda Remesh, Ph.D. Postdoctoral Fellow at Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Road MS 6R2100 Berkeley, CA 94720 (phone) 510-495-8179 (cell) 804-402-8730 sgremesh(a)lbl.gov

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Re: [Chimera-users] CHIMERA ERROR
by Eric Pettersen 10 Feb '17

10 Feb '17

> On Feb 8, 2017, at 9:07 AM, Stellamaris Sotomayor Burneo <stellamaris_sb(a)yahoo.com> wrote: > > > Dear Dr. Eric, > > My name is Stellamaris. I am an undergraduate student from Ecuador. There is almost no one working in molecular docking in my country so far. So, it is very difficult to find somebody to ask for help. I would like to kindly ask you a question about the problem I am having with Chimera and I would really appreciate your help. > > I am trying to convert a set of receptors (named receptor.pdb) to receptor.mol2. using chimera. However i am having problems with the charges of FAD, NAD, NDP, and FMN. Receptors that have problems in those groups are not being transformed. > > Is there a way to transform those files without having to change to charges? I have tried changing the charges and it seems to work. However, I am very afraid of changing the conditions of my simulations if I change the charges. > > I have gotten the following message: > NAD) Error: cannot run "/opt/UCSF/Chimera64-1.10.2/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit > Failure running ANTECHAMBER for residue NAD Hi Stellamaris, As you have discovered, the underlying tools that Chimera relies on to derive charges (AmberTools/antechamber/sqm) sometimes fail for entities with concentrated areas of negative charge. It is for this reason that Chimera already includes pre-calculated charges for ADP, ATP, GDP, and GTP. These charges were taken from the AMBER parameter database <http://research.bmh.manchester.ac.uk/bryce/amber>. Charges for the moieties you mentioned are also in that database, and I’ve gone ahead and added NAD and NDP to the ones that Chimera knows about without needing to do a calculation. Precalculated NAD/NDP charges will be available in daily builds dated Feb. 9 or later. Unfortunately, FMN and FAD are more problematic in that Chimera doesn’t protonate them in the standard way used in the database. It adds a proton (and positive charge) to the isoalloxazine ring system so that the central ring becomes aromatic. Obviously, the simplest way to deal with this if you don’t need FAD/FMN as a cofactor is to simply delete them. If you do need them then things get hairy. I guess what I would do is: 1) Delete FMN/FAD. 2) Run Dock Prep which will get you a Mol2 file of the remainder of the system with charges. 3) Close your system and reopen it. 4) Delete everything but the FMN/FAD. 5) Set the IDATM types of the FMN/FAD so that they correspond to the standard protonation pattern. 6) Add hydrogens. 7) Write another Mol2 file with just FMN/FAD. 8) Edit this second Mol2 file and transcribe the charges found in the corresponding Amber parameter database file to the atoms. 9) Combine your two Mol2 files. Step 6 is a little tricky in that the atom names in the “OFF” parameter files aren’t all the same as the PDB standard names, but there is connectivity information in the OFF file, so you can figure out which atom is which. You can do step 5 by running the “defattr” command with the file I have attached, which will set the types of FMN/FAD heavy atoms to the standard protonation pattern. Also, instead of step 8, you could work up another “defattr” file to assign charges to the FMN/FAD before you write out the Mol2 file. Probably easier. —Eric Eric Pettersen UCSF Computer Graphics Lab

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