Dear Rui and All, For the initial PDB file for my MD, it contains chain A (residue 1-400) and B (residue 1-40). After I load the trajectory file to VMD, I find it has converted both chain A and B to chain X. And in chain X it contains the original sequences of both chain A and chain B, which means in Chain X it has residue 1-400 (originall from chain A) followed by residue 1-40 (originally from chain B). And if I select residue 1-40, the residue 1-40 from both the original chain A and chain B are selected. If I only want to highlight the X chain residue 1-40 which correspond to residue 1-40 in chain B by VMD, will you please advice a correct method? Cheers, Acoot
----- Original Message ----- From: Joaquim Rui de Castro Rodrigues <joaquim.rodrig...@ipleiria.pt> To: Acoot Brett <acootbr...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Saturday, 18 August 2012 8:43 PM Subject: RE: [gmx-users] 2 chain protein and VMD Hi, You could do something like this: set sel1 [atomselect top "residue 0 to 499"] $sel1 set chain A set sel2 [atomselect top "residue 500 to 999"] $sel2 set chain B Hope this helps, Rui Rodrigues ________________________________________ De: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] Em Nome De Acoot Brett [acootbr...@yahoo.com] Enviado: sábado, 18 de Agosto de 2012 9:35 Para: Discussion list for GROMACS users Assunto: [gmx-users] 2 chain protein and VMD Dear All, After the production MD for a 2-chain protein complex (chain A and chain B) was done, I used VMD to observe the trajectory. I want to color the 2 chains in different color. However it seems during the observation of the trajectory by VMD, VMD treated both of the 2 chains as chain X, and thus the 2 chains cannot be colored differently. Do you have any method or suggestion to color the 2 chains in different color by VMD in the trajectory observation process? Cheers, Acoot -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
