- Chimera-users - RBVI Mailing Lists

view along a crystal axis
by Michael Elbaum 11 Jan '21

11 Jan '21

Hi. I would like to view a lattice of molecules generated by "Unit Cell" along a given axis. Is there a way to set the view accordingly, say along a, b, or c axis? Other than showing the I'm showing the outline box and eye-balling, but probably there's a more precise way to do this. thanks for your help, Michael

3 6

Identifying type of interaction
by nitya yerabandi 09 Jan '21

09 Jan '21

Hi, I'm using UCSF Chimera right now to analyze the contact residues between two proteins, Hsp70 and BAG3. I have created a distance monitor table on chimera that shows residues, atoms, and the distances between them. I am now trying to identify the type of interaction between each pair of atoms, like polar, nonpolar, hydrogen,etc. However, I am having difficulty doing this. I was wondering if you could assist me with this. Thank you, Nitya Yerabandi

2 2

command line "vol all style surface plane z,60,8
by Dieter Blaas 08 Jan '21

08 Jan '21

Hi, I am trying to display a volume (128 px box) sliced through the middle as seen down the z axis but 8 slices thick instead of just one. I can render a single slice with "vol #0 style surface plane z,64" but I could not find out how to make it e.g. 8 slices thick. In VolumeViewer there is the parameter 'Depth' but it is not accepted as parameter in the command line! Rater, adding one more number at the end of the command starts playing a movie of one slice after the other.... Thanks a lot for hints, bw Dieter ------------------------------------------------------------------------ Dieter Blaas, Max 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, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

3 3

Make a new pdb model from a part of pdb file
by C.J. 07 Jan '21

07 Jan '21

Hi, I have a pdb with a A chain of 1000 amino acids. How can I make a new model with a part of A chain (i.e. 500 amino acids) using command line? Thank you! Best, Jianhao

2 2

(no subject)
by Hemapriya Kumar 07 Jan '21

07 Jan '21

While clicking on the fetch, its getting like certificate no verified as command -- With Regards Hemapriya Kumar

2 1

RMSD after superimposition
by Subhabrata Majumder, PhD 07 Jan '21

07 Jan '21

Dear Support, I have recently started using chimera_ucsf. I was trying to look at Calpha RMSD list after superimposition two conformation of a particular protein. Do you know where should I get the list after superimposition? Thanks, Subhabrata -- Subhabrata Majumder, PhD Assistant Professor Biophysics & Structural Genomics Saha Institute of Nuclear Physics HBNI Sector 1, Block AF Saltlake Kolkata -700064 India Email subhabrata.majumder(a)saha.ac.in ; subhabrata.sinp(a)gmail.com

2 2

Deleting lipid molecules
by Moradkhan, Tiglath A 04 Jan '21

04 Jan '21

Hi I've built a lipid particle containing 252 molecules and I'm trying to randomly delete 20 lipid molecules. Does the delete command allow this? I've tried using it but it doesn't seem to work for this case. Thanks Tiglath

