- Chimera-users - RBVI Mailing Lists

Solvent Accessibility
by Vincent Lynch 12 Oct '05

12 Oct '05

To Whom It May Concern, I am new to Chimera (and molecular modeling in general) and cant figure out if I can color by residue accessibility to solvent and see the raw value of solvent accessibility. Thanks Vinny

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matchmaker alignment
by Boaz Shaanan 11 Oct '05

11 Oct '05

Hi, Is it possible to save as a file (or print) the alignment that is produced by matchmaker between two structures that are read in ? Thanks, Boaz

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DBFILTER_2.2.8 released
by Sheng-Hung Wang 10 Oct '05

10 Oct '05

Dear all: DBFILTER_2.2.8 has been released. This version fixed the bug in counting for H-bond donors & acceptors! Please UPDATE your version to v2.2.8. Download site: CADD toos in Drug R&D http://home.pchome.com.tw/team/gentamicin/mol/mol.htm ------------------------------------------------------------------------- DBFILTER can check the mol2 format database, and pick out any problematic structure which results in "segmentation fault" of DOCK during flexible docking. (for example, salt or structure which contains multi-moleculars built in....) And DBFILTER will output a new database which you want. There are also 12 kinds of filters for spotlighting drug-like properties. Including: Allowed_atoms, Molecular_weight, LogP, H_bond_donors, H_bond_acceptors, Sum_of_N+O, Halogens, Rings, Max_ring_members, Rotatable_bonds, CH3(CH2)n- , CF3(CF2)n-. To enable LogP filter, XLOGP should be run first to calculate your database by: xlogp -m database.mol2>logp.in File 'logp.in' is needed for dbfilter. XLOGP can be download from FTP site of Institute of Physical Chemistry, Peking University. ( ftp://ftp2.ipc.pku.edu.cn/pub/software/xlogp ) ___________________________________________________ ��°� Yahoo!��Ħ��rͨӍ 7.0 beta��M�W·�Ԓ�� http://messenger.yahoo.com.tw/beta.html

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adding chain IDs
by Eric Pettersen 07 Oct '05

07 Oct '05

Hi, Since it's a lot easier to do things in Chimera when a file has chain IDs, Maximilian Andrews wrote a script (below) for adding chain IDs to files that lack them. It does require that TER cards be present at the end of chains, but those are a lot easier to add than chain IDs. Enjoy! Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu #! /usr/bin/env python # Filename: rename_pdb_for_chimera.py ###################################################################### # # # Created: Maximilian N. Andrews, July 18, 2005 # # Ciamician, Bologna University # # # # Function: # # # # This script adds a chain ID to all the subunits (column 22) in # # the PDB file. # # The chains are named 'A','B','C',etc. until all of the subunits # # have been labeled. # # # # For the subunits to be renamed properly the PDB must contain a # # line beginning with TER after each subunit, for example: # # ... # # ATOM 1570 OXT HIE 103 24.590 -9.249 30.054 # # TER # # ATOM 1571 N SER 104 16.936 7.767 30.236 # # ... # # # # Notes: # # # # The original file is first read by the script, then copied to a # # backup file - with the same name, but with "~" added at the end # # of it - and then it is renamed and saved with the original name. # # # # Usage: # # # # rename_pdb.py arg1 arg2 # # arg1 is the the number of chains that have to be renamed; # # arg2 is the name of the input file; # # example: rename_pdb.py 4 MY_PDB.pdb # # # ###################################################################### import sys import os def BAILING_OUT(N_ARG): """ The srcipt needs two arguments: [int] The number of subunits to be renamed; [str] The name of the PDB file to be renamed. The correct use of this script is: rename_pdb.py arg1 arg2 arg1 is the number of chains in the protein; arg2 is the name of the input file; example: rename_pdb.py 4 MY_PDB.pdb """ if N_ARG != 3: print BAILING_OUT.__doc__ sys.exit() else: return BAILING_OUT(len(sys.argv)) NUMBER_CHAINS = sys.argv[1] PDB_IN = sys.argv[2] print 'Number of chains is: ',sys.argv[1] print 'The PDB file to rename is: ',sys.argv[2] PDB_OUT = PDB_IN PDB_BAK = PDB_IN+'~' f = open(PDB_IN,'r') lines = f.readlines() f.close() print 'Making backup file '+PDB_BAK+'...' os.rename(PDB_IN,PDB_BAK) print '...done!' print 'Renaming '+PDB_IN+'...' CHAIN = 65 # this is the integer that corrisponds to the character "A" MAX_CHAIN = int(NUMBER_CHAINS) + CHAIN LETTER = chr(CHAIN) NEW_PDB = [] for i in range(len(lines)): line = lines[i] if line.startswith('TER'): CHAIN = CHAIN + 1 if CHAIN < MAX_CHAIN: LETTER = chr(CHAIN) else: LETTER = ' ' if line.startswith('ATOM'): newline=line[0:21]+LETTER+line[22:] NEW_PDB.append(newline) elif line.startswith('TER') and len(line) > 21: # just in case there's a chain identifier in the "TER" line... (the condition len (line) is added just in case the TER line is a just few characters long... i.e. it would add a blank space at the start of the following line) newline=line[0:21]+' '+line[22:] NEW_PDB.append(newline) else: # if line doesn't start with either ATOM or TER, it will print it as is NEW_PDB.append(line) print '...done!' print 'Writing renamed file '+PDB_OUT+'...' f = open(PDB_OUT,'w') for i in range(len(NEW_PDB)): f.write(NEW_PDB[i]) f.close() print '...done!'

