[PyMOL] Consistent coloring between sticks of sidechains and cartoon backbones in spectrum coloring

Hi, Pymol-users I have my protein shown as cartoon and colored with spectrum. Now I would like to show several residues at different places with sticks representation. when I tried, I can not get the color consistent between the backbone CA and the carbons on the sidechain. I searched the

Re: [PyMOL] Consistent coloring between sticks of sidechains and cartoon backbones in spectrum coloring

I tried that. that is actually how I found this is a way to color them according the CA color assigned in the spectrum. Charles From: Olson, Linda Sent: Thursday, May 21, 2020 12:24 PM To: Chen, Qiang Subject: Re: Consistent coloring between sticks

Re: [PyMOL] Consistent coloring between sticks of sidechains and cartoon backbones in spectrum coloring

: Thursday, May 21, 2020 9:19 AM To: Chen, Qiang ; pymol-users@lists.sourceforge.net Subject: RE: Consistent coloring between sticks of sidechains and cartoon backbones in spectrum coloring Hi Charles, This pml script does want you want, # Color the carvons atoms of the sidechain the same as the color

Re: [PyMOL] choice of color in util.cbc

Thanks! This works well. "Spectrum chain" is more flexible and powerful in this case. Charles From: Thomas Holder Sent: Tuesday, July 14, 2020 2:24 PM To: Chen, Qiang Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] choice of color in ut

[PyMOL] choice of color in util.cbc

Hi, Pymol Users Is it possible to choose different color pattern when using util.cbc? Wiki says I could use the following to choose the first_color util.cbc 6uwz, first_color=1, quiet=0 6uwz is just an example of a pentameric protein. However, there is no change when specify any other number

[PyMOL] hydrogen bond list for a series of files

Hi, Pymol users Could you help me do this in an efficient way? Let me describe the task I try to do. I have a series of numerically ordered files, say model00.pdb model.01.pdb …… model.30.pdb All the pdb have the same protein composition, chain A, B, C, D, and E. Their relative position is

Re: [PyMOL] renumber (Oganesyan, Vaheh)

Coot is also an option. CCP4 is much better/flexible though. > On Jun 15, 2020, at 3:57 PM, pymol-users-requ...@lists.sourceforge.net wrote: > > Send PyMOL-users mailing list submissions to > pymol-users@lists.sourceforge.net > > To subscribe or unsubscribe via the World Wide Web, visit

Re: [PyMOL] hydrogen bond list for a series of files

From: Mooers, Blaine H.M. (HSC) Sent: Monday, June 15, 2020 9:44 PM To: Chen, Qiang ; pymol-users@lists.sourceforge.net Subject: RE: hydrogen bond list for a series of files Hi Charles, Make sure that PyMOL's present working directory is where the pdb files are stored. Copy and paste each of the

[PyMOL] color by index

Will spectrum just works for your purpose? spectrum count, blue red, yourprotein, byres=1 you can switch off byres if you really want color by atom index. Charles > hello everyone! > I am trying to color an explicit distribution by color (say blue to red) > pls help me with the command color

Re: [PyMOL] hydrogen bond list for a series of files

Great, thanks! Really appreciate your help! Charles From: Mooers, Blaine H.M. (HSC) Sent: Tuesday, June 16, 2020 10:51 AM To: Chen, Qiang ; pymol-users@lists.sourceforge.net Subject: RE: hydrogen bond list for a series of files Hi Charlie, This will give

Re: [PyMOL] hydrogen bond list for a series of files

Hi, Blaine, Then the question becomes how to generate a list with 30 or 300 numbers. Will this work? file_list=list(range(00, 30)) Thanks! Charles From: Mooers, Blaine H.M. (HSC) Sent: Tuesday, June 16, 2020 9:57 AM To: Chen, Qiang ; pymol-users

[PyMOL] hydrogen bond list for a series of files

eforge.net You can reach the person managing the list at pymol-users-ow...@lists.sourceforge.net When replying, please edit your Subject line so it is more specific than "Re: Contents of PyMOL-users digest..." Today's Topics: 1. Re: hydrogen bond list for a serie

[PyMOL] transform an channel pore profile

Hi, Pymol users, Would anyone help me to transform the calculated pore profile along with the protein. I have a couple of proteins and I calculated the pore profiles using MOLE. I downloaded the pymol scripts to regenerate the pores with the protein. when I aligned these proteins, the pore

Re: [PyMOL] transform an channel pore profile

I got the answer. Actually, the solution is so simple, matrix_copy. Charles From: Chen, Qiang Sent: Friday, July 24, 2020 12:46 PM To: pymol-users@lists.sourceforge.net Subject: transform an channel pore profile Hi, Pymol users, Would anyone help me

[PyMOL] Salt bridges in same chains

Hi, All, I am writing a script to find all salt bridges in a pentameric proteins in 50 models. The issues are 1. There are no salt bridges found in the same chain. But I find some if I use this command. >pairwise_dist /model0//A/LYS+ARG/NZ+NE+NH*, >/model0//A/ASP+GLU/OD*+OE*, 4,

[PyMOL] generate non crystallic subunit

Hi, Pymol-users I have a pentameric protein. However, the PDB only contain one subunit with Biomt info provided as the follows. How can I generate the other four subunit and get the whole pentamer in pymol? Thanks! REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, O, B, C REMARK 350 BIOMT1 1

[PyMOL] list_hb.py

Hi, Pymol Users, I used this script to find hydrogen-bond in protein, list_hb.py. list_hb all, all, write_distances_file=hb I find there are some pairs are clearly not hydrogen bonds, e.g. A/VAL`257/O/774A/MET`261/O/8342.87 Also, the angle is not right for certain pair

Re: [PyMOL] CCP4 maps not aligning to my PDB file

try this. Matrix Copy - PyMOLWiki Matrix Copy - PyMOLWiki Matrix_copy copies the object matrix from one object to another.. This command is often used after a protein structure alignment to bring other

Re: [PyMOL] PyMOL-users Digest, Vol 177, Issue 5

u...@lists.sourceforge.net You can reach the person managing the list at pymol-users-ow...@lists.sourceforge.net When replying, please edit your Subject line so it is more specific than "Re: Contents of PyMOL-users digest..." Today's Topics: 1. Salt bridges in same chains (Chen, Qiang)

[PyMOL] counting salt bridge pairs

/429/OD1 to model1/A/ARG/424/NE: 2.589 model1/E/ASP/429/OD2 to model1/A/ARG/424/NE: 3.604 model1/E/GLU/437/OE2 to model1/E/ARG/310/NE: 3.311 model1/E/ASP/446/OD2 to model1/E/LYS/239/NZ: 3.776 Message: 3 Date: Fri, 12 Feb 2021 14:07:13 + From: "

[PyMOL] Exporting data from PyMOL into OriginLab

I often process the images from pymol or originLab in GIMP or photoshop. You could set the pixel content of your pymol image, Png - PyMOLWiki. But I guess this is not the "crop" you expect. Best, Charles Png - PyMOLWiki

[PyMOL] r, theta, and phi of a helix

Hi, Pymol Users, How can I extract the orientation of the helix region of a protein? For example, I have a pentameric membrane protein, I would like to know the orientation angle of one helix region relative to the pentameric symmetry axis (Z)? I found there is a script to calculate the angle