2 1

Re: [Chimera-users] betacavity web and chimera
by Elaine Meng 03 Jan '21

03 Jan '21

On Jan 2, 2021, at 10:42 PM, Jacqueline Vitali <jackie.vitali(a)gmail.com> wrote: > > Hi Elaine, > is there a way to incorporate in chimera the option to read cavities from betacavity web (Nucleic Acids Res 2015 vol 43 W413-W418) ? Right now you do it for CASTP. > Please let me know. > THank you. > Jackie Vitali > Cleveland State University Hi Jackie, Unfortunately we don't have resources to provide visualization capability for the many useful web servers that exist. A related server with Chimera visualization capability is MOLEonline: <https://mole.upol.cz/> I hadn't heard of betacavity before. In general it would be useful to say or give examples of what outputs they do provide, to give some idea of whether it might be possible... I had to run it myself to figure that out. Looks like they just give Jmol visualization in the web browser and a script for Pymol. Maybe you could ask the authors of betacavity if they would also provide a Chimera script too, but it's probably unlikely. I also see they give lists of atoms on the right side of the results page, but not in PDB format. You could try manually showing surface for those atoms in Chimera (with a Chimera command) but it would be (1) tedious, and (2) just the molecular surface of those atoms, so there may be jagged edges and bits sticking out, not a nice enclosed blob as in their Jmol visualization. Our Castp visualization has this same issue. E.g. for 2gbp I get in the betacavity results: VOID 3 VOID-VOLUME 8.468 A^3 VOID-BNDRY-AREA 41.050 A^2 VOID-DEFINING-ATOMS 27 ATOM 131 CE1 PHE A 16 0.064 A^2 ATOM 689 CA ASN A 91 0.978 A^2 ATOM 691 O ASN A 91 3.921 A^2 ATOM 695 ND2 ASN A 91 1.857 A^2 ATOM 705 N GLU A 93 0.796 A^2 ATOM 709 CB GLU A 93 1.116 A^2 ATOM 713 OE2 GLU A 93 1.118 A^2 ATOM 829 CE2 TYR A 107 0.001 A^2 ATOM 831 OH TYR A 107 5.812 A^2 ATOM 840 CA GLY A 109 0.897 A^2 ATOM 843 N THR A 110 0.696 A^2 ATOM 846 O THR A 110 1.145 A^2 ATOM 848 OG1 THR A 110 2.830 A^2 ATOM 849 CG2 THR A 110 2.985 A^2 ATOM 863 OG SER A 112 2.918 A^2 ATOM 1174 CE1 HIS A 152 0.504 A^2 ATOM 1180 CB PRO A 153 2.424 A^2 ATOM 1182 CD PRO A 153 0.061 A^2 ATOM 1183 N ASP A 154 0.007 A^2 ATOM 1188 CG ASP A 154 1.146 A^2 ATOM 1189 OD1 ASP A 154 3.493 A^2 ATOM 1190 OD2 ASP A 154 1.781 A^2 ATOM 1944 OD1 ASN A 256 0.193 A^2 ATOM 1945 ND2 ASN A 256 0.811 A^2 ATOM 1982 OE1 GLN A 261 2.372 A^2 ATOM 2240 OH TYR A 295 0.069 A^2 ATOM 2356 O1 BGC A 310 1.045 A^2 ...and then in Chimera I could open 2gbp surf :16@ce1:91@o,nd2:93@n,cb,oe2:107@c32,oh:109@ca:110@n,o,og1,cg2:112@og:152@ce1:153@cb,cd:154@n,cg,od1,od2:256@od1,nd2:261@oe1:195@oh:310@o1 ...where the surf command is all one line although the mail program may break it up. (Or you could have multiple surf commands for subsets of those atoms.) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

2 1

Accession number
by Yasmeen Nasr 31 Dec '20

31 Dec '20

Hello there, This doesn’t seem very much chimera related but I hope someone could help me out. I’m trying to use phD-SNP server and SNP&GO server and they require a Swiss prot code and a uni-prot accession number respectively. Does anyone know where I retrieve such numbers for SNPs? Thank you in advance. Yasmeen Abdulhadi Sent from my iPhone

1 0

Clustering saving PDB
by Lorena Roldán 28 Dec '20

28 Dec '20

Good afternoon, I contact you as I would really appreciate your help. I have a MD trajectory which I have processed into Clusters with the Analysis ... Cluster tool. I have saved the resulting file with the members and the representative frame, but now I would like to save those representative frames in separate PDB files. This process is extremely tedious if manually done, so I have tried to perform a script: with open("/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/clusters_frame.txt", "r") as f: lines=f.readlines() cluster_number = 1 for i in range(len(lines)): frame = i if mdInfo["frame number"] == frame: name = "/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/Clusters/_" + str(cluster_number) runCommand('write format pdb 0 $name) which would be run in the "Per-frame Commands", in order to 1) encounter the frames of the cluster and 2) save each frame in a PDB file, correctly numbered. However, this script is not working, and I would greatly thank any help you could provide me with. Lorena. -- <http://www.uab.cat> Lorena Roldán Martín *PhD Student in Bioinformatics* Departament de Química Unitat de Química Física Campus de la UAB · 08193 Bellaterra (Cerdanyola del Vallès) · Barcelona · Spain +34 690799431 www.uab.cat <http://www.uab.cat> <https://orcid.org/0000-0002-6902-8285><https://www.linkedin.com/in/lorena-roldan-biomedica/>

3 4