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chimera trouble
by flints16 cvd 07 Oct '05

07 Oct '05

Hi Sorry to say this but chimera does not work on win xp, and every computer on campus uses xp, ah so no luck there. Thanks --------------------------------- Yahoo! for Good Click here to donate to the Hurricane Katrina relief effort.

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movie recorder command file help
by Pullan, Lee 05 Oct '05

05 Oct '05

Hi, I am using the movie recorder in Chimera with the command line file, as suggested in the tutorial. What do I enter into the command file in order to switch objects on and off and also how do I change properties like transparencies/colors? Thanks Lee Pullan, PhD Center for Structural Biology Department of Biochemistry and Molecular Biology University of Texas - Houston Medical School Houston TX 77030 Tel: 713 500 6121

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Invitation: Chimera Workshop Announcement - UCSF November 17&18, 2005
by Scooter Morris 05 Oct '05

05 Oct '05

Dear Chimera User: The Resource on Biocomputing, Visualization, and Informatics (RBVI) is going to be holding our Fall UCSF Chimera Workshop on November 17&18, 2005 at the UCSF Mission Bay Campus in San Francisco, CA. More details about the workshop, and a link to the registration form are available at http://www.cgl.ucsf.edu/Outreach/Workshops/. We have also attached a brochure about the workshop which may be distributed amongst any interested colleagues. There are only 30 slots available, so we would recommend that you sign up as soon as possible. Thanks! -- scooter

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Moving molecules independently in chimera
by David Chenoweth 29 Sep '05

29 Sep '05

Hi! I am a new chimera user and was just wondering if someone could tell me how to move a single molecule in chimera when I have two open. I have two separate small molecule pdb files and I want to open both in the same chimera session. I also want to be able to move one independent of the other so I can overlay the two. Once they are overlayed I would also like the option of adjusting either or moving both together. Thanks in advance for the help. David C.

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Re: [Chimera-users] color-by-element in v. 2172
by Elaine Meng 22 Sep '05

22 Sep '05

Hi Boaz, It is the same procedure as before. However, it sounds like the coloring target is set to something that does not include atoms and bonds. Look in the Actions... Color menu; the default is "all of the above" which would include "atoms/bonds." However, if the coloring target is set to "ribbons" or "background" (for example) there is nothing to color by element. This is most likely what is happening, since with the "all of the above" setting, the copy of 1.2172 I'm using does color by element as before. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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color-by-element in v. 2172
by Boaz Shaanan 22 Sep '05

22 Sep '05

Hi, On the new v. 2172 release candidate, I tried to 'colour by element' a selection of residues in the color panel and got a reply "Nothing applicable to color by element". This is true for both windows and linux. I did this many times before, so has something gone wrong or is there a different path I have to follow to get this type of coloring with the new release ? Thanks for your help. Boaz